Zinc in PDB 5x4j: The Crystal Structure of Pyrococcus Furiosus Recj (Zn-Soaking)

The structure of The Crystal Structure of Pyrococcus Furiosus Recj (Zn-Soaking), PDB code: 5x4j was solved by M.J.Li, G.S.Yi, F.Yu, H.Zhou, J.N.Chen, C.Y.Xu, F.P.Wang, X.Xiao, J.H.He, X.P.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.89 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.614, 67.347, 60.511, 90.00, 112.54, 90.00
R / Rfree (%)	17.7 / 21.2

The structure of The Crystal Structure of Pyrococcus Furiosus Recj (Zn-Soaking) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the The Crystal Structure of Pyrococcus Furiosus Recj (Zn-Soaking) (pdb code 5x4j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of Pyrococcus Furiosus Recj (Zn-Soaking), PDB code: 5x4j:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Crystal Structure of Pyrococcus Furiosus Recj (Zn-Soaking)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Pyrococcus Furiosus Recj (Zn-Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:21.7 occ:0.87 OD2 A:ASP165 2.0 25.3 1.0 O A:HOH883 2.1 26.4 1.0 OD2 A:ASP36 2.2 15.2 1.0 NE2 A:HIS106 2.2 14.7 1.0 CG A:ASP165 2.8 21.4 1.0 OD1 A:ASP165 3.0 21.0 1.0 CD2 A:HIS106 3.1 14.1 1.0 CG A:ASP36 3.1 16.5 1.0 CE1 A:HIS106 3.1 15.5 1.0 CB A:ASP36 3.6 16.0 1.0 O A:HOH857 3.7 22.1 1.0 ZN A:ZN502 3.7 25.9 1.0 CE1 A:HIS107 4.1 16.1 1.0 N A:GLY136 4.1 11.7 1.0 OD1 A:ASP36 4.1 14.3 1.0 CB A:ASP165 4.2 19.0 1.0 ND1 A:HIS106 4.2 17.0 1.0 CG A:HIS106 4.3 15.0 1.0 NE2 A:HIS107 4.3 15.4 1.0 CB A:SER135 4.5 12.7 1.0 CA A:GLY136 4.8 13.1 1.0 CA A:SER135 4.8 12.2 1.0 CB A:ALA83 4.9 14.8 1.0 O A:ALA83 4.9 14.7 1.0 C A:SER135 5.0 13.0 1.0 ND1 A:HIS107 5.0 16.4 1.0

Zinc binding site 2 out of 4 in the The Crystal Structure of Pyrococcus Furiosus Recj (Zn-Soaking)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Pyrococcus Furiosus Recj (Zn-Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:25.9 occ:0.97 NE2 A:HIS107 2.2 15.4 1.0 O A:HOH878 2.3 29.9 1.0 O A:HOH883 2.3 26.4 1.0 O A:HOH857 2.8 22.1 1.0 CE1 A:HIS107 3.1 16.1 1.0 CD2 A:HIS107 3.2 14.1 1.0 ZN A:ZN501 3.7 21.7 0.9 NE2 A:HIS440 3.8 19.6 1.0 ND1 A:HIS107 4.2 16.4 1.0 O A:HOH907 4.3 25.5 1.0 CG A:HIS107 4.3 14.2 1.0 CD2 A:HIS440 4.4 12.9 1.0 NE2 A:HIS106 4.4 14.7 1.0 OD2 A:ASP165 4.6 25.3 1.0 OD1 A:ASP165 4.8 21.0 1.0 CE1 A:HIS440 4.8 19.1 1.0 CE1 A:HIS106 4.9 15.5 1.0 O A:HOH889 5.0 37.1 1.0 O A:HOH900 5.0 39.4 1.0

Zinc binding site 3 out of 4 in the The Crystal Structure of Pyrococcus Furiosus Recj (Zn-Soaking)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Pyrococcus Furiosus Recj (Zn-Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:0.9 occ:1.00 NE2 A:HIS0 2.3 62.9 1.0 CD2 A:HIS0 3.2 59.8 1.0 CE1 A:HIS0 3.2 63.1 1.0 ND1 A:HIS0 4.3 60.9 1.0 CG A:HIS0 4.4 56.9 1.0 O A:MSE1 4.6 26.3 1.0

Zinc binding site 4 out of 4 in the The Crystal Structure of Pyrococcus Furiosus Recj (Zn-Soaking)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Pyrococcus Furiosus Recj (Zn-Soaking) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:34.1 occ:0.99 O A:HOH725 2.0 19.6 1.0 O A:HOH856 2.1 29.6 1.0 ND1 A:HIS174 2.2 21.1 1.0 CG A:HIS174 3.1 15.4 1.0 CE1 A:HIS174 3.2 19.2 1.0 CB A:HIS174 3.3 13.3 1.0 CA A:HIS174 3.9 15.6 1.0 CD2 A:HIS174 4.2 17.3 1.0 NE2 A:HIS174 4.2 19.9 1.0 O A:PHE173 4.4 19.6 1.0 N A:GLY175 4.7 16.8 1.0 O A:HOH732 4.8 36.8 1.0 N A:HIS174 4.9 17.1 1.0 C A:HIS174 4.9 17.9 1.0

M.J.Li, G.S.Yi, F.Yu, H.Zhou, J.N.Chen, C.Y.Xu, F.P.Wang, X.Xiao, J.H.He, X.P.Liu. The Crystal Structure of Pyrococcus Furiosus Recj Implicates It As An Ancestor of Eukaryotic CDC45 Nucleic Acids Res. V. 45 12551 2017.
ISSN: ISSN 0305-1048
DOI: 10.1093/NAR/GKX887