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Magnesium in PDB 7kth: Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN), PDB code: 7kth was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.82 / 1.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.089, 68.373, 111.095, 90, 90, 90
R / Rfree (%) 16.6 / 19

Other elements in 7kth:

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN) also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN) (pdb code 7kth). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN), PDB code: 7kth:

Magnesium binding site 1 out of 1 in 7kth

Go back to Magnesium Binding Sites List in 7kth
Magnesium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:26.4
occ:0.58
 OD1 A:ASP330 1.9 41.8 1.0
O12 A:GOA501 2.1 43.4 0.9
O A:HOH602 2.2 34.6 1.0
OP1 P:8OG5 2.4 23.2 1.0
OD2 A:ASP332 2.6 26.0 1.0
CG A:ASP330 2.8 57.4 1.0
OD2 A:ASP330 3.2 69.8 1.0
C1 A:GOA501 3.2 27.1 0.9
CG A:ASP332 3.5 20.0 1.0
P P:8OG5 3.5 20.1 1.0
O A:HOH869 3.6 42.1 1.0
NA A:NA503 3.7 22.3 1.0
OD1 A:ASP332 3.8 20.0 1.0
O5' P:8OG5 3.8 18.5 1.0
C5' P:8OG5 4.0 19.3 1.0
CB A:ASP330 4.2 43.5 1.0
O11 A:GOA501 4.2 27.7 0.9
OP2 P:8OG5 4.2 21.8 1.0
O A:ASP330 4.3 27.9 1.0
N A:GLY320 4.3 12.2 1.0
CA A:GLY319 4.3 13.7 1.0
C A:ASP330 4.4 33.7 1.0
O A:HOH604 4.5 20.7 1.0
O A:HOH607 4.6 25.0 1.0
CB A:ASP332 4.7 14.9 1.0
N A:VAL331 4.7 26.3 1.0
CA A:ASP330 4.7 25.7 1.0
O3' P:DA4 4.8 20.6 1.0
O A:HOH787 4.8 28.8 1.0
C A:GLY319 4.9 11.7 1.0
N A:ASP330 4.9 22.6 1.0
O A:HOH728 5.0 36.0 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Watching A Double Strand Break Repair Polymerase Insert A Pro-Mutagenic Oxidized Nucleotide. Nat Commun V. 12 2059 2021.
ISSN: ESSN 2041-1723
PubMed: 33824325
DOI: 10.1038/S41467-021-21354-6
Page generated: Wed Oct 2 22:39:21 2024

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