Magnesium in PDB 5vz7: Pre-Catalytic Ternary Complex of Human Polymerase Mu (G433A) Mutant with Incoming Nonhydrolyzable Umpnpp

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Polymerase Mu (G433A) Mutant with Incoming Nonhydrolyzable Umpnpp:
2.7.7.7;

The structure of Pre-Catalytic Ternary Complex of Human Polymerase Mu (G433A) Mutant with Incoming Nonhydrolyzable Umpnpp, PDB code: 5vz7 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)	40.44 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.805, 68.825, 109.757, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 18.8

The structure of Pre-Catalytic Ternary Complex of Human Polymerase Mu (G433A) Mutant with Incoming Nonhydrolyzable Umpnpp also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (G433A) Mutant with Incoming Nonhydrolyzable Umpnpp (pdb code 5vz7). 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 (G433A) Mutant with Incoming Nonhydrolyzable Umpnpp, PDB code: 5vz7:
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 (G433A) 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 (G433A) Mutant with Incoming Nonhydrolyzable Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:5.3 occ:1.00 OD2 A:ASP330 2.0 7.0 1.0 OD1 A:ASP332 2.0 6.0 1.0 O P:HOH105 2.1 10.9 1.0 OD2 A:ASP418 2.1 10.2 1.0 O A:HOH942 2.2 8.8 0.2 O3' P:DA4 2.2 8.4 0.8 O2A A:2KH701 2.3 6.2 1.0 CG A:ASP330 3.0 7.9 1.0 CG A:ASP332 3.1 6.1 1.0 C3' P:DA4 3.2 9.1 0.8 CG A:ASP418 3.3 10.1 1.0 OD1 A:ASP330 3.3 5.9 1.0 PA A:2KH701 3.3 5.0 1.0 OD2 A:ASP332 3.5 5.3 1.0 MG A:MG703 3.6 5.0 1.0 O5' A:2KH701 3.7 6.4 1.0 O1A A:2KH701 3.8 9.3 1.0 C4' P:DA4 3.8 11.3 0.8 CB A:ASP418 3.9 7.8 1.0 C5' P:DA4 3.9 12.1 0.8 C5' A:2KH701 4.0 7.9 1.0 CE1 A:HIS329 4.1 9.2 0.9 OD1 A:ASP418 4.3 11.4 1.0 CB A:ASP330 4.3 6.5 1.0 O5' P:DA4 4.4 13.4 0.8 CB A:ASP332 4.4 5.3 1.0 O P:HOH113 4.4 32.8 1.0 OP1 P:DA4 4.5 12.6 0.8 C2' P:DA4 4.5 11.2 0.8 NH2 A:ARG416 4.6 10.4 1.0 O3G A:2KH701 4.8 6.2 1.0 N3A A:2KH701 4.8 7.1 1.0 ND1 A:HIS329 4.8 7.2 0.5 O1B A:2KH701 4.9 5.7 1.0 NE2 A:HIS329 5.0 10.6 0.7

Magnesium binding site 2 out of 2 in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (G433A) 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 (G433A) Mutant with Incoming Nonhydrolyzable Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:5.0 occ:1.00 OD1 A:ASP330 2.0 5.9 1.0 O1B A:2KH701 2.1 5.7 1.0 OD2 A:ASP332 2.1 5.3 1.0 O3G A:2KH701 2.1 6.2 1.0 O A:HOH902 2.2 5.6 1.0 O2A A:2KH701 2.2 6.2 1.0 CG A:ASP330 3.1 7.9 1.0 CG A:ASP332 3.1 6.1 1.0 PB A:2KH701 3.1 5.4 1.0 PA A:2KH701 3.3 5.0 1.0 PG A:2KH701 3.3 9.0 1.0 N3A A:2KH701 3.5 7.1 1.0 OD1 A:ASP332 3.5 6.0 1.0 OD2 A:ASP330 3.5 7.0 1.0 O3B A:2KH701 3.6 5.1 1.0 MG A:MG702 3.6 5.3 1.0 O A:ASP330 4.0 6.5 1.0 ND1 A:HIS329 4.1 7.2 0.5 C5' A:2KH701 4.2 7.9 1.0 O1G A:2KH701 4.2 11.3 1.0 O A:HOH873 4.2 9.6 1.0 O A:HOH840 4.2 6.7 1.0 O5' A:2KH701 4.3 6.4 1.0 N A:GLY320 4.3 4.3 1.0 C A:ASP330 4.3 5.5 1.0 CE1 A:HIS329 4.4 9.2 0.9 CB A:ASP330 4.4 6.5 1.0 CB A:ASP332 4.5 5.3 1.0 O1A A:2KH701 4.5 9.3 1.0 O2G A:2KH701 4.5 10.3 1.0 O2B A:2KH701 4.5 9.9 1.0 N A:ASP330 4.5 6.9 1.0 CA A:ASP330 4.6 6.6 1.0 CA A:GLY319 4.7 5.0 1.0 O P:HOH105 4.7 10.9 1.0 N A:ASP332 4.7 5.3 1.0 N A:VAL331 4.9 6.0 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