Magnesium in PDB 5vzb: Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Utp

All present enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Utp:
2.7.7.7;

The structure of Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Utp, PDB code: 5vzb was solved by A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.33 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.807, 68.843, 109.848, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 18.7

The structure of Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Utp also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Utp (pdb code 5vzb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Utp, PDB code: 5vzb:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Utp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:8.2 occ:1.00 OD2 A:ASP330 2.0 9.3 1.0 OD1 A:ASP332 2.0 8.3 1.0 OD2 A:ASP418 2.0 14.6 1.0 O2 A:EDO507 2.1 14.0 0.9 O1 A:EDO507 2.1 10.3 0.9 O2A A:UTP506 2.5 8.6 1.0 C2 A:EDO507 3.0 24.0 0.9 C1 A:EDO507 3.0 18.1 0.9 CG A:ASP330 3.0 9.7 1.0 CG A:ASP332 3.1 5.9 1.0 CG A:ASP418 3.2 10.6 1.0 OD1 A:ASP330 3.3 7.3 1.0 PA A:UTP506 3.5 10.7 1.0 OD2 A:ASP332 3.5 6.0 1.0 MG A:MG502 3.7 7.0 1.0 O5' A:UTP506 3.8 13.2 1.0 CB A:ASP418 3.8 9.5 1.0 O1A A:UTP506 4.0 14.9 1.0 C5' A:UTP506 4.0 12.6 1.0 CE1 A:HIS329 4.2 11.2 1.0 OD1 A:ASP418 4.2 12.8 1.0 O A:HOH749 4.3 25.8 1.0 CB A:ASP330 4.3 6.9 1.0 CB A:ASP332 4.4 6.0 1.0 OP1 P:DA4 4.4 10.8 1.0 NH2 A:ARG416 4.5 10.4 1.0 O3A A:UTP506 4.9 8.5 1.0 ND1 A:HIS329 5.0 11.8 1.0 O1G A:UTP506 5.0 9.3 1.0

Magnesium binding site 2 out of 3 in the Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Utp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:7.0 occ:1.00 OD1 A:ASP330 2.0 7.3 1.0 O2A A:UTP506 2.1 8.6 1.0 OD2 A:ASP332 2.1 6.0 1.0 O1B A:UTP506 2.1 7.2 1.0 O A:HOH729 2.1 6.8 1.0 O1G A:UTP506 2.1 9.3 1.0 CG A:ASP332 3.1 5.9 1.0 CG A:ASP330 3.1 9.7 1.0 PB A:UTP506 3.1 7.8 1.0 PA A:UTP506 3.2 10.7 1.0 O3A A:UTP506 3.4 8.5 1.0 PG A:UTP506 3.4 9.9 1.0 OD1 A:ASP332 3.4 8.3 1.0 OD2 A:ASP330 3.5 9.3 1.0 O3B A:UTP506 3.6 7.8 1.0 MG A:MG501 3.7 8.2 1.0 O A:ASP330 4.0 7.0 1.0 ND1 A:HIS329 4.1 11.8 1.0 C5' A:UTP506 4.1 12.6 1.0 O3G A:UTP506 4.2 14.6 1.0 O A:HOH669 4.2 8.3 1.0 O5' A:UTP506 4.2 13.2 1.0 N A:GLY320 4.3 4.5 1.0 C A:ASP330 4.3 6.4 1.0 O A:HOH645 4.3 11.8 1.0 CE1 A:HIS329 4.4 11.2 1.0 O1A A:UTP506 4.4 14.9 1.0 CB A:ASP332 4.4 6.0 1.0 CB A:ASP330 4.4 6.9 1.0 O2B A:UTP506 4.5 9.1 1.0 N A:ASP330 4.5 7.1 1.0 O2G A:UTP506 4.5 13.7 1.0 CA A:ASP330 4.7 6.4 1.0 CA A:GLY319 4.7 6.1 1.0 N A:ASP332 4.8 5.9 1.0 N A:VAL331 4.9 6.1 1.0 O2 A:EDO507 4.9 14.0 0.9 O1 A:EDO507 4.9 10.3 0.9

Magnesium binding site 3 out of 3 in the Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Utp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Post-Catalytic Complex of Human Polymerase Mu (G433S) Mutant with Incoming Utp within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg101 b:29.7 occ:0.83 O T:HOH215 2.0 22.8 1.0 O T:HOH242 2.1 41.9 1.0 O T:HOH206 2.1 26.4 1.0 O T:HOH218 2.1 29.8 1.0 O D:HOH111 3.8 50.4 0.9 O T:HOH238 3.9 41.9 0.8 O D:HOH117 4.1 24.5 0.5 N7 T:DG2 4.2 21.9 1.0 O D:HOH117 4.2 23.2 0.5 O6 T:DG3 4.2 16.5 1.0 O T:HOH202 4.3 25.9 0.7 N4 D:DC2 4.4 16.9 1.0 O6 T:DG2 4.4 17.3 1.0 O T:HOH207 4.4 24.2 1.0 C5 T:DC1 5.0 20.0 1.0

A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Structural Accommodation of Ribonucleotide Incorporation By the Dna Repair Enzyme Polymerase Mu. Nucleic Acids Res. V. 45 9138 2017.
ISSN: ESSN 1362-4962
PubMed: 28911097
DOI: 10.1093/NAR/GKX527