Zinc in PDB 6xpe: Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation

The binding sites of Zinc atom in the Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation (pdb code 6xpe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation, PDB code: 6xpe:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:0.3 occ:1.00 ND1 B:HIS318 2.0 94.6 1.0 NE2 B:HIS301 2.2 98.4 1.0 SG A:CYS53 2.5 0.1 1.0 OE1 B:GLU352 2.7 0.7 1.0 CG B:HIS318 2.7 94.6 1.0 CE1 B:HIS301 2.8 98.4 1.0 CB B:HIS318 2.9 94.6 1.0 OE1 B:GLN350 2.9 83.7 1.0 CE1 B:HIS318 3.0 94.6 1.0 CD2 B:HIS301 3.4 98.4 1.0 CD B:GLU352 3.6 0.7 1.0 CD2 B:HIS318 3.9 94.6 1.0 ND1 B:HIS301 4.0 98.4 1.0 NE2 B:HIS318 4.0 94.6 1.0 CB B:GLU352 4.1 0.7 1.0 CD B:GLN350 4.2 83.7 1.0 OG B:SER302 4.2 89.6 1.0 CB A:CYS53 4.2 0.1 1.0 CG B:HIS301 4.3 98.4 1.0 CG B:GLU352 4.4 0.7 1.0 CA B:HIS318 4.4 94.6 1.0 OE2 B:GLU352 4.4 0.7 1.0 O A:HIS52 4.5 0.2 1.0

Zinc binding site 2 out of 8 in the Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:0.3 occ:1.00 NE2 B:HIS137 2.0 0.1 1.0 NE2 B:HIS345 2.1 0.0 1.0 CE1 B:HIS345 2.4 0.0 1.0 CE1 B:HIS137 2.7 0.1 1.0 CD2 B:HIS137 2.7 0.1 1.0 CD2 B:HIS345 3.3 0.0 1.0 ND1 B:HIS137 3.5 0.1 1.0 ND1 B:HIS345 3.6 0.0 1.0 CG B:HIS137 3.6 0.1 1.0 O B:PHE134 3.9 86.5 1.0 CG B:HIS345 4.0 0.0 1.0 CB B:HIS137 4.9 0.1 1.0

Zinc binding site 3 out of 8 in the Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:0.2 occ:1.00 OD2 B:ASP224 1.5 0.1 1.0 OD1 B:ASP224 1.6 0.1 1.0 CG B:ASP224 1.7 0.1 1.0 NE2 B:HIS106 2.7 0.5 1.0 OD1 B:ASP110 2.9 0.8 1.0 CB B:ASP224 3.2 0.1 1.0 CD2 B:HIS106 3.3 0.5 1.0 OD2 B:ASP110 3.5 0.8 1.0 CE1 B:HIS106 3.6 0.5 1.0 CG B:ASP110 3.6 0.8 1.0 NE2 B:HIS220 3.7 0.2 1.0 CA B:ASP224 4.1 0.1 1.0 CD2 B:HIS220 4.2 0.2 1.0 CD1 B:ILE151 4.2 98.3 1.0 O B:HIS220 4.3 0.2 1.0 CG B:HIS106 4.4 0.5 1.0 ND1 B:HIS106 4.4 0.5 1.0 CE1 B:HIS220 4.5 0.2 1.0 CG1 B:VAL154 4.5 0.9 1.0 N B:ASP224 4.6 0.1 1.0 O B:HIS106 4.9 0.5 1.0 CB B:ASP110 5.0 0.8 1.0

Zinc binding site 4 out of 8 in the Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:0.9 occ:1.00 NE2 A:HIS52 2.1 0.2 1.0 SG B:CYS361 2.3 0.6 1.0 CB B:CYS364 2.4 0.2 1.0 SG B:CYS364 2.5 0.2 1.0 NE2 A:HIS54 2.6 0.8 1.0 N B:CYS364 2.9 0.2 1.0 CD2 A:HIS52 3.0 0.2 1.0 CE1 A:HIS54 3.1 0.8 1.0 CA B:CYS364 3.1 0.2 1.0 CE1 A:HIS52 3.1 0.2 1.0 CB B:CYS361 3.4 0.6 1.0 CD2 A:HIS54 3.4 0.8 1.0 C B:PHE363 3.9 0.3 1.0 ND1 A:HIS54 3.9 0.8 1.0 C B:CYS364 4.1 0.2 1.0 CG A:HIS54 4.1 0.8 1.0 CG A:HIS52 4.1 0.2 1.0 ND1 A:HIS52 4.2 0.2 1.0 CB B:PHE363 4.2 0.3 1.0 O B:CYS361 4.3 0.6 1.0 CA B:PHE363 4.4 0.3 1.0 N B:PHE363 4.6 0.3 1.0 C B:CYS361 4.6 0.6 1.0 CA B:CYS361 4.6 0.6 1.0 O B:CYS364 4.6 0.2 1.0 N B:GLU365 4.7 0.2 1.0 O B:PHE363 4.8 0.3 1.0 O A:HIS52 4.9 0.2 1.0

Zinc binding site 5 out of 8 in the Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:0.3 occ:1.00 NE2 A:HIS301 2.0 98.4 1.0 OE1 A:GLU352 2.2 0.7 1.0 CE1 A:HIS301 2.2 98.4 1.0 ND1 A:HIS318 2.5 94.6 1.0 SG B:CYS53 2.7 0.1 1.0 CB A:HIS318 2.8 94.6 1.0 CG A:HIS318 2.9 94.6 1.0 CD A:GLU352 3.2 0.7 1.0 OE1 A:GLN350 3.3 83.7 1.0 CD2 A:HIS301 3.3 98.4 1.0 ND1 A:HIS301 3.5 98.4 1.0 CB A:GLU352 3.5 0.7 1.0 CE1 A:HIS318 3.6 94.6 1.0 CG A:GLU352 3.9 0.7 1.0 CG A:HIS301 4.0 98.4 1.0 OE2 A:GLU352 4.1 0.7 1.0 CD2 A:HIS318 4.2 94.6 1.0 CA A:HIS318 4.2 94.6 1.0 CD A:GLN350 4.4 83.7 1.0 OG A:SER302 4.4 89.6 1.0 CB B:CYS53 4.5 0.1 1.0 NE2 A:HIS318 4.5 94.6 1.0 O B:HIS52 4.7 0.2 1.0 C A:HIS318 4.8 94.6 1.0 CA A:GLU352 4.9 0.7 1.0 O A:HIS301 5.0 98.4 1.0

Zinc binding site 6 out of 8 in the Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:0.9 occ:1.00 NE2 B:HIS52 2.1 0.2 1.0 SG A:CYS361 2.3 0.6 1.0 CB A:CYS364 2.4 0.2 1.0 SG A:CYS364 2.5 0.2 1.0 NE2 B:HIS54 2.6 0.8 1.0 N A:CYS364 2.9 0.2 1.0 CD2 B:HIS52 3.0 0.2 1.0 CE1 B:HIS54 3.1 0.8 1.0 CA A:CYS364 3.1 0.2 1.0 CE1 B:HIS52 3.1 0.2 1.0 CB A:CYS361 3.4 0.6 1.0 CD2 B:HIS54 3.4 0.8 1.0 C A:PHE363 3.9 0.3 1.0 ND1 B:HIS54 3.9 0.8 1.0 C A:CYS364 4.1 0.2 1.0 CG B:HIS54 4.1 0.8 1.0 CG B:HIS52 4.1 0.2 1.0 ND1 B:HIS52 4.2 0.2 1.0 CB A:PHE363 4.2 0.3 1.0 O A:CYS361 4.3 0.6 1.0 CA A:PHE363 4.4 0.3 1.0 N A:PHE363 4.6 0.3 1.0 C A:CYS361 4.6 0.6 1.0 CA A:CYS361 4.6 0.6 1.0 O A:CYS364 4.6 0.2 1.0 N A:GLU365 4.7 0.2 1.0 O A:PHE363 4.8 0.3 1.0 O B:HIS52 4.9 0.2 1.0

Zinc binding site 7 out of 8 in the Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:0.3 occ:1.00 NE2 A:HIS137 2.0 0.1 1.0 NE2 A:HIS345 2.1 0.0 1.0 CE1 A:HIS345 2.4 0.0 1.0 CE1 A:HIS137 2.7 0.1 1.0 CD2 A:HIS137 2.7 0.1 1.0 CD2 A:HIS345 3.3 0.0 1.0 ND1 A:HIS137 3.5 0.1 1.0 ND1 A:HIS345 3.6 0.0 1.0 CG A:HIS137 3.6 0.1 1.0 O A:PHE134 3.9 86.5 1.0 CG A:HIS345 4.0 0.0 1.0 CB A:HIS137 4.9 0.1 1.0

Zinc binding site 8 out of 8 in the Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Human ZNT8 Wt, in the Presence of Zinc, Determined in Outward-Facing Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:0.2 occ:1.00 OD2 A:ASP224 1.5 0.1 1.0 CG A:ASP224 1.6 0.1 1.0 OD1 A:ASP224 1.6 0.1 1.0 OD1 A:ASP110 2.7 0.8 1.0 NE2 A:HIS106 2.7 0.5 1.0 CE1 A:HIS106 3.0 0.5 1.0 OD2 A:ASP110 3.0 0.8 1.0 CB A:ASP224 3.1 0.1 1.0 CG A:ASP110 3.2 0.8 1.0 NE2 A:HIS220 3.9 0.2 1.0 CD2 A:HIS106 3.9 0.5 1.0 CA A:ASP224 4.0 0.1 1.0 ND1 A:HIS106 4.1 0.5 1.0 CD2 A:HIS220 4.4 0.2 1.0 O A:HIS220 4.5 0.2 1.0 CD1 A:ILE151 4.5 98.3 1.0 CG A:HIS106 4.6 0.5 1.0 CB A:ASP110 4.6 0.8 1.0 CG1 A:VAL154 4.6 0.9 1.0 N A:ASP224 4.7 0.1 1.0 CE1 A:HIS220 4.7 0.2 1.0

J.Xue, T.Xie, W.Zeng, Y.Jiang, X.C.Bai. Cryo-Em Structures of Human ZNT8 in Both Outward- and Inward-Facing Conformations. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 32723473
DOI: 10.7554/ELIFE.58823