Magnesium in PDB 5twr: Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp:
2.7.7.7;

The structure of Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp, PDB code: 5twr 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)	28.71 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.703, 68.606, 109.767, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.4

The structure of Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp (pdb code 5twr). 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 (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp, PDB code: 5twr:
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 (H329A) 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 (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:13.0 occ:1.00 OD2 A:ASP418 2.0 14.1 1.0 OD2 A:ASP330 2.0 16.1 1.0 OD1 A:ASP332 2.0 11.5 1.0 O A:HOH847 2.1 14.0 1.0 O3' P:DA4 2.1 11.8 1.0 O2A A:2KH701 2.2 9.4 1.0 CG A:ASP332 3.1 13.5 1.0 CG A:ASP330 3.1 14.6 1.0 CG A:ASP418 3.2 15.0 1.0 C3' P:DA4 3.2 12.5 1.0 PA A:2KH701 3.3 13.2 1.0 OD1 A:ASP330 3.4 15.2 1.0 OD2 A:ASP332 3.5 12.3 1.0 MG A:MG703 3.6 11.9 1.0 O1A A:2KH701 3.7 15.0 1.0 O5' A:2KH701 3.7 11.8 1.0 C4' P:DA4 3.8 14.6 1.0 CB A:ASP418 3.8 12.5 1.0 O A:HOH981 3.9 26.3 1.0 C5' P:DA4 3.9 12.6 1.0 C5' A:2KH701 4.0 7.8 1.0 OD1 A:ASP418 4.2 14.9 1.0 CB A:ASP332 4.4 10.5 1.0 CB A:ASP330 4.4 13.9 1.0 OP1 P:DA4 4.5 14.0 1.0 C2' P:DA4 4.5 12.2 1.0 O5' P:DA4 4.6 15.4 1.0 O3G A:2KH701 4.7 12.1 1.0 CZ3 A:TRP434 4.7 10.2 0.7 NH2 A:ARG416 4.7 15.5 1.0 N3A A:2KH701 4.8 14.0 1.0 O1B A:2KH701 4.9 10.3 1.0

Magnesium binding site 2 out of 2 in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) 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 (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:11.9 occ:1.00 OD1 A:ASP330 2.0 15.2 1.0 O3G A:2KH701 2.0 12.1 1.0 OD2 A:ASP332 2.1 12.3 1.0 O1B A:2KH701 2.1 10.3 1.0 O2A A:2KH701 2.1 9.4 1.0 O A:HOH870 2.2 13.8 1.0 CG A:ASP330 3.0 14.6 1.0 CG A:ASP332 3.1 13.5 1.0 PB A:2KH701 3.1 12.8 1.0 PA A:2KH701 3.3 13.2 1.0 PG A:2KH701 3.4 13.9 1.0 OD2 A:ASP330 3.4 16.1 1.0 OD1 A:ASP332 3.5 11.5 1.0 N3A A:2KH701 3.5 14.0 1.0 O3B A:2KH701 3.5 12.9 1.0 MG A:MG702 3.6 13.0 1.0 O A:HOH981 3.9 26.3 1.0 C5' A:2KH701 4.1 7.8 1.0 O A:ASP330 4.1 13.0 1.0 O A:HOH822 4.2 14.1 1.0 O1G A:2KH701 4.2 16.6 1.0 N A:GLY320 4.2 11.1 1.0 O5' A:2KH701 4.3 11.8 1.0 O A:HOH889 4.3 12.8 1.0 C A:ASP330 4.3 14.9 1.0 CB A:ASP330 4.4 13.9 1.0 O1A A:2KH701 4.4 15.0 1.0 CB A:ASP332 4.4 10.5 1.0 O2G A:2KH701 4.4 14.5 1.0 O2B A:2KH701 4.5 15.2 1.0 N A:ASP330 4.5 11.4 1.0 CA A:GLY319 4.6 13.9 1.0 O A:HOH847 4.6 14.0 1.0 CA A:ASP330 4.7 14.8 1.0 N A:ASP332 4.7 12.5 1.0 N A:VAL331 4.9 11.4 1.0 C A:GLY319 5.0 15.0 1.0 O3' P:DA4 5.0 11.8 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