Magnesium in PDB 5vzg: Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp:
2.7.7.7;

The structure of Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp, PDB code: 5vzg 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)	34.85 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.668, 68.555, 110.108, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.2

The structure of Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp also contains other interesting chemical elements:

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

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

Magnesium binding site 1 out of 2 in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:12.7 occ:1.00 OD2 A:ASP330 2.0 13.5 1.0 OD1 A:ASP332 2.1 9.6 1.0 OD2 A:ASP418 2.1 13.4 1.0 O3' P:DA4 2.1 9.2 0.9 O A:HOH826 2.2 14.0 1.0 O2A A:2KH701 2.3 7.8 1.0 CG A:ASP330 3.1 11.8 1.0 CG A:ASP332 3.1 10.9 1.0 C3' P:DA4 3.1 12.0 0.9 CG A:ASP418 3.2 15.4 1.0 PA A:2KH701 3.3 11.9 1.0 OD1 A:ASP330 3.5 9.4 1.0 OD2 A:ASP332 3.5 10.3 1.0 MG A:MG703 3.6 9.9 1.0 O5' A:2KH701 3.7 10.9 1.0 O1A A:2KH701 3.7 11.5 1.0 C4' P:DA4 3.8 16.9 0.9 CB A:ASP418 3.8 12.0 1.0 C5' P:DA4 3.9 17.7 0.9 CE1 A:HIS329 4.0 12.6 1.0 C5' A:2KH701 4.0 6.7 1.0 O P:HOH105 4.3 17.6 1.0 OD1 A:ASP418 4.3 13.3 1.0 CB A:ASP330 4.4 9.5 1.0 CB A:ASP332 4.4 7.3 1.0 O5' P:DA4 4.4 18.4 0.9 C2' P:DA4 4.5 11.6 0.9 OP1 P:DA4 4.5 14.3 0.9 NH2 A:ARG416 4.6 13.7 1.0 O3G A:2KH701 4.8 10.3 1.0 N3A A:2KH701 4.8 8.4 1.0 ND1 A:HIS329 4.9 23.7 1.0 NE2 A:HIS329 4.9 23.9 1.0 O1B A:2KH701 5.0 8.4 1.0

Magnesium binding site 2 out of 2 in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:9.9 occ:1.00 O1B A:2KH701 2.0 8.4 1.0 OD1 A:ASP330 2.0 9.4 1.0 OD2 A:ASP332 2.1 10.3 1.0 O2A A:2KH701 2.1 7.8 1.0 O3G A:2KH701 2.1 10.3 1.0 O A:HOH871 2.2 10.8 1.0 CG A:ASP330 3.1 11.8 1.0 CG A:ASP332 3.1 10.9 1.0 PB A:2KH701 3.1 10.8 1.0 PA A:2KH701 3.3 11.9 1.0 PG A:2KH701 3.4 13.4 1.0 N3A A:2KH701 3.5 8.4 1.0 OD1 A:ASP332 3.5 9.6 1.0 OD2 A:ASP330 3.5 13.5 1.0 O3B A:2KH701 3.6 10.7 1.0 MG A:MG702 3.6 12.7 1.0 ND1 A:HIS329 4.0 23.7 1.0 O A:ASP330 4.1 10.8 1.0 O1G A:2KH701 4.1 14.8 1.0 C5' A:2KH701 4.1 6.7 1.0 O A:HOH807 4.1 14.2 1.0 CE1 A:HIS329 4.2 12.6 1.0 O A:HOH867 4.2 12.7 1.0 N A:GLY320 4.2 9.7 1.0 O5' A:2KH701 4.3 10.9 1.0 C A:ASP330 4.3 13.0 1.0 CB A:ASP330 4.4 9.5 1.0 CB A:ASP332 4.4 7.3 1.0 O1A A:2KH701 4.4 11.5 1.0 O2B A:2KH701 4.5 12.9 1.0 O2G A:2KH701 4.5 16.0 1.0 N A:ASP330 4.5 11.3 1.0 CA A:GLY319 4.6 11.1 1.0 CA A:ASP330 4.6 13.9 1.0 O A:HOH826 4.8 14.0 1.0 N A:ASP332 4.8 11.2 1.0 N A:VAL331 4.9 9.2 1.0 O3' P:DA4 5.0 9.2 0.9 C A:GLY319 5.0 9.4 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