Magnesium 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:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Chlorovirus Pbcv-1 Bi-Functional Dcmp/Dctp Deaminase Bi-Dcd, PDB code: 7fh4:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg204 b:38.5 occ:1.00 O2A A:DCP202 2.0 32.9 1.0 O1B A:DCP202 2.0 34.0 1.0 O2G A:DCP202 2.1 46.5 1.0 O A:HOH314 2.1 38.8 1.0 OE2 A:GLU51 2.1 43.3 1.0 O A:HOH316 2.2 38.0 1.0 PB A:DCP202 3.1 37.5 1.0 CD A:GLU51 3.2 45.0 1.0 PG A:DCP202 3.2 44.4 1.0 PA A:DCP202 3.2 36.5 1.0 O3B A:DCP202 3.4 41.0 1.0 O3A A:DCP202 3.4 41.9 1.0 NZ A:LYS20 3.8 35.8 1.0 CG A:GLU51 3.8 36.0 1.0 O A:HOH340 3.8 43.8 1.0 O1G A:DCP202 3.9 49.5 1.0 C5' A:DCP202 4.1 35.1 1.0 O A:HOH321 4.1 42.3 1.0 O5' A:DCP202 4.2 35.8 1.0 O A:HOH361 4.2 50.6 1.0 OE1 A:GLU51 4.2 44.0 1.0 O A:PHE49 4.3 44.6 1.0 O A:PRO46 4.4 32.9 1.0 O1A A:DCP202 4.4 38.1 1.0 O3G A:DCP202 4.5 41.5 1.0 O2B A:DCP202 4.5 34.7 1.0 N A:GLY48 4.5 41.1 1.0 O A:LEU45 4.6 36.2 1.0 CE A:LYS20 4.7 37.7 1.0 CA A:ARG47 5.0 34.7 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg204 b:39.0 occ:1.00 O2G B:DCP202 1.8 40.0 1.0 O1A B:DCP202 2.0 33.5 1.0 O2B B:DCP202 2.0 37.7 1.0 OE2 B:GLU51 2.1 40.3 1.0 O B:HOH319 2.1 38.9 1.0 O B:HOH329 2.2 38.0 1.0 PB B:DCP202 3.0 39.5 1.0 PG B:DCP202 3.0 43.7 1.0 CD B:GLU51 3.2 44.4 1.0 PA B:DCP202 3.2 37.9 1.0 O3B B:DCP202 3.2 37.2 1.0 O3A B:DCP202 3.4 38.1 1.0 O3G B:DCP202 3.8 46.9 1.0 NZ B:LYS20 3.8 36.9 1.0 CG B:GLU51 3.8 37.2 1.0 O B:HOH333 3.9 35.6 1.0 O B:HOH353 4.2 47.3 1.0 OE1 B:GLU51 4.2 46.2 1.0 C5' B:DCP202 4.2 43.0 1.0 O1G B:DCP202 4.2 45.1 1.0 O5' B:DCP202 4.2 36.2 1.0 O2A B:DCP202 4.3 34.1 1.0 O1B B:DCP202 4.4 39.3 1.0 N B:GLY48 4.5 42.8 1.0 O B:PHE49 4.5 40.9 1.0 O B:PRO46 4.5 37.9 1.0 CE B:LYS20 4.8 37.3 1.0 O B:LEU45 4.9 39.5 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