Zinc in PDB 5x4k: The Complex Crystal Structure of Pyrococcus Furiosus Recj and Cmp

The structure of The Complex Crystal Structure of Pyrococcus Furiosus Recj and Cmp, PDB code: 5x4k 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)	49.11 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.426, 66.172, 59.929, 90.00, 112.22, 90.00
R / Rfree (%)	16.3 / 18.9

The binding sites of Zinc atom in the The Complex Crystal Structure of Pyrococcus Furiosus Recj and Cmp (pdb code 5x4k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the The Complex Crystal Structure of Pyrococcus Furiosus Recj and Cmp, PDB code: 5x4k:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the The Complex Crystal Structure of Pyrococcus Furiosus Recj and Cmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Complex Crystal Structure of Pyrococcus Furiosus Recj and Cmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:13.7 occ:0.97 O A:HOH686 1.9 11.7 1.0 OD2 A:ASP165 1.9 16.2 1.0 O2P A:C5P505 2.1 16.8 1.0 NE2 A:HIS106 2.2 12.8 1.0 OD2 A:ASP36 2.4 13.4 1.0 CG A:ASP165 2.9 15.8 1.0 CE1 A:HIS106 3.0 11.6 1.0 OD1 A:ASP165 3.2 16.2 1.0 P A:C5P505 3.3 18.7 1.0 ZN A:ZN502 3.3 12.9 0.9 CD2 A:HIS106 3.3 11.5 1.0 CG A:ASP36 3.4 11.9 1.0 O1P A:C5P505 3.4 14.9 1.0 CB A:ASP36 3.7 11.4 1.0 O5' A:C5P505 4.0 24.7 1.0 ND1 A:HIS106 4.2 9.5 1.0 CE1 A:HIS107 4.2 15.7 1.0 CB A:ASP165 4.3 12.5 1.0 O A:ALA83 4.3 12.9 1.0 CG A:HIS106 4.4 12.1 1.0 N A:GLY136 4.4 11.0 1.0 OD1 A:ASP36 4.5 14.7 1.0 OD2 A:ASP34 4.5 16.5 1.0 O A:HOH609 4.5 21.7 1.0 O3P A:C5P505 4.5 25.2 1.0 C5' A:C5P505 4.7 23.5 1.0 NE2 A:HIS107 4.7 15.7 1.0 CB A:ALA83 4.7 13.2 1.0 NE2 A:HIS440 4.7 10.7 1.0 CB A:SER135 4.8 12.4 1.0

Zinc binding site 2 out of 3 in the The Complex Crystal Structure of Pyrococcus Furiosus Recj and Cmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Complex Crystal Structure of Pyrococcus Furiosus Recj and Cmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:12.9 occ:0.94 O1P A:C5P505 1.9 14.9 1.0 ND1 A:HIS32 2.0 13.2 1.0 OD2 A:ASP34 2.0 16.5 1.0 O A:HOH686 2.4 11.7 1.0 CE1 A:HIS32 2.8 16.0 1.0 CG A:ASP34 2.8 14.6 1.0 OD1 A:ASP34 3.0 13.1 1.0 CG A:HIS32 3.2 13.7 1.0 P A:C5P505 3.2 18.7 1.0 ZN A:ZN501 3.3 13.7 1.0 O A:HOH609 3.3 21.7 1.0 O2P A:C5P505 3.5 16.8 1.0 CB A:HIS32 3.7 10.9 1.0 OD1 A:ASP165 3.9 16.2 1.0 O A:ALA83 3.9 12.9 1.0 NE2 A:HIS32 4.0 15.7 1.0 O5' A:C5P505 4.1 24.7 1.0 CB A:ASP36 4.2 11.4 1.0 CD2 A:HIS32 4.2 17.2 1.0 O3P A:C5P505 4.2 25.2 1.0 CB A:ASP34 4.2 11.3 1.0 O A:HOH945 4.4 17.3 1.0 OD2 A:ASP36 4.5 13.4 1.0 OD2 A:ASP165 4.5 16.2 1.0 CG A:ASP165 4.6 15.8 1.0 CE1 A:HIS107 4.6 15.7 1.0 O3' A:C5P504 4.7 31.1 1.0 CB A:ALA83 4.8 13.2 1.0 CG A:ASP36 4.9 11.9 1.0 NE2 A:HIS107 4.9 15.7 1.0 N A:GLY37 5.0 10.7 1.0 O A:HOH808 5.0 18.7 1.0

Zinc binding site 3 out of 3 in the The Complex Crystal Structure of Pyrococcus Furiosus Recj and Cmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Complex Crystal Structure of Pyrococcus Furiosus Recj and Cmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:40.7 occ:0.80 O A:HOH654 1.9 31.1 1.0 NE2 A:HIS0 2.0 40.5 1.0 CE1 A:HIS0 2.8 42.2 1.0 CD2 A:HIS0 3.2 40.5 1.0 ND1 A:HIS0 4.0 41.6 1.0 CG A:HIS0 4.2 38.9 1.0 O A:HOH968 4.3 33.0 1.0 O A:MSE1 4.6 26.6 1.0 O A:HOH932 4.7 32.5 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