Zinc in PDB 7zvy: Thermococcus Kadokarensis Phosphomannose Isomerase

The structure of Thermococcus Kadokarensis Phosphomannose Isomerase, PDB code: 7zvy was solved by F.Hoh, A.Calio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.79 / 2.16
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	91.158, 91.158, 113.378, 90, 90, 120
R / Rfree (%)	22.1 / 28.9

The binding sites of Zinc atom in the Thermococcus Kadokarensis Phosphomannose Isomerase (pdb code 7zvy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Thermococcus Kadokarensis Phosphomannose Isomerase, PDB code: 7zvy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Thermococcus Kadokarensis Phosphomannose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermococcus Kadokarensis Phosphomannose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:50.0 occ:1.00 OE1 A:GLU51 2.4 92.9 1.0 NE2 A:HIS46 2.4 90.8 1.0 NE2 A:HIS85 2.5 81.7 1.0 OE2 A:GLU51 2.6 73.5 1.0 CD A:GLU51 2.8 84.0 1.0 CE1 A:HIS46 3.2 84.0 1.0 NE2 A:HIS44 3.2 69.4 1.0 CE1 A:HIS85 3.3 87.2 1.0 CD2 A:HIS46 3.6 77.1 1.0 CD2 A:HIS85 3.7 69.3 1.0 CD2 A:HIS44 3.7 74.7 1.0 CG A:GLU51 4.2 68.0 1.0 CE1 A:HIS44 4.4 74.5 1.0 ND1 A:HIS46 4.4 100.9 1.0 ND1 A:HIS85 4.5 88.9 1.0 CG A:HIS46 4.6 96.0 1.0 CZ A:PHE53 4.7 64.8 1.0 CG A:HIS85 4.7 68.9 1.0 CE1 A:PHE53 4.9 58.1 1.0 CB A:GLU51 5.0 70.7 1.0

Zinc binding site 2 out of 4 in the Thermococcus Kadokarensis Phosphomannose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermococcus Kadokarensis Phosphomannose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:50.0 occ:1.00 CD1 A:PHE77 3.6 56.4 1.0 O A:HOH311 3.6 64.6 1.0 CZ G:PHE20 3.8 72.5 1.0 O A:ILE76 3.9 69.6 1.0 CE1 A:PHE77 4.0 47.9 1.0 CE1 G:PHE20 4.4 79.2 1.0 CA A:PHE77 4.5 53.8 1.0 CG A:PHE77 4.6 49.4 1.0 CE2 G:PHE20 4.6 84.8 1.0 CE1 A:TYR69 4.7 60.1 1.0 OH A:TYR69 4.8 60.5 1.0 CZ A:TYR69 4.9 74.5 1.0 CB A:PHE77 4.9 50.7 1.0 C A:ILE76 5.0 47.8 1.0

Zinc binding site 3 out of 4 in the Thermococcus Kadokarensis Phosphomannose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thermococcus Kadokarensis Phosphomannose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:50.0 occ:1.00 O F:HOH307 2.2 62.5 1.0 OE1 F:GLU51 2.9 86.5 1.0 OE2 F:GLU51 3.0 72.6 1.0 NE2 F:HIS46 3.1 50.0 1.0 NE2 F:HIS44 3.1 79.3 1.0 CD F:GLU51 3.3 84.8 1.0 CD2 F:HIS44 3.9 79.2 1.0 CD2 F:HIS46 4.1 50.0 1.0 CE1 F:HIS46 4.1 50.0 1.0 NE2 F:HIS85 4.1 81.6 1.0 CE1 F:HIS44 4.2 77.7 1.0 CD2 F:HIS85 4.4 81.2 1.0 CG F:GLU51 4.7 66.5 1.0 CZ F:PHE53 5.0 51.7 1.0

Zinc binding site 4 out of 4 in the Thermococcus Kadokarensis Phosphomannose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thermococcus Kadokarensis Phosphomannose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn201 b:50.0 occ:1.00 CE1 G:HIS44 3.2 61.2 1.0 NE2 G:HIS44 3.4 56.7 1.0 OE1 G:GLU51 3.6 61.4 1.0 CD2 G:HIS85 3.6 58.5 1.0 OE2 G:GLU51 3.9 66.6 1.0 NE2 G:HIS85 4.1 62.0 1.0 CD G:GLU51 4.2 65.5 1.0 CZ G:PHE53 4.3 50.0 1.0 ND1 G:HIS44 4.5 60.7 1.0 CG1 G:VAL41 4.5 66.1 1.0 CD2 G:HIS44 4.8 56.7 1.0 CG G:HIS85 4.9 52.8 1.0

A.Calio, C.Dubois, S.Fontanay, M.M.Koza, F.Hoh, C.Roumestand, P.Oger, J.Peters. Unravelling the Adaptation Mechanisms to High Pressure in Proteins. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 35955607
DOI: 10.3390/IJMS23158469