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Sodium in PDB 7ktd: Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN), PDB code: 7ktd 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) 43.38 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.316, 62.42, 119.135, 90, 90, 90
R / Rfree (%) 16 / 17.8

Other elements in 7ktd:

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) also contains other interesting chemical elements:

Manganese (Mn) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) (pdb code 7ktd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN), PDB code: 7ktd:

Sodium binding site 1 out of 1 in 7ktd

Go back to Sodium Binding Sites List in 7ktd
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na510

b:19.5
occ:1.00
 O P:HOH215 2.3 27.0 1.0
O A:VAL246 2.3 20.8 1.0
O A:THR241 2.3 23.2 1.0
O A:HOH819 2.4 28.8 1.0
O A:ILE243 2.5 22.6 1.0
OP1 P:DT3 2.7 19.8 1.0
C A:VAL246 3.4 19.9 1.0
C A:THR241 3.4 21.8 1.0
C A:ILE243 3.5 24.9 1.0
O P:HOH212 3.7 35.6 1.0
P P:DT3 3.7 20.6 1.0
N A:VAL246 3.8 20.8 1.0
OP2 P:DT3 4.0 20.8 1.0
O A:HOH783 4.0 53.7 1.0
CA A:VAL246 4.1 20.5 1.0
N A:ILE243 4.1 22.7 1.0
CA A:THR241 4.2 22.6 1.0
C A:GLN242 4.2 24.4 1.0
N A:PHE244 4.3 20.6 1.0
N A:GLY245 4.3 19.9 1.0
CA A:PHE244 4.3 22.3 1.0
N A:GLN242 4.4 23.8 1.0
O A:HOH837 4.4 37.8 1.0
CA A:ILE243 4.4 21.0 1.0
N A:GLY247 4.4 20.2 1.0
CA A:GLN242 4.5 27.3 1.0
CB A:VAL246 4.5 21.1 1.0
O A:GLN242 4.6 27.2 1.0
O3' P:DG2 4.7 20.7 1.0
C A:PHE244 4.7 21.4 1.0
CA A:GLY247 4.8 21.6 1.0
CB A:THR241 4.8 23.3 1.0
C A:GLY245 4.8 19.7 1.0
O A:PHE240 4.8 22.6 1.0
O5' P:DT3 5.0 20.7 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: Mon Aug 18 10:35:09 2025

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