Zinc in PDB 7y5h: Cryo-Em Structure of A Eukaryotic ZNT8 at A Low pH

The binding sites of Zinc atom in the Cryo-Em Structure of A Eukaryotic ZNT8 at A Low pH (pdb code 7y5h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of A Eukaryotic ZNT8 at A Low pH, PDB code: 7y5h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of A Eukaryotic ZNT8 at A Low pH


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 A Eukaryotic ZNT8 at A Low pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:34.1 occ:1.00 OE2 B:GLU357 2.0 25.7 1.0 ND1 B:HIS323 2.3 21.2 1.0 NE2 B:HIS306 2.3 19.7 1.0 SG A:CYS46 2.3 43.4 1.0 OE1 B:GLU357 2.6 25.7 1.0 CD B:GLU357 2.6 25.7 1.0 CE1 B:HIS323 3.0 21.2 1.0 CE1 B:HIS306 3.3 19.7 1.0 CD2 B:HIS306 3.3 19.7 1.0 CG B:HIS323 3.5 21.2 1.0 CB A:CYS46 3.9 43.4 1.0 CB B:HIS323 3.9 21.2 1.0 NE2 A:HIS47 4.1 45.7 1.0 CG B:GLU357 4.1 25.7 1.0 NE2 B:HIS323 4.3 21.2 1.0 ND1 B:HIS306 4.4 19.7 1.0 CG B:HIS306 4.4 19.7 1.0 CD2 B:HIS323 4.5 21.2 1.0 CE1 A:HIS47 4.6 45.7 1.0 OE1 B:GLN362 4.7 61.3 1.0 CD2 A:HIS47 4.7 45.7 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of A Eukaryotic ZNT8 at A Low pH


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 A Eukaryotic ZNT8 at A Low pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:95.8 occ:1.00 NE2 B:HIS45 2.0 50.8 1.0 ND1 B:HIS47 2.0 45.7 1.0 SG A:CYS369 2.3 55.5 1.0 SG A:CYS366 2.3 59.3 1.0 CB A:CYS366 2.5 59.3 1.0 CD2 B:HIS45 2.6 50.8 1.0 CE1 B:HIS47 2.9 45.7 1.0 CE1 B:HIS45 3.1 50.8 1.0 CG B:HIS47 3.2 45.7 1.0 CB B:HIS47 3.6 45.7 1.0 CG B:HIS45 3.7 50.8 1.0 ND1 B:HIS45 3.9 50.8 1.0 CB A:CYS369 4.0 55.5 1.0 CA A:CYS366 4.0 59.3 1.0 NE2 B:HIS47 4.0 45.7 1.0 CD2 B:HIS47 4.2 45.7 1.0 N A:CYS369 4.3 55.5 1.0 CB A:SER363 4.4 71.7 1.0 CA A:CYS369 4.6 55.5 1.0 C A:CYS366 4.7 59.3 1.0 N A:CYS366 4.8 59.3 1.0 CA B:HIS47 4.9 45.7 1.0 OG A:SER363 4.9 71.7 1.0 N B:HIS47 5.0 45.7 1.0 CB B:HIS45 5.0 50.8 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of A Eukaryotic ZNT8 at A Low pH


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 A Eukaryotic ZNT8 at A Low pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:95.8 occ:1.00 NE2 A:HIS45 2.0 50.8 1.0 ND1 A:HIS47 2.0 45.7 1.0 SG B:CYS369 2.3 55.5 1.0 SG B:CYS366 2.3 59.3 1.0 CE1 A:HIS47 2.7 45.7 1.0 CD2 A:HIS45 2.7 50.8 1.0 CB B:CYS366 2.8 59.3 1.0 CE1 A:HIS45 3.1 50.8 1.0 CG A:HIS47 3.3 45.7 1.0 CB A:HIS47 3.9 45.7 1.0 CG A:HIS45 3.9 50.8 1.0 CB B:CYS369 3.9 55.5 1.0 NE2 A:HIS47 3.9 45.7 1.0 ND1 A:HIS45 4.0 50.8 1.0 CD2 A:HIS47 4.2 45.7 1.0 CA B:CYS366 4.3 59.3 1.0 N B:CYS369 4.3 55.5 1.0 CB B:SER363 4.5 71.7 1.0 CA B:CYS369 4.6 55.5 1.0 OG B:SER363 4.7 71.7 1.0 N B:CYS366 4.8 59.3 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of A Eukaryotic ZNT8 at A Low pH


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 A Eukaryotic ZNT8 at A Low pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:34.1 occ:1.00 OE2 A:GLU357 2.0 25.7 1.0 ND1 A:HIS323 2.3 21.2 1.0 NE2 A:HIS306 2.3 19.7 1.0 SG B:CYS46 2.3 43.4 1.0 OE1 A:GLU357 2.5 25.7 1.0 CD A:GLU357 2.6 25.7 1.0 CE1 A:HIS323 3.1 21.2 1.0 CD2 A:HIS306 3.3 19.7 1.0 CE1 A:HIS306 3.3 19.7 1.0 CG A:HIS323 3.5 21.2 1.0 CB B:CYS46 3.9 43.4 1.0 CB A:HIS323 3.9 21.2 1.0 CG A:GLU357 4.1 25.7 1.0 NE2 B:HIS47 4.1 45.7 1.0 NE2 A:HIS323 4.3 21.2 1.0 ND1 A:HIS306 4.4 19.7 1.0 CG A:HIS306 4.4 19.7 1.0 CD2 A:HIS323 4.5 21.2 1.0 CE1 B:HIS47 4.5 45.7 1.0 OE1 A:GLN362 4.8 61.3 1.0 CD2 B:HIS47 4.8 45.7 1.0

S.Zhang, C.Fu, Y.Luo, Q.Xie, T.Xu, Z.Sun, Z.Su, X.Zhou. Cryo-Em Structure of A Eukaryotic Zinc Transporter at A Low pH Suggests Its Zn 2+ -Releasing Mechanism. J.Struct.Biol. V. 215 07926 2022.
ISSN: ESSN 1095-8657
PubMed: 36464198
DOI: 10.1016/J.JSB.2022.107926