Magnesium in PDB 5vzh: Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Utp

All present enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Utp:
2.7.7.7;

The structure of Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Utp, PDB code: 5vzh 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)	45.04 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.637, 68.722, 109.404, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.1

The structure of Post-Catalytic Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Utp (pdb code 5vzh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Utp, PDB code: 5vzh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:12.4 occ:1.00 OD2 A:ASP330 2.0 12.4 1.0 OD1 A:ASP332 2.0 12.0 1.0 OD2 A:ASP418 2.0 12.1 1.0 O12 A:GOA507 2.1 16.9 1.0 O2 A:GOA507 2.1 13.1 1.0 O2A A:UTP506 2.4 8.8 1.0 C1 A:GOA507 2.8 34.0 1.0 C2 A:GOA507 2.9 24.9 1.0 CG A:ASP330 3.0 13.9 1.0 CG A:ASP332 3.1 11.5 1.0 CG A:ASP418 3.2 15.4 1.0 OD1 A:ASP330 3.4 10.0 1.0 PA A:UTP506 3.5 13.9 1.0 OD2 A:ASP332 3.6 10.5 1.0 MG A:MG502 3.7 10.1 1.0 CB A:ASP418 3.8 11.6 1.0 O5' A:UTP506 3.8 13.1 1.0 O1A A:UTP506 3.9 13.3 1.0 O11 A:GOA507 4.0 37.0 1.0 C5' A:UTP506 4.1 9.1 1.0 CE1 A:HIS329 4.2 13.7 1.0 OD1 A:ASP418 4.2 17.1 1.0 CB A:ASP330 4.3 12.2 1.0 OP1 P:DA4 4.3 13.6 1.0 O A:HOH703 4.3 26.7 1.0 CB A:ASP332 4.4 7.4 1.0 NH2 A:ARG416 4.4 10.3 1.0 O3A A:UTP506 4.9 12.5 1.0 NE2 A:HIS329 4.9 17.1 1.0 O1G A:UTP506 5.0 12.4 1.0

Magnesium binding site 2 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:10.1 occ:1.00 OD1 A:ASP330 2.0 10.0 1.0 O1B A:UTP506 2.0 8.8 1.0 O A:HOH656 2.1 11.9 1.0 OD2 A:ASP332 2.1 10.5 1.0 O1G A:UTP506 2.1 12.4 1.0 O2A A:UTP506 2.1 8.8 1.0 CG A:ASP330 3.1 13.9 1.0 PB A:UTP506 3.1 10.8 1.0 CG A:ASP332 3.1 11.5 1.0 PA A:UTP506 3.3 13.9 1.0 PG A:UTP506 3.4 15.1 1.0 O3A A:UTP506 3.4 12.5 1.0 OD1 A:ASP332 3.4 12.0 1.0 OD2 A:ASP330 3.5 12.4 1.0 O3B A:UTP506 3.6 12.6 1.0 MG A:MG501 3.7 12.4 1.0 O A:ASP330 4.0 12.3 1.0 ND1 A:HIS329 4.1 18.3 1.0 O A:HOH604 4.1 13.1 1.0 C5' A:UTP506 4.1 9.1 1.0 O3G A:UTP506 4.1 18.3 1.0 O A:HOH623 4.2 9.9 1.0 O5' A:UTP506 4.2 13.1 1.0 CE1 A:HIS329 4.3 13.7 1.0 N A:GLY320 4.3 9.8 1.0 C A:ASP330 4.3 13.2 1.0 CB A:ASP330 4.4 12.2 1.0 O2B A:UTP506 4.4 11.5 1.0 O1A A:UTP506 4.4 13.3 1.0 CB A:ASP332 4.4 7.4 1.0 O2G A:UTP506 4.5 15.1 1.0 N A:ASP330 4.5 9.6 1.0 CA A:GLY319 4.6 9.1 1.0 CA A:ASP330 4.6 14.9 1.0 N A:ASP332 4.8 8.0 1.0 N A:VAL331 4.9 10.3 1.0 O2 A:GOA507 4.9 13.1 1.0 O12 A:GOA507 5.0 16.9 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