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Magnesium in PDB 5vzh: Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Utp

Enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Utp

All present enzymatic activity of Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Utp:
2.7.7.7;

Protein crystallography data

The structure of Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Utp, PDB code: 5vzh 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) 45.04 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.637, 68.722, 109.404, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.1

Other elements in 5vzh:

The structure of Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Utp also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Post-Catalytic Complex of Human Polymerase Mu (W434H) Mutant with Incoming Utp (pdb code 5vzh). 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 (W434H) Mutant with Incoming Utp, PDB code: 5vzh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5vzh

Go back to Magnesium Binding Sites List in 5vzh
Magnesium binding site 1 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:12.4
occ:1.00
OD2 A:ASP330 2.0 12.4 1.0
OD1 A:ASP332 2.0 12.0 1.0
OD2 A:ASP418 2.0 12.1 1.0
O12 A:GOA507 2.1 16.9 1.0
O2 A:GOA507 2.1 13.1 1.0
O2A A:UTP506 2.4 8.8 1.0
C1 A:GOA507 2.8 34.0 1.0
C2 A:GOA507 2.9 24.9 1.0
CG A:ASP330 3.0 13.9 1.0
CG A:ASP332 3.1 11.5 1.0
CG A:ASP418 3.2 15.4 1.0
OD1 A:ASP330 3.4 10.0 1.0
PA A:UTP506 3.5 13.9 1.0
OD2 A:ASP332 3.6 10.5 1.0
MG A:MG502 3.7 10.1 1.0
CB A:ASP418 3.8 11.6 1.0
O5' A:UTP506 3.8 13.1 1.0
O1A A:UTP506 3.9 13.3 1.0
O11 A:GOA507 4.0 37.0 1.0
C5' A:UTP506 4.1 9.1 1.0
CE1 A:HIS329 4.2 13.7 1.0
OD1 A:ASP418 4.2 17.1 1.0
CB A:ASP330 4.3 12.2 1.0
OP1 P:DA4 4.3 13.6 1.0
O A:HOH703 4.3 26.7 1.0
CB A:ASP332 4.4 7.4 1.0
NH2 A:ARG416 4.4 10.3 1.0
O3A A:UTP506 4.9 12.5 1.0
NE2 A:HIS329 4.9 17.1 1.0
O1G A:UTP506 5.0 12.4 1.0

Magnesium binding site 2 out of 2 in 5vzh

Go back to Magnesium Binding Sites List in 5vzh
Magnesium binding site 2 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:10.1
occ:1.00
OD1 A:ASP330 2.0 10.0 1.0
O1B A:UTP506 2.0 8.8 1.0
O A:HOH656 2.1 11.9 1.0
OD2 A:ASP332 2.1 10.5 1.0
O1G A:UTP506 2.1 12.4 1.0
O2A A:UTP506 2.1 8.8 1.0
CG A:ASP330 3.1 13.9 1.0
PB A:UTP506 3.1 10.8 1.0
CG A:ASP332 3.1 11.5 1.0
PA A:UTP506 3.3 13.9 1.0
PG A:UTP506 3.4 15.1 1.0
O3A A:UTP506 3.4 12.5 1.0
OD1 A:ASP332 3.4 12.0 1.0
OD2 A:ASP330 3.5 12.4 1.0
O3B A:UTP506 3.6 12.6 1.0
MG A:MG501 3.7 12.4 1.0
O A:ASP330 4.0 12.3 1.0
ND1 A:HIS329 4.1 18.3 1.0
O A:HOH604 4.1 13.1 1.0
C5' A:UTP506 4.1 9.1 1.0
O3G A:UTP506 4.1 18.3 1.0
O A:HOH623 4.2 9.9 1.0
O5' A:UTP506 4.2 13.1 1.0
CE1 A:HIS329 4.3 13.7 1.0
N A:GLY320 4.3 9.8 1.0
C A:ASP330 4.3 13.2 1.0
CB A:ASP330 4.4 12.2 1.0
O2B A:UTP506 4.4 11.5 1.0
O1A A:UTP506 4.4 13.3 1.0
CB A:ASP332 4.4 7.4 1.0
O2G A:UTP506 4.5 15.1 1.0
N A:ASP330 4.5 9.6 1.0
CA A:GLY319 4.6 9.1 1.0
CA A:ASP330 4.6 14.9 1.0
N A:ASP332 4.8 8.0 1.0
N A:VAL331 4.9 10.3 1.0
O2 A:GOA507 4.9 13.1 1.0
O12 A:GOA507 5.0 16.9 1.0

Reference:

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
Page generated: Mon Sep 30 06:24:35 2024

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