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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5vz8:

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

Magnesium Binding Sites:

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 5vz8

Go back to Magnesium Binding Sites List in 5vz8
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 5vz8

Go back to Magnesium Binding Sites List in 5vz8
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

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 06:22:54 2024

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