Dysprosium in PDB 8fnr: X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7
Protein crystallography data
The structure of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7, PDB code: 8fnr
was solved by
J.J.Jung,
C.-Y.Lin,
A.K.Boal,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
27.41 /
1.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
56,
54.234,
65.275,
90,
93.57,
90
|
R / Rfree (%)
|
16.1 /
18.1
|
Dysprosium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
14;
Binding sites:
The binding sites of Dysprosium atom in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7
(pdb code 8fnr). This binding sites where shown within
5.0 Angstroms radius around Dysprosium atom.
In total 14 binding sites of Dysprosium where determined in the
X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7, PDB code: 8fnr:
Jump to Dysprosium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Dysprosium binding site 1 out
of 14 in 8fnr
Go back to
Dysprosium Binding Sites List in 8fnr
Dysprosium binding site 1 out
of 14 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7
 Mono view
 Stereo pair view
|
A full contact list of Dysprosium with other atoms in the Dy binding
site number 1 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Dy201
b:19.2
occ:0.91
|
OD1
|
A:ASN34
|
2.3
|
30.8
|
1.0
|
OD1
|
A:ASP36
|
2.3
|
35.7
|
1.0
|
OD1
|
A:ASP38
|
2.4
|
26.8
|
1.0
|
OE1
|
A:GLU42
|
2.5
|
26.2
|
1.0
|
OD2
|
A:ASP38
|
2.5
|
27.7
|
1.0
|
O
|
A:SER40
|
2.5
|
22.7
|
1.0
|
OE1
|
A:GLU45
|
2.6
|
15.9
|
1.0
|
OE2
|
A:GLU45
|
2.6
|
16.0
|
1.0
|
CG
|
A:ASP38
|
2.8
|
28.6
|
1.0
|
OD2
|
A:ASP36
|
2.9
|
35.1
|
1.0
|
CD
|
A:GLU45
|
2.9
|
15.8
|
1.0
|
CG
|
A:ASP36
|
2.9
|
36.3
|
1.0
|
CD
|
A:GLU42
|
3.3
|
25.2
|
1.0
|
OE2
|
A:GLU42
|
3.3
|
26.8
|
1.0
|
CG
|
A:ASN34
|
3.3
|
29.8
|
1.0
|
C
|
A:SER40
|
3.7
|
19.5
|
1.0
|
ND2
|
A:ASN34
|
3.8
|
30.3
|
1.0
|
CB
|
A:ASP38
|
4.3
|
32.5
|
1.0
|
CA
|
A:LEU41
|
4.4
|
17.4
|
1.0
|
CG
|
A:GLU45
|
4.4
|
15.1
|
1.0
|
CB
|
A:ASP36
|
4.4
|
37.9
|
1.0
|
N
|
A:GLU42
|
4.5
|
18.5
|
1.0
|
N
|
A:LEU41
|
4.5
|
17.8
|
1.0
|
OG
|
A:SER40
|
4.5
|
24.1
|
1.0
|
N
|
A:SER40
|
4.6
|
24.4
|
1.0
|
CB
|
A:ASN34
|
4.6
|
27.2
|
1.0
|
CG
|
A:GLU42
|
4.7
|
22.1
|
1.0
|
CA
|
A:SER40
|
4.7
|
21.6
|
1.0
|
O
|
A:HOH363
|
4.7
|
41.5
|
1.0
|
N
|
A:ASP36
|
4.9
|
36.7
|
1.0
|
C
|
A:LEU41
|
4.9
|
17.0
|
1.0
|
O
|
A:HOH317
|
4.9
|
42.7
|
1.0
|
|
Dysprosium binding site 2 out
of 14 in 8fnr
Go back to
Dysprosium Binding Sites List in 8fnr
Dysprosium binding site 2 out
of 14 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7
 Mono view
 Stereo pair view
|
A full contact list of Dysprosium with other atoms in the Dy binding
site number 2 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Dy202
b:17.3
occ:1.00
|
OE1
|
A:GLU66
|
2.3
|
19.0
|
1.0
|
OD1
|
A:ASN58
|
2.3
|
16.3
|
1.0
|
O
|
A:THR64
|
2.4
|
15.9
|
1.0
|
OD1
|
A:ASP60
|
2.4
|
19.9
|
1.0
|
OD2
|
A:ASP60
|
2.4
|
20.7
|
1.0
|
OD2
|
A:ASP62
|
2.5
|
18.1
|
1.0
|
OE2
|
A:GLU69
|
2.5
|
16.8
|
1.0
|
OE1
|
A:GLU69
|
2.5
|
15.6
|
1.0
|
OD1
|
A:ASP62
|
2.5
|
16.3
|
1.0
|
CG
|
A:ASP60
|
2.8
|
20.7
|
1.0
|
CG
|
A:ASP62
|
2.8
|
17.5
|
1.0
|
CD
|
A:GLU69
|
2.8
|
16.0
|
1.0
|
CD
|
A:GLU66
|
3.4
|
19.8
|
1.0
|
CG
|
A:ASN58
|
3.4
|
16.0
|
1.0
|
C
|
A:THR64
|
3.6
|
16.0
|
1.0
|
OE2
|
A:GLU66
|
3.7
|
20.1
|
1.0
|
ND2
|
A:ASN58
|
3.9
|
16.3
|
1.0
|
O
|
A:HOH375
|
4.1
|
32.1
|
1.0
|
OG1
|
A:THR64
|
4.3
|
17.4
|
1.0
|
CB
|
A:ASP60
|
4.3
|
22.1
|
1.0
|
CB
|
A:ASP62
|
4.3
|
18.6
|
1.0
|
CA
|
A:LEU65
|
4.4
|
14.7
|
1.0
|
CG
|
A:GLU69
|
4.4
|
16.2
|
1.0
|
N
|
A:LEU65
|
4.4
|
15.0
|
1.0
|
N
|
A:GLU66
|
4.4
|
18.6
|
1.0
|
N
|
A:THR64
|
4.6
|
16.0
|
1.0
|
CA
|
A:THR64
|
4.6
|
16.3
|
1.0
|
CB
|
A:ASN58
|
4.7
|
15.0
|
1.0
|
CG
|
A:GLU66
|
4.7
|
20.5
|
1.0
|
O
|
A:HOH329
|
4.7
|
34.0
|
1.0
|
C
|
A:LEU65
|
4.8
|
15.9
|
1.0
|
N
|
A:ASP60
|
4.9
|
20.7
|
1.0
|
CA
|
A:ASN58
|
4.9
|
15.1
|
1.0
|
O
|
A:HOH358
|
4.9
|
22.7
|
1.0
|
N
|
A:ASP62
|
5.0
|
18.9
|
1.0
|
CB
|
A:THR64
|
5.0
|
17.0
|
1.0
|
|
Dysprosium binding site 3 out
of 14 in 8fnr
Go back to
Dysprosium Binding Sites List in 8fnr
Dysprosium binding site 3 out
of 14 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7
 Mono view
 Stereo pair view
|
A full contact list of Dysprosium with other atoms in the Dy binding
site number 3 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Dy203
b:14.2
occ:1.00
|
OD1
|
A:ASN83
|
2.3
|
18.1
|
1.0
|
OE1
|
A:GLU91
|
2.3
|
15.1
|
1.0
|
O
|
A:THR89
|
2.3
|
18.0
|
1.0
|
OD1
|
A:ASP85
|
2.4
|
16.8
|
1.0
|
OE1
|
A:GLU94
|
2.5
|
13.6
|
1.0
|
OD2
|
A:ASP87
|
2.5
|
18.5
|
1.0
|
OD2
|
A:ASP85
|
2.5
|
15.8
|
1.0
|
OD1
|
A:ASP87
|
2.5
|
19.3
|
1.0
|
OE2
|
A:GLU94
|
2.5
|
14.8
|
1.0
|
CG
|
A:ASP85
|
2.8
|
16.8
|
1.0
|
CG
|
A:ASP87
|
2.8
|
19.2
|
1.0
|
CD
|
A:GLU94
|
2.9
|
13.6
|
1.0
|
CD
|
A:GLU91
|
3.3
|
15.1
|
1.0
|
CG
|
A:ASN83
|
3.4
|
18.8
|
1.0
|
OE2
|
A:GLU91
|
3.6
|
15.9
|
1.0
|
C
|
A:THR89
|
3.6
|
18.1
|
1.0
|
ND2
|
A:ASN83
|
4.0
|
19.5
|
1.0
|
OG1
|
A:THR89
|
4.1
|
18.1
|
1.0
|
CB
|
A:ASP85
|
4.3
|
18.3
|
1.0
|
CB
|
A:ASP87
|
4.4
|
20.7
|
1.0
|
N
|
A:GLU91
|
4.4
|
13.7
|
1.0
|
CG
|
A:GLU94
|
4.4
|
12.7
|
1.0
|
CA
|
A:LEU90
|
4.4
|
14.9
|
1.0
|
N
|
A:LEU90
|
4.4
|
16.2
|
1.0
|
CA
|
A:THR89
|
4.5
|
18.4
|
1.0
|
N
|
A:THR89
|
4.6
|
19.0
|
1.0
|
NH2
|
B:ARG100
|
4.6
|
15.9
|
1.0
|
CB
|
A:ASN83
|
4.7
|
18.6
|
1.0
|
CG
|
A:GLU91
|
4.7
|
14.2
|
1.0
|
O
|
A:HOH314
|
4.8
|
19.7
|
1.0
|
NH1
|
B:ARG100
|
4.8
|
16.5
|
1.0
|
CB
|
A:THR89
|
4.8
|
18.1
|
1.0
|
CA
|
A:ASN83
|
4.9
|
17.8
|
1.0
|
C
|
A:LEU90
|
4.9
|
13.6
|
1.0
|
O
|
A:HOH345
|
4.9
|
27.7
|
1.0
|
|
Dysprosium binding site 4 out
of 14 in 8fnr
Go back to
Dysprosium Binding Sites List in 8fnr
Dysprosium binding site 4 out
of 14 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7
 Mono view
 Stereo pair view
|
A full contact list of Dysprosium with other atoms in the Dy binding
site number 4 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Dy204
b:19.3
occ:0.71
|
O
|
A:LYS113
|
2.2
|
19.8
|
1.0
|
OD1
|
A:ASN109
|
2.3
|
15.9
|
1.0
|
O
|
A:HOH405
|
2.3
|
22.9
|
1.0
|
OD1
|
A:ASP107
|
2.4
|
16.2
|
1.0
|
OE1
|
A:GLU118
|
2.4
|
13.4
|
1.0
|
OD1
|
A:ASP111
|
2.4
|
17.2
|
1.0
|
OE2
|
A:GLU118
|
2.5
|
13.8
|
1.0
|
CD
|
A:GLU118
|
2.8
|
13.7
|
1.0
|
CG
|
A:ASP111
|
3.3
|
17.9
|
1.0
|
CG
|
A:ASN109
|
3.3
|
16.1
|
1.0
|
C
|
A:LYS113
|
3.4
|
19.6
|
1.0
|
CG
|
A:ASP107
|
3.6
|
16.1
|
1.0
|
OD2
|
A:ASP111
|
3.6
|
18.2
|
1.0
|
ND2
|
A:ASN109
|
3.8
|
16.8
|
1.0
|
N
|
A:LYS113
|
4.2
|
20.6
|
1.0
|
O
|
A:HOH313
|
4.2
|
31.2
|
1.0
|
OD2
|
A:ASP107
|
4.3
|
16.9
|
1.0
|
CA
|
A:LYS113
|
4.3
|
20.1
|
1.0
|
CG
|
A:GLU118
|
4.3
|
13.8
|
1.0
|
N
|
A:LEU114
|
4.4
|
14.6
|
1.0
|
N
|
A:ASP111
|
4.4
|
17.9
|
1.0
|
CA
|
A:LEU114
|
4.5
|
14.0
|
1.0
|
CA
|
A:ASP107
|
4.5
|
14.3
|
1.0
|
N
|
A:ASN109
|
4.5
|
15.1
|
1.0
|
CB
|
A:LYS113
|
4.5
|
20.9
|
1.0
|
CB
|
A:ASP107
|
4.5
|
14.9
|
1.0
|
CB
|
A:ASP111
|
4.6
|
18.5
|
1.0
|
CB
|
A:ASN109
|
4.6
|
16.0
|
1.0
|
C
|
A:ASP107
|
4.7
|
15.0
|
1.0
|
N
|
A:THR115
|
4.7
|
20.2
|
1.0
|
N
|
A:LYS110
|
4.8
|
22.4
|
1.0
|
CA
|
A:ASN109
|
4.8
|
15.8
|
1.0
|
C
|
A:ASN109
|
4.9
|
16.1
|
1.0
|
N
|
A:ALA108
|
4.9
|
14.2
|
1.0
|
CA
|
A:ASP111
|
4.9
|
18.4
|
1.0
|
O
|
A:HOH368
|
4.9
|
22.3
|
1.0
|
CD2
|
A:LEU114
|
5.0
|
12.2
|
1.0
|
N
|
A:GLY112
|
5.0
|
17.8
|
1.0
|
|
Dysprosium binding site 5 out
of 14 in 8fnr
Go back to
Dysprosium Binding Sites List in 8fnr
Dysprosium binding site 5 out
of 14 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7
 Mono view
 Stereo pair view
|
A full contact list of Dysprosium with other atoms in the Dy binding
site number 5 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Dy201
b:14.4
occ:1.00
|
OE1
|
B:GLU66
|
2.3
|
17.0
|
1.0
|
OD1
|
B:ASN58
|
2.3
|
18.2
|
1.0
|
O
|
B:THR64
|
2.4
|
13.8
|
1.0
|
OD1
|
B:ASP60
|
2.4
|
19.7
|
1.0
|
OD1
|
B:ASP62
|
2.4
|
16.4
|
1.0
|
OD2
|
B:ASP60
|
2.5
|
20.4
|
1.0
|
OE2
|
B:GLU69
|
2.5
|
17.5
|
1.0
|
OD2
|
B:ASP62
|
2.5
|
17.5
|
1.0
|
OE1
|
B:GLU69
|
2.5
|
17.6
|
1.0
|
CG
|
B:ASP60
|
2.8
|
20.1
|
1.0
|
CG
|
B:ASP62
|
2.8
|
16.9
|
1.0
|
CD
|
B:GLU69
|
2.9
|
17.4
|
1.0
|
CD
|
B:GLU66
|
3.3
|
17.3
|
1.0
|
CG
|
B:ASN58
|
3.4
|
17.5
|
1.0
|
C
|
B:THR64
|
3.6
|
13.3
|
1.0
|
OE2
|
B:GLU66
|
3.7
|
17.6
|
1.0
|
ND2
|
B:ASN58
|
3.9
|
16.8
|
1.0
|
OG1
|
B:THR64
|
4.2
|
14.9
|
1.0
|
CB
|
B:ASP60
|
4.3
|
20.0
|
1.0
|
CB
|
B:ASP62
|
4.3
|
16.8
|
1.0
|
N
|
B:GLU66
|
4.3
|
15.7
|
1.0
|
CG
|
B:GLU69
|
4.4
|
17.1
|
1.0
|
CA
|
B:LEU65
|
4.4
|
14.2
|
1.0
|
N
|
B:LEU65
|
4.4
|
14.5
|
1.0
|
N
|
B:THR64
|
4.5
|
12.8
|
1.0
|
CA
|
B:THR64
|
4.6
|
13.4
|
1.0
|
CB
|
B:ASN58
|
4.7
|
17.0
|
1.0
|
CG
|
B:GLU66
|
4.7
|
17.3
|
1.0
|
O
|
B:HOH320
|
4.7
|
27.3
|
1.0
|
C
|
B:LEU65
|
4.8
|
14.8
|
1.0
|
CA
|
B:ASN58
|
4.9
|
17.3
|
1.0
|
N
|
B:ASP60
|
4.9
|
19.1
|
1.0
|
CB
|
B:THR64
|
5.0
|
14.6
|
1.0
|
|
Dysprosium binding site 6 out
of 14 in 8fnr
Go back to
Dysprosium Binding Sites List in 8fnr
Dysprosium binding site 6 out
of 14 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7
 Mono view
 Stereo pair view
|
A full contact list of Dysprosium with other atoms in the Dy binding
site number 6 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Dy202
b:12.6
occ:1.00
|
OD1
|
B:ASN83
|
2.3
|
16.5
|
1.0
|
OE1
|
B:GLU91
|
2.3
|
14.2
|
1.0
|
O
|
B:THR89
|
2.4
|
16.2
|
1.0
|
OD1
|
B:ASP85
|
2.4
|
16.9
|
1.0
|
OD2
|
B:ASP85
|
2.4
|
16.4
|
1.0
|
OD2
|
B:ASP87
|
2.5
|
17.1
|
1.0
|
OE1
|
B:GLU94
|
2.5
|
13.0
|
1.0
|
OD1
|
B:ASP87
|
2.5
|
17.1
|
1.0
|
OE2
|
B:GLU94
|
2.5
|
14.1
|
1.0
|
CG
|
B:ASP85
|
2.8
|
16.9
|
1.0
|
CG
|
B:ASP87
|
2.8
|
17.3
|
1.0
|
CD
|
B:GLU94
|
2.9
|
13.3
|
1.0
|
CD
|
B:GLU91
|
3.3
|
14.0
|
1.0
|
CG
|
B:ASN83
|
3.4
|
16.3
|
1.0
|
OE2
|
B:GLU91
|
3.6
|
14.2
|
1.0
|
C
|
B:THR89
|
3.6
|
15.6
|
1.0
|
ND2
|
B:ASN83
|
4.0
|
16.6
|
1.0
|
OG1
|
B:THR89
|
4.1
|
16.6
|
1.0
|
CB
|
B:ASP85
|
4.3
|
17.2
|
1.0
|
CB
|
B:ASP87
|
4.3
|
17.7
|
1.0
|
N
|
B:GLU91
|
4.4
|
11.8
|
1.0
|
CG
|
B:GLU94
|
4.4
|
12.5
|
1.0
|
CA
|
B:LEU90
|
4.4
|
14.2
|
1.0
|
N
|
B:LEU90
|
4.5
|
14.7
|
1.0
|
NH2
|
A:ARG100
|
4.5
|
15.2
|
1.0
|
N
|
B:THR89
|
4.6
|
16.2
|
1.0
|
CA
|
B:THR89
|
4.6
|
15.7
|
1.0
|
CB
|
B:ASN83
|
4.7
|
15.6
|
1.0
|
CG
|
B:GLU91
|
4.7
|
12.9
|
1.0
|
O
|
B:HOH341
|
4.8
|
34.0
|
1.0
|
NH1
|
A:ARG100
|
4.8
|
14.8
|
1.0
|
CA
|
B:ASN83
|
4.9
|
15.6
|
1.0
|
C
|
B:LEU90
|
4.9
|
13.9
|
1.0
|
CB
|
B:THR89
|
4.9
|
15.9
|
1.0
|
O
|
B:HOH345
|
5.0
|
17.6
|
1.0
|
|
Dysprosium binding site 7 out
of 14 in 8fnr
Go back to
Dysprosium Binding Sites List in 8fnr
Dysprosium binding site 7 out
of 14 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7
 Mono view
 Stereo pair view
|
A full contact list of Dysprosium with other atoms in the Dy binding
site number 7 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Dy203
b:22.5
occ:0.77
|
O
|
B:LYS113
|
2.3
|
23.8
|
1.0
|
OD1
|
B:ASN109
|
2.3
|
23.9
|
1.0
|
OD1
|
B:ASP107
|
2.3
|
20.9
|
1.0
|
O
|
B:HOH377
|
2.4
|
32.4
|
1.0
|
OD1
|
B:ASP111
|
2.4
|
23.2
|
1.0
|
OE1
|
B:GLU118
|
2.5
|
20.3
|
1.0
|
OE2
|
B:GLU118
|
2.5
|
22.3
|
1.0
|
CD
|
B:GLU118
|
2.9
|
21.2
|
1.0
|
CG
|
B:ASP111
|
3.3
|
24.3
|
1.0
|
CG
|
B:ASN109
|
3.4
|
25.2
|
1.0
|
C
|
B:LYS113
|
3.5
|
24.2
|
1.0
|
CG
|
B:ASP107
|
3.5
|
20.7
|
1.0
|
OD2
|
B:ASP111
|
3.7
|
24.8
|
1.0
|
ND2
|
B:ASN109
|
3.9
|
25.7
|
1.0
|
N
|
B:LYS113
|
4.2
|
23.8
|
1.0
|
OD2
|
B:ASP107
|
4.3
|
20.9
|
1.0
|
CA
|
B:LYS113
|
4.3
|
24.5
|
1.0
|
CG
|
B:GLU118
|
4.4
|
20.9
|
1.0
|
CA
|
B:ASP107
|
4.4
|
20.0
|
1.0
|
N
|
B:ASP111
|
4.4
|
24.8
|
1.0
|
N
|
B:LEU114
|
4.5
|
16.9
|
1.0
|
CB
|
B:ASP107
|
4.5
|
20.1
|
1.0
|
CA
|
B:LEU114
|
4.6
|
16.6
|
1.0
|
CB
|
B:ASP111
|
4.6
|
25.7
|
1.0
|
CB
|
B:LYS113
|
4.6
|
25.3
|
1.0
|
N
|
B:ASN109
|
4.6
|
24.9
|
1.0
|
C
|
B:ASP107
|
4.7
|
21.1
|
1.0
|
O
|
B:HOH334
|
4.7
|
37.4
|
1.0
|
CB
|
B:ASN109
|
4.7
|
26.5
|
1.0
|
N
|
B:LYS110
|
4.8
|
28.7
|
1.0
|
N
|
B:ALA108
|
4.9
|
27.4
|
1.0
|
CA
|
B:ASP111
|
4.9
|
25.2
|
1.0
|
N
|
B:THR115
|
4.9
|
20.8
|
1.0
|
N
|
B:GLY112
|
5.0
|
20.5
|
1.0
|
|
Dysprosium binding site 8 out
of 14 in 8fnr
Go back to
Dysprosium Binding Sites List in 8fnr
Dysprosium binding site 8 out
of 14 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7
 Mono view
 Stereo pair view
|
A full contact list of Dysprosium with other atoms in the Dy binding
site number 8 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Dy201
b:18.3
occ:1.00
|
OD1
|
C:ASN58
|
2.3
|
23.8
|
1.0
|
OE1
|
C:GLU66
|
2.3
|
22.8
|
1.0
|
O
|
C:THR64
|
2.3
|
19.9
|
1.0
|
OD1
|
C:ASP62
|
2.4
|
22.3
|
1.0
|
OE2
|
C:GLU69
|
2.4
|
21.1
|
1.0
|
OD1
|
C:ASP60
|
2.4
|
28.9
|
1.0
|
OD2
|
C:ASP60
|
2.5
|
29.2
|
1.0
|
OD2
|
C:ASP62
|
2.5
|
23.4
|
1.0
|
OE1
|
C:GLU69
|
2.5
|
20.9
|
1.0
|
CG
|
C:ASP60
|
2.8
|
28.8
|
1.0
|
CG
|
C:ASP62
|
2.8
|
22.9
|
1.0
|
CD
|
C:GLU69
|
2.8
|
21.0
|
1.0
|
CD
|
C:GLU66
|
3.3
|
23.1
|
1.0
|
CG
|
C:ASN58
|
3.4
|
23.2
|
1.0
|
C
|
C:THR64
|
3.6
|
19.2
|
1.0
|
OE2
|
C:GLU66
|
3.7
|
22.8
|
1.0
|
ND2
|
C:ASN58
|
3.8
|
23.4
|
1.0
|
O
|
C:HOH366
|
4.1
|
35.9
|
1.0
|
CB
|
C:ASP60
|
4.3
|
28.7
|
1.0
|
CB
|
C:ASP62
|
4.3
|
23.3
|
1.0
|
OG1
|
C:THR64
|
4.3
|
21.0
|
1.0
|
N
|
C:GLU66
|
4.3
|
21.2
|
1.0
|
CG
|
C:GLU69
|
4.3
|
21.3
|
1.0
|
CA
|
C:LEU65
|
4.3
|
19.0
|
1.0
|
N
|
C:LEU65
|
4.4
|
18.8
|
1.0
|
N
|
C:THR64
|
4.5
|
19.5
|
1.0
|
CA
|
C:THR64
|
4.6
|
19.2
|
1.0
|
CB
|
C:ASN58
|
4.7
|
22.2
|
1.0
|
CG
|
C:GLU66
|
4.7
|
23.4
|
1.0
|
C
|
C:LEU65
|
4.8
|
19.6
|
1.0
|
O
|
C:HOH385
|
4.8
|
35.0
|
1.0
|
N
|
C:ASP60
|
4.9
|
27.4
|
1.0
|
CA
|
C:ASN58
|
4.9
|
22.2
|
1.0
|
O
|
C:HOH342
|
5.0
|
31.3
|
1.0
|
N
|
C:ASP62
|
5.0
|
22.9
|
1.0
|
|
Dysprosium binding site 9 out
of 14 in 8fnr
Go back to
Dysprosium Binding Sites List in 8fnr
Dysprosium binding site 9 out
of 14 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7
 Mono view
 Stereo pair view
|
A full contact list of Dysprosium with other atoms in the Dy binding
site number 9 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Dy202
b:18.8
occ:1.00
|
OD1
|
C:ASN83
|
2.3
|
22.7
|
1.0
|
OE1
|
C:GLU91
|
2.3
|
19.7
|
1.0
|
O
|
C:THR89
|
2.4
|
22.6
|
1.0
|
OD2
|
C:ASP87
|
2.4
|
22.0
|
1.0
|
OD1
|
C:ASP87
|
2.5
|
24.1
|
1.0
|
OD1
|
C:ASP85
|
2.5
|
25.3
|
1.0
|
OE2
|
C:GLU94
|
2.5
|
19.6
|
1.0
|
OD2
|
C:ASP85
|
2.5
|
22.8
|
1.0
|
OE1
|
C:GLU94
|
2.5
|
18.2
|
1.0
|
CG
|
C:ASP87
|
2.8
|
23.9
|
1.0
|
CG
|
C:ASP85
|
2.8
|
24.4
|
1.0
|
CD
|
C:GLU94
|
2.9
|
18.7
|
1.0
|
CD
|
C:GLU91
|
3.3
|
18.5
|
1.0
|
CG
|
C:ASN83
|
3.4
|
24.7
|
1.0
|
C
|
C:THR89
|
3.6
|
22.3
|
1.0
|
OE2
|
C:GLU91
|
3.6
|
18.6
|
1.0
|
ND2
|
C:ASN83
|
3.9
|
26.5
|
1.0
|
OG1
|
C:THR89
|
4.1
|
22.0
|
1.0
|
CB
|
C:ASP87
|
4.3
|
26.2
|
1.0
|
CB
|
C:ASP85
|
4.4
|
26.3
|
1.0
|
N
|
C:GLU91
|
4.4
|
17.5
|
1.0
|
CG
|
C:GLU94
|
4.4
|
17.9
|
1.0
|
CA
|
C:LEU90
|
4.5
|
20.6
|
1.0
|
NH2
|
D:ARG100
|
4.5
|
19.5
|
1.0
|
N
|
C:LEU90
|
4.5
|
21.1
|
1.0
|
N
|
C:THR89
|
4.6
|
24.8
|
1.0
|
CA
|
C:THR89
|
4.6
|
22.6
|
1.0
|
CB
|
C:ASN83
|
4.7
|
25.7
|
1.0
|
CG
|
C:GLU91
|
4.7
|
16.8
|
1.0
|
NH1
|
D:ARG100
|
4.8
|
22.0
|
1.0
|
O
|
C:HOH377
|
4.8
|
35.7
|
1.0
|
C
|
C:LEU90
|
4.9
|
18.6
|
1.0
|
CA
|
C:ASN83
|
4.9
|
25.5
|
1.0
|
CB
|
C:THR89
|
4.9
|
21.6
|
1.0
|
N
|
C:ASP85
|
5.0
|
29.2
|
1.0
|
|
Dysprosium binding site 10 out
of 14 in 8fnr
Go back to
Dysprosium Binding Sites List in 8fnr
Dysprosium binding site 10 out
of 14 in the X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7
 Mono view
 Stereo pair view
|
A full contact list of Dysprosium with other atoms in the Dy binding
site number 10 of X-Ray Crystal Structure of Hansschlegelia Quercus Lanmodulin (Lanm) with Dysprosium (III) Bound at pH 7 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Dy203
b:18.6
occ:0.38
|
O
|
C:LYS113
|
2.2
|
26.4
|
1.0
|
OD1
|
C:ASN109
|
2.3
|
25.9
|
1.0
|
O
|
C:HOH341
|
2.4
|
27.1
|
1.0
|
OD1
|
C:ASP111
|
2.4
|
24.2
|
1.0
|
OE1
|
C:GLU118
|
2.5
|
19.2
|
1.0
|
OD1
|
C:ASP107
|
2.5
|
21.7
|
1.0
|
OE2
|
C:GLU118
|
2.7
|
19.6
|
1.0
|
CD
|
C:GLU118
|
3.0
|
19.8
|
1.0
|
CG
|
C:ASP111
|
3.2
|
24.6
|
1.0
|
CG
|
C:ASN109
|
3.4
|
26.2
|
1.0
|
C
|
C:LYS113
|
3.4
|
26.2
|
1.0
|
OD2
|
C:ASP111
|
3.5
|
25.4
|
1.0
|
CG
|
C:ASP107
|
3.7
|
21.6
|
1.0
|
ND2
|
C:ASN109
|
4.0
|
26.8
|
1.0
|
N
|
C:LYS113
|
4.1
|
24.9
|
1.0
|
CA
|
C:LYS113
|
4.2
|
25.7
|
1.0
|
N
|
C:LEU114
|
4.4
|
16.3
|
1.0
|
N
|
C:ASP111
|
4.4
|
23.1
|
1.0
|
N
|
C:ASN109
|
4.4
|
25.6
|
1.0
|
OD2
|
C:ASP107
|
4.4
|
21.9
|
1.0
|
CG
|
C:GLU118
|
4.5
|
20.9
|
1.0
|
CA
|
C:LEU114
|
4.5
|
16.4
|
1.0
|
CB
|
C:LYS113
|
4.5
|
26.6
|
1.0
|
CB
|
C:ASP111
|
4.5
|
23.9
|
1.0
|
CA
|
C:ASP107
|
4.6
|
21.6
|
1.0
|
CB
|
C:ASN109
|
4.6
|
26.4
|
1.0
|
CB
|
C:ASP107
|
4.7
|
20.8
|
1.0
|
O
|
C:HOH355
|
4.7
|
36.6
|
1.0
|
N
|
C:LYS110
|
4.7
|
23.3
|
1.0
|
C
|
C:ASP107
|
4.8
|
22.5
|
1.0
|
N
|
C:ALA108
|
4.8
|
22.7
|
1.0
|
CA
|
C:ASN109
|
4.8
|
25.7
|
1.0
|
CA
|
C:ASP111
|
4.9
|
23.0
|
1.0
|
N
|
C:THR115
|
4.9
|
17.6
|
1.0
|
C
|
C:ASN109
|
4.9
|
24.8
|
1.0
|
O
|
C:HOH410
|
5.0
|
47.1
|
1.0
|
N
|
C:GLY112
|
5.0
|
21.8
|
1.0
|
|
Reference:
J.A.Mattocks,
J.J.Jung,
C.Y.Lin,
Z.Dong,
N.H.Yennawar,
E.R.Featherston,
C.S.Kang-Yun,
T.A.Hamilton,
D.M.Park,
A.K.Boal,
J.A.Cotruvo.
Enhanced Rare-Earth Separation with A Metal-Sensitive Lanmodulin Dimer Nature V. 618 87 2023.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-05945-5
Page generated: Wed Jul 31 10:35:09 2024
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