Dysprosium in PDB 4ll7: Structure of SHE3P Amino Terminus.

The structure of Structure of SHE3P Amino Terminus., PDB code: 4ll7 was solved by H.Shi, N.Singh, F.Esselborn, G.Blobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.86 / 2.31
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	28.069, 49.576, 149.950, 89.96, 84.67, 89.98
R / Rfree (%)	23.1 / 26.4

The structure of Structure of SHE3P Amino Terminus. also contains other interesting chemical elements:

Platinum

(Pt)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Dysprosium atom in the Structure of SHE3P Amino Terminus. (pdb code 4ll7). This binding sites where shown within 5.0 Angstroms radius around Dysprosium atom.
In total 30 binding sites of Dysprosium where determined in the Structure of SHE3P Amino Terminus., PDB code: 4ll7:
Jump to Dysprosium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Dysprosium binding site 1 out of 30 in the Structure of SHE3P Amino Terminus.


Mono view


Stereo pair view

A full contact list of Dysprosium with other atoms in the Dy binding site number 1 of Structure of SHE3P Amino Terminus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Dy201 b:33.0 occ:0.80 DY A:DY201 0.0 33.0 0.8 DY A:DY201 1.4 18.4 0.2 OE1 A:GLU128 2.3 42.4 1.0 OE1 B:GLU113 2.4 42.6 1.0 OE1 A:GLU125 2.5 38.6 1.0 OE2 E:GLU113 2.6 28.1 1.0 OE1 E:GLU113 2.8 27.7 1.0 O B:HOH305 2.9 40.2 1.0 OE2 A:GLU128 2.9 19.0 1.0 CD A:GLU128 3.0 32.1 1.0 CD E:GLU113 3.0 25.9 1.0 OE2 A:GLU125 3.2 66.7 1.0 CD A:GLU125 3.2 60.1 1.0 DY E:DY202 3.5 85.7 0.3 CD B:GLU113 3.6 50.0 1.0 OE2 B:GLU113 4.3 31.3 1.0 NZ E:LYS110 4.3 44.6 1.0 O B:LYS110 4.4 34.0 1.0 CG A:GLU128 4.5 25.4 1.0 CG E:GLU113 4.5 42.6 1.0 CG B:GLU113 4.6 34.8 1.0 CG A:GLU125 4.7 54.6 1.0 CB B:GLU113 4.8 28.3 1.0 CA B:LYS110 4.9 35.4 1.0 CB B:LYS110 5.0 37.1 1.0

Dysprosium binding site 2 out of 30 in the Structure of SHE3P Amino Terminus.


Mono view


Stereo pair view

A full contact list of Dysprosium with other atoms in the Dy binding site number 2 of Structure of SHE3P Amino Terminus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Dy201 b:18.4 occ:0.20 DY A:DY201 0.0 18.4 0.2 DY A:DY201 1.4 33.0 0.8 OE2 E:GLU113 2.4 28.1 1.0 OE1 A:GLU125 2.4 38.6 1.0 DY E:DY202 2.6 85.7 0.3 CD E:GLU113 2.8 25.9 1.0 OE1 E:GLU113 2.9 27.7 1.0 OE2 A:GLU128 3.2 19.0 1.0 O B:HOH305 3.3 40.2 1.0 OE1 A:GLU128 3.5 42.4 1.0 CD A:GLU125 3.5 60.1 1.0 OE1 B:GLU113 3.6 42.6 1.0 CD A:GLU128 3.7 32.1 1.0 C3 A:DTT212 3.8 87.7 1.0 OE2 A:GLU125 3.9 66.7 1.0 CG E:GLU113 4.0 42.6 1.0 CG B:LYS110 4.3 23.8 1.0 CB E:GLU113 4.3 37.1 1.0 CB B:LYS110 4.3 37.1 1.0 C2 A:DTT212 4.4 89.8 1.0 C1 A:DTT212 4.5 88.7 1.0 C4 A:DTT212 4.6 86.8 1.0 CA B:LYS110 4.6 35.4 1.0 CD B:GLU113 4.7 50.0 1.0 S4 A:DTT212 4.7 84.1 1.0 CG A:GLU125 4.8 54.6 1.0 O B:LYS110 4.8 34.0 1.0 NZ B:LYS110 4.8 49.6 1.0 O3 A:DTT212 5.0 97.8 1.0 CD B:LYS110 5.0 62.3 1.0

Dysprosium binding site 3 out of 30 in the Structure of SHE3P Amino Terminus.


Mono view


Stereo pair view

A full contact list of Dysprosium with other atoms in the Dy binding site number 3 of Structure of SHE3P Amino Terminus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Dy202 b:56.2 occ:0.23 OE1 A:GLU113 2.0 26.8 1.0 OE2 E:GLU125 2.3 38.4 1.0 O E:HOH304 2.8 65.8 1.0 DY E:DY201 2.8 13.2 0.2 CD A:GLU113 2.9 42.5 1.0 CD E:GLU125 3.0 18.8 1.0 DY E:DY201 3.2 29.1 0.8 CG E:GLU125 3.2 42.7 1.0 CG A:GLU113 3.4 33.3 1.0 CB A:GLU113 3.5 41.5 1.0 O A:LYS110 3.8 34.5 1.0 O E:HOH312 4.0 40.1 1.0 OE2 A:GLU113 4.0 17.9 1.0 OE1 E:GLU125 4.1 38.8 1.0 O E:HOH313 4.2 62.7 1.0 CG A:LYS114 4.2 40.2 1.0 CA A:LYS110 4.4 20.7 1.0 CB A:LYS110 4.5 26.7 1.0 C A:LYS110 4.5 25.3 1.0 CG A:LYS110 4.7 24.7 1.0 CB E:GLU125 4.7 29.2 1.0 C A:GLU113 4.7 29.1 1.0 N A:LYS114 4.8 28.1 1.0 CA A:GLU113 4.8 31.7 1.0 OE1 F:GLU113 4.8 42.1 1.0 OE2 E:GLU128 4.8 26.2 1.0 CD A:LYS114 4.9 58.7 1.0

Dysprosium binding site 4 out of 30 in the Structure of SHE3P Amino Terminus.


Mono view


Stereo pair view

A full contact list of Dysprosium with other atoms in the Dy binding site number 4 of Structure of SHE3P Amino Terminus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Dy203 b:71.4 occ:0.16 OE2 A:GLU103 2.4 69.7 1.0 CD A:GLU103 3.4 64.7 1.0 OE1 A:GLU103 3.7 64.1 1.0 OE2 A:GLU96 3.8 65.9 1.0 O A:HOH319 4.5 44.9 1.0 CG A:GLU103 4.7 42.5 1.0 CD A:GLU96 4.7 78.3 1.0 OD1 F:ASN124 4.8 45.4 1.0 OE1 A:GLU96 4.9 90.7 1.0

Dysprosium binding site 5 out of 30 in the Structure of SHE3P Amino Terminus.


Mono view


Stereo pair view

A full contact list of Dysprosium with other atoms in the Dy binding site number 5 of Structure of SHE3P Amino Terminus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Dy204 b:71.5 occ:0.26 OD1 A:ASP115 2.8 35.6 1.0 O4 G:SO4204 3.0 0.6 1.0 O A:HOH320 3.1 65.7 1.0 OD2 A:ASP115 3.3 39.7 1.0 CG A:ASP115 3.4 38.5 1.0 NZ G:LYS105 4.1 26.9 1.0 S G:SO4204 4.2 1.0 1.0 O2 G:SO4204 4.2 99.3 1.0 O3 G:SO4204 4.8 0.9 1.0 CB A:ASP115 4.9 39.3 1.0 OE1 A:GLU111 5.0 57.3 1.0

Dysprosium binding site 6 out of 30 in the Structure of SHE3P Amino Terminus.


Mono view


Stereo pair view

A full contact list of Dysprosium with other atoms in the Dy binding site number 6 of Structure of SHE3P Amino Terminus. within 5.0Å range: probe atom residue distance (Å) B Occ B:Dy201 b:63.4 occ:0.33 OD1 B:ASP115 2.4 52.4 1.0 CG B:ASP115 3.2 41.2 1.0 OD2 B:ASP115 3.3 46.1 1.0 O2 H:EDO206 4.6 44.1 1.0 CB B:ASP115 4.7 21.3 1.0 CG B:GLU111 4.7 53.8 1.0 NZ H:LYS105 4.8 31.5 1.0 O B:GLU111 4.9 32.2 1.0 OE2 B:GLU111 4.9 68.5 1.0 O1 B:SO4207 4.9 0.6 1.0

Dysprosium binding site 7 out of 30 in the Structure of SHE3P Amino Terminus.


Mono view


Stereo pair view

A full contact list of Dysprosium with other atoms in the Dy binding site number 7 of Structure of SHE3P Amino Terminus. within 5.0Å range: probe atom residue distance (Å) B Occ B:Dy202 b:73.0 occ:0.20 O B:HOH321 2.6 63.7 1.0 OE2 B:GLU103 2.6 57.9 1.0 OE1 B:GLU103 2.9 52.9 1.0 CD B:GLU103 3.1 41.9 1.0 OE2 B:GLU96 4.0 63.3 1.0 OG B:SER100 4.6 58.0 1.0 O B:HOH308 4.6 36.3 1.0 CG B:GLU103 4.6 19.3 1.0 OD1 E:ASN124 4.8 50.2 1.0 O F:HOH318 4.8 46.8 1.0 CA B:SER100 4.9 19.4 1.0

Dysprosium binding site 8 out of 30 in the Structure of SHE3P Amino Terminus.


Mono view


Stereo pair view

A full contact list of Dysprosium with other atoms in the Dy binding site number 8 of Structure of SHE3P Amino Terminus. within 5.0Å range: probe atom residue distance (Å) B Occ B:Dy203 b:67.0 occ:0.25 OE1 B:GLU128 2.1 67.9 1.0 O B:HOH322 2.9 68.7 1.0 CD B:GLU128 3.3 74.4 1.0 OE2 B:GLU128 3.7 66.5 1.0 CG B:GLU125 4.4 67.2 1.0 CG B:GLU128 4.5 49.6 1.0 OE2 B:GLU125 4.6 93.1 1.0 CB B:GLU128 5.0 46.3 1.0

Dysprosium binding site 9 out of 30 in the Structure of SHE3P Amino Terminus.


Mono view


Stereo pair view

A full contact list of Dysprosium with other atoms in the Dy binding site number 9 of Structure of SHE3P Amino Terminus. within 5.0Å range: probe atom residue distance (Å) B Occ C:Dy201 b:35.4 occ:0.80 DY C:DY201 0.0 35.4 0.8 DY C:DY201 1.3 18.2 0.2 OE1 C:GLU128 2.2 46.0 1.0 O C:HOH321 2.4 17.2 1.0 CD C:GLU128 3.0 26.9 1.0 OE2 C:GLU128 3.0 17.6 1.0 OE1 C:GLU125 3.0 52.6 1.0 OE2 C:GLU125 3.1 71.8 1.0 CD C:GLU125 3.2 53.2 1.0 CG C:GLU125 4.3 51.8 1.0 CG C:GLU128 4.4 18.1 1.0 O C:HOH304 5.0 43.0 1.0 CB C:GLU128 5.0 23.9 1.0

Dysprosium binding site 10 out of 30 in the Structure of SHE3P Amino Terminus.


Mono view


Stereo pair view

A full contact list of Dysprosium with other atoms in the Dy binding site number 10 of Structure of SHE3P Amino Terminus. within 5.0Å range: probe atom residue distance (Å) B Occ C:Dy201 b:18.2 occ:0.20 DY C:DY201 0.0 18.2 0.2 DY C:DY201 1.3 35.4 0.8 O C:HOH321 2.3 17.2 1.0 OE2 C:GLU128 3.0 17.6 1.0 OE1 C:GLU128 3.0 46.0 1.0 CD C:GLU128 3.4 26.9 1.0 OE2 C:GLU125 3.5 71.8 1.0 CD C:GLU125 3.6 53.2 1.0 OE1 C:GLU125 3.7 52.6 1.0 O C:HOH304 3.9 43.0 1.0 CG C:GLU125 4.3 51.8 1.0 CG C:GLU128 4.9 18.1 1.0

H.Shi, N.Singh, F.Esselborn, G.Blobel. Structure of A Myosinbulletadaptor Complex and Pairing By Cargo. Proc.Natl.Acad.Sci.Usa V. 111 E1082 2014.
ISSN: ISSN 0027-8424
PubMed: 24522109
DOI: 10.1073/PNAS.1401428111