Magnesium in PDB 5vz8: Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Utp

All present enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Utp:
2.7.7.7;

The structure of Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Utp, PDB code: 5vz8 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)	29.91 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.934, 69.031, 109.825, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.4

The structure of Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Utp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Post-Catalytic Complex of Human Polymerase Mu (G433A) Mutant with Incoming Utp (pdb code 5vz8). 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 (G433A) Mutant with Incoming Utp, PDB code: 5vz8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (G433A) 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 (G433A) Mutant with Incoming Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:9.9 occ:1.00 OD2 A:ASP330 1.9 7.3 1.0 OD1 A:ASP332 2.0 8.0 1.0 O2 A:EDO505 2.1 11.4 1.0 OD2 A:ASP418 2.1 12.6 1.0 O1 A:EDO505 2.1 9.5 1.0 O2A A:UTP504 2.4 6.5 1.0 CG A:ASP330 2.9 8.4 1.0 C2 A:EDO505 3.0 20.1 1.0 C1 A:EDO505 3.1 15.4 1.0 CG A:ASP332 3.1 5.5 1.0 CG A:ASP418 3.2 12.9 1.0 OD1 A:ASP330 3.3 5.7 1.0 OD2 A:ASP332 3.5 4.8 1.0 PA A:UTP504 3.5 9.7 1.0 MG A:MG502 3.7 6.3 1.0 O5' A:UTP504 3.9 7.6 1.0 CB A:ASP418 3.9 8.1 1.0 C5' A:UTP504 4.0 9.3 1.0 O1A A:UTP504 4.1 12.2 1.0 CE1 A:HIS329 4.2 11.7 1.0 OD1 A:ASP418 4.2 12.9 1.0 CB A:ASP330 4.2 6.1 1.0 O A:HOH727 4.3 23.5 1.0 OP1 P:DA4 4.4 10.2 1.0 CB A:ASP332 4.4 5.8 1.0 NH2 A:ARG416 4.4 10.7 1.0 O3A A:UTP504 4.9 7.4 1.0 O1G A:UTP504 4.9 9.6 1.0 ND1 A:HIS329 5.0 13.5 1.0 CA A:ASP332 5.0 3.1 1.0

Magnesium binding site 2 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (G433A) 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 (G433A) Mutant with Incoming Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:6.3 occ:1.00 OD1 A:ASP330 2.0 5.7 1.0 OD2 A:ASP332 2.0 4.8 1.0 O1B A:UTP504 2.1 5.1 1.0 O A:HOH706 2.1 6.5 1.0 O2A A:UTP504 2.1 6.5 1.0 O1G A:UTP504 2.1 9.6 1.0 CG A:ASP332 3.1 5.5 1.0 CG A:ASP330 3.1 8.4 1.0 PB A:UTP504 3.1 8.7 1.0 PA A:UTP504 3.2 9.7 1.0 O3A A:UTP504 3.4 7.4 1.0 PG A:UTP504 3.4 9.7 1.0 OD1 A:ASP332 3.5 8.0 1.0 OD2 A:ASP330 3.5 7.3 1.0 O3B A:UTP504 3.6 7.9 1.0 MG A:MG501 3.7 9.9 1.0 O A:ASP330 4.0 6.2 1.0 ND1 A:HIS329 4.1 13.5 1.0 C5' A:UTP504 4.1 9.3 1.0 O5' A:UTP504 4.2 7.6 1.0 O3G A:UTP504 4.2 14.2 1.0 O A:HOH668 4.2 6.6 1.0 C A:ASP330 4.3 5.3 1.0 O A:HOH662 4.3 10.8 1.0 N A:GLY320 4.3 2.4 1.0 CB A:ASP330 4.4 6.1 1.0 CE1 A:HIS329 4.4 11.7 1.0 O1A A:UTP504 4.4 12.2 1.0 CB A:ASP332 4.4 5.8 1.0 O2B A:UTP504 4.5 8.0 1.0 N A:ASP330 4.5 7.0 1.0 O2G A:UTP504 4.5 12.4 1.0 CA A:ASP330 4.6 6.0 1.0 CA A:GLY319 4.7 5.0 1.0 N A:ASP332 4.8 4.9 1.0 N A:VAL331 4.9 5.4 1.0 O2 A:EDO505 4.9 11.4 1.0 O1 A:EDO505 5.0 9.5 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