Magnesium in PDB 5vza: Pre-Catalytic Ternary Complex of Human Polymerase Mu (G433S) Mutant with Incoming Nonhydrolyzable Umpnpp

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Polymerase Mu (G433S) Mutant with Incoming Nonhydrolyzable Umpnpp:
2.7.7.7;

The structure of Pre-Catalytic Ternary Complex of Human Polymerase Mu (G433S) Mutant with Incoming Nonhydrolyzable Umpnpp, PDB code: 5vza 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)	32.37 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.866, 68.838, 110.044, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 18.4

The structure of Pre-Catalytic Ternary Complex of Human Polymerase Mu (G433S) Mutant with Incoming Nonhydrolyzable Umpnpp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (G433S) Mutant with Incoming Nonhydrolyzable Umpnpp (pdb code 5vza). 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 (G433S) Mutant with Incoming Nonhydrolyzable Umpnpp, PDB code: 5vza:
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 (G433S) 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 (G433S) Mutant with Incoming Nonhydrolyzable Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:7.8 occ:1.00 OD2 A:ASP330 2.0 8.2 1.0 OD1 A:ASP332 2.0 7.4 1.0 OD2 A:ASP418 2.1 9.8 1.0 O P:HOH105 2.1 11.7 1.0 O A:HOH917 2.1 9.4 0.3 O3' P:DA4 2.1 11.0 0.7 O2A A:2KH701 2.3 7.2 1.0 CG A:ASP330 3.0 8.2 1.0 CG A:ASP332 3.1 6.1 1.0 CG A:ASP418 3.2 9.9 1.0 C3' P:DA4 3.2 9.8 0.7 OD1 A:ASP330 3.3 7.6 1.0 PA A:2KH701 3.4 7.7 1.0 OD2 A:ASP332 3.5 5.9 1.0 MG A:MG703 3.6 6.9 1.0 O5' A:2KH701 3.7 10.2 1.0 O1A A:2KH701 3.7 10.7 1.0 C4' P:DA4 3.8 10.5 0.7 CB A:ASP418 3.9 8.6 1.0 C5' P:DA4 3.9 9.7 0.7 C5' A:2KH701 4.0 10.5 1.0 CE1 A:HIS329 4.1 9.4 1.0 OD1 A:ASP418 4.2 10.7 1.0 CB A:ASP330 4.3 7.9 1.0 CB A:ASP332 4.4 6.0 1.0 O5' P:DA4 4.5 12.1 0.7 OP1 P:DA4 4.5 11.1 0.7 C2' P:DA4 4.5 10.3 0.7 O P:HOH112 4.5 18.6 0.6 NH2 A:ARG416 4.7 11.1 1.0 O3G A:2KH701 4.8 9.4 1.0 N3A A:2KH701 4.8 7.2 1.0 ND1 A:HIS329 4.9 7.8 0.5 NE2 A:HIS329 4.9 12.8 0.8 O1B A:2KH701 4.9 7.3 1.0

Magnesium binding site 2 out of 2 in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (G433S) 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 (G433S) Mutant with Incoming Nonhydrolyzable Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:6.9 occ:1.00 OD1 A:ASP330 2.0 7.6 1.0 OD2 A:ASP332 2.0 5.9 1.0 O1B A:2KH701 2.1 7.3 1.0 O A:HOH937 2.1 6.5 1.0 O3G A:2KH701 2.1 9.4 1.0 O2A A:2KH701 2.2 7.2 1.0 CG A:ASP332 3.1 6.1 1.0 CG A:ASP330 3.1 8.2 1.0 PB A:2KH701 3.2 7.5 1.0 PA A:2KH701 3.3 7.7 1.0 PG A:2KH701 3.4 9.2 1.0 OD1 A:ASP332 3.4 7.4 1.0 N3A A:2KH701 3.5 7.2 1.0 OD2 A:ASP330 3.5 8.2 1.0 O3B A:2KH701 3.6 7.1 1.0 MG A:MG702 3.6 7.8 1.0 O A:ASP330 4.0 7.2 1.0 ND1 A:HIS329 4.0 7.8 0.5 O1G A:2KH701 4.2 12.2 1.0 C5' A:2KH701 4.2 10.5 1.0 O A:HOH865 4.2 7.3 1.0 O A:HOH861 4.2 11.0 1.0 N A:GLY320 4.3 4.9 1.0 O5' A:2KH701 4.3 10.2 1.0 CE1 A:HIS329 4.3 9.4 1.0 C A:ASP330 4.3 8.1 1.0 CB A:ASP330 4.4 7.9 1.0 CB A:ASP332 4.4 6.0 1.0 O1A A:2KH701 4.5 10.7 1.0 N A:ASP330 4.5 7.8 1.0 O2G A:2KH701 4.5 12.6 1.0 O2B A:2KH701 4.5 8.9 1.0 CA A:GLY319 4.6 6.2 1.0 CA A:ASP330 4.6 8.1 1.0 O P:HOH105 4.7 11.7 1.0 N A:ASP332 4.7 6.8 1.0 N A:VAL331 4.9 6.9 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