Magnesium in PDB 5vze: Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Utp

All present enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Utp:
2.7.7.7;

The structure of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Utp, PDB code: 5vze 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)	32.91 / 1.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.921, 68.987, 109.996, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20

The structure of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Utp also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Utp (pdb code 5vze). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Utp, PDB code: 5vze:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Post-Catalytic Complex of Human Polymerase Mu (W434A) 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 (W434A) Mutant with Incoming Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:10.3 occ:1.00 OD2 A:ASP330 2.0 11.9 1.0 OD1 A:ASP332 2.0 10.2 1.0 O2 A:GOA506 2.1 11.7 1.0 OD2 A:ASP418 2.1 15.1 1.0 O12 A:GOA506 2.1 17.7 1.0 O2A A:UTP505 2.4 10.4 1.0 C1 A:GOA506 2.9 30.3 1.0 CG A:ASP330 3.0 11.1 1.0 C2 A:GOA506 3.0 22.9 1.0 CG A:ASP332 3.1 8.3 1.0 CG A:ASP418 3.2 12.4 1.0 OD1 A:ASP330 3.3 8.8 1.0 PA A:UTP505 3.5 12.9 1.0 OD2 A:ASP332 3.5 7.2 1.0 MG A:MG502 3.7 8.8 1.0 CB A:ASP418 3.8 11.0 1.0 O5' A:UTP505 3.9 12.1 1.0 C5' A:UTP505 4.0 13.5 1.0 O1A A:UTP505 4.0 16.6 1.0 O11 A:GOA506 4.1 34.6 1.0 CE1 A:HIS329 4.2 12.9 1.0 OD1 A:ASP418 4.3 14.8 1.0 CB A:ASP330 4.3 9.7 1.0 OP1 P:DA4 4.4 13.8 1.0 O A:HOH742 4.4 23.0 1.0 CB A:ASP332 4.4 7.7 1.0 NH2 A:ARG416 4.5 13.0 1.0 O3A A:UTP505 4.9 11.3 1.0 O1G A:UTP505 4.9 10.2 1.0 ND1 A:HIS329 5.0 14.3 1.0

Magnesium binding site 2 out of 3 in the Post-Catalytic Complex of Human Polymerase Mu (W434A) 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 (W434A) Mutant with Incoming Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:8.8 occ:1.00 OD1 A:ASP330 2.0 8.8 1.0 O2A A:UTP505 2.1 10.4 1.0 O A:HOH710 2.1 9.6 1.0 OD2 A:ASP332 2.1 7.2 1.0 O1B A:UTP505 2.1 9.3 1.0 O1G A:UTP505 2.1 10.2 1.0 CG A:ASP332 3.1 8.3 1.0 CG A:ASP330 3.1 11.1 1.0 PB A:UTP505 3.1 9.8 1.0 PA A:UTP505 3.2 12.9 1.0 O3A A:UTP505 3.4 11.3 1.0 PG A:UTP505 3.4 11.4 1.0 OD1 A:ASP332 3.5 10.2 1.0 OD2 A:ASP330 3.5 11.9 1.0 O3B A:UTP505 3.6 10.5 1.0 MG A:MG501 3.7 10.3 1.0 O A:ASP330 4.0 9.5 1.0 ND1 A:HIS329 4.1 14.3 1.0 C5' A:UTP505 4.2 13.5 1.0 O A:HOH632 4.2 9.2 1.0 O5' A:UTP505 4.2 12.1 1.0 O3G A:UTP505 4.2 16.7 1.0 O A:HOH663 4.3 13.6 1.0 C A:ASP330 4.3 9.2 1.0 N A:GLY320 4.3 5.5 1.0 CE1 A:HIS329 4.4 12.9 1.0 CB A:ASP330 4.4 9.7 1.0 O1A A:UTP505 4.4 16.6 1.0 CB A:ASP332 4.4 7.7 1.0 O2B A:UTP505 4.5 10.9 1.0 O2G A:UTP505 4.5 15.2 1.0 N A:ASP330 4.6 9.0 1.0 CA A:ASP330 4.7 9.8 1.0 CA A:GLY319 4.7 7.5 1.0 N A:ASP332 4.8 7.0 1.0 N A:VAL331 4.9 8.8 1.0 O2 A:GOA506 4.9 11.7 1.0 O12 A:GOA506 5.0 17.7 1.0

Magnesium binding site 3 out of 3 in the Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Utp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Post-Catalytic Complex of Human Polymerase Mu (W434A) Mutant with Incoming Utp within 5.0Å range: probe atom residue distance (Å) B Occ T:Mg101 b:42.8 occ:0.75 O T:HOH207 2.0 28.8 1.0 O T:HOH240 2.0 33.1 0.6 O T:HOH211 2.2 32.5 1.0 O T:HOH239 2.2 39.7 0.8 O T:HOH219 2.2 40.4 0.8 O D:HOH111 3.6 39.5 1.0 O6 T:DG3 4.1 19.4 1.0 N7 T:DG2 4.2 24.4 1.0 N4 D:DC2 4.3 19.8 1.0 O6 T:DG2 4.4 20.6 1.0 O T:HOH202 4.4 28.2 0.8 O T:HOH213 4.5 25.8 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