Zinc in PDB 7fh4: Chlorovirus Pbcv-1 Bi-Functional Dcmp/Dctp Deaminase Bi-Dcd

The structure of Chlorovirus Pbcv-1 Bi-Functional Dcmp/Dctp Deaminase Bi-Dcd, PDB code: 7fh4 was solved by Z.She, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.79 / 2.00
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	81.582, 81.582, 80.396, 90, 90, 120
R / Rfree (%)	17 / 21.4

The structure of Chlorovirus Pbcv-1 Bi-Functional Dcmp/Dctp Deaminase Bi-Dcd also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Chlorovirus Pbcv-1 Bi-Functional Dcmp/Dctp Deaminase Bi-Dcd (pdb code 7fh4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Chlorovirus Pbcv-1 Bi-Functional Dcmp/Dctp Deaminase Bi-Dcd, PDB code: 7fh4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Chlorovirus Pbcv-1 Bi-Functional Dcmp/Dctp Deaminase Bi-Dcd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Chlorovirus Pbcv-1 Bi-Functional Dcmp/Dctp Deaminase Bi-Dcd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:58.7 occ:1.00 ND1 A:HIS67 2.2 34.6 1.0 SG A:CYS95 2.3 37.4 1.0 SG A:CYS98 2.3 34.7 1.0 N4 A:DCM201 2.7 36.5 1.0 C4 A:DCM201 3.1 41.7 1.0 CE1 A:HIS67 3.1 42.2 1.0 CB A:CYS98 3.1 30.5 1.0 CG A:HIS67 3.2 38.4 1.0 CB A:CYS95 3.3 43.2 1.0 N3 A:DCM201 3.5 46.8 1.0 CB A:HIS67 3.6 34.5 1.0 O A:HOH359 3.6 44.8 1.0 N A:CYS95 3.6 44.8 1.0 C5 A:DCM201 3.7 51.7 1.0 N A:CYS98 3.8 37.8 1.0 CA A:CYS95 4.0 43.2 1.0 CA A:CYS98 4.1 36.1 1.0 OE1 A:GLN69 4.2 44.1 1.0 NE2 A:HIS67 4.2 44.4 1.0 CD2 A:HIS67 4.3 41.4 1.0 C A:CYS95 4.5 39.4 1.0 C2 A:DCM201 4.5 50.2 1.0 O A:CYS95 4.5 33.8 1.0 C6 A:DCM201 4.6 52.2 1.0 O B:HOH361 4.7 47.9 1.0 C A:PRO94 4.7 39.8 1.0 CD A:GLN69 4.9 55.9 1.0 C A:GLU97 4.9 36.9 1.0 CA A:PRO94 4.9 42.4 1.0 N1 A:DCM201 5.0 52.0 1.0

Zinc binding site 2 out of 2 in the Chlorovirus Pbcv-1 Bi-Functional Dcmp/Dctp Deaminase Bi-Dcd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Chlorovirus Pbcv-1 Bi-Functional Dcmp/Dctp Deaminase Bi-Dcd within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:58.5 occ:1.00 ND1 B:HIS67 2.0 39.6 1.0 SG B:CYS98 2.2 34.5 1.0 SG B:CYS95 2.4 38.2 1.0 N4 B:DCM201 2.7 27.8 1.0 CE1 B:HIS67 3.0 41.0 1.0 CG B:HIS67 3.1 37.2 1.0 C4 B:DCM201 3.1 42.4 1.0 CB B:CYS98 3.1 33.9 1.0 O B:HOH362 3.4 49.5 1.0 CB B:HIS67 3.4 31.4 1.0 CB B:CYS95 3.4 43.4 1.0 N3 B:DCM201 3.5 47.0 1.0 N B:CYS95 3.7 40.0 1.0 C5 B:DCM201 3.8 53.9 1.0 N B:CYS98 3.9 33.6 1.0 CA B:CYS98 4.1 33.5 1.0 CA B:CYS95 4.1 44.6 1.0 NE2 B:HIS67 4.1 45.2 1.0 CD2 B:HIS67 4.2 40.8 1.0 OE1 B:GLN69 4.2 40.5 1.0 O A:HOH358 4.4 41.9 1.0 C2 B:DCM201 4.4 48.2 1.0 C B:CYS95 4.7 41.7 1.0 C6 B:DCM201 4.7 55.7 1.0 O B:CYS95 4.7 33.9 1.0 C B:PRO94 4.8 37.9 1.0 CD B:GLN69 4.8 54.6 1.0 CA B:PRO94 4.9 40.0 1.0 CA B:HIS67 5.0 27.8 1.0 N1 B:DCM201 5.0 52.9 1.0

Y.H.Li, H.F.Hou, Z.Geng, H.Zhang, Z.She, Y.H.Dong. Structural Basis of A Multi-Functional Deaminase in Chlorovirus Pbcv-1. Arch.Biochem.Biophys. V. 727 09339 2022.
ISSN: ESSN 1096-0384
PubMed: 35764100
DOI: 10.1016/J.ABB.2022.109339