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Sodium in PDB 7ktc: Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN), PDB code: 7ktc 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) 35.02 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.272, 62.354, 118.901, 90, 90, 90
R / Rfree (%) 15.6 / 17.6

Other elements in 7ktc:

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN) also contains other interesting chemical elements:

Manganese (Mn) 7 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+ (120MIN) (pdb code 7ktc). 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+ (120MIN), PDB code: 7ktc:

Sodium binding site 1 out of 1 in 7ktc

Go back to Sodium Binding Sites List in 7ktc
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:7.4
occ:1.00
 O A:HOH847 2.3 14.3 1.0
O A:VAL246 2.4 8.4 1.0
O A:THR241 2.4 9.9 1.0
O A:ILE243 2.4 8.4 1.0
O P:HOH214 2.4 13.7 1.0
OP1 P:DT3 2.7 8.2 1.0
C A:VAL246 3.4 7.3 1.0
C A:ILE243 3.4 9.2 1.0
C A:THR241 3.5 8.8 1.0
N A:VAL246 3.8 6.9 1.0
P P:DT3 3.8 7.1 1.0
O P:HOH211 4.0 30.9 1.0
OP2 P:DT3 4.0 7.8 1.0
N A:ILE243 4.0 10.8 1.0
O A:HOH780 4.1 34.0 1.0
CA A:VAL246 4.1 8.4 1.0
C A:GLN242 4.2 12.1 1.0
CA A:THR241 4.2 8.1 1.0
N A:PHE244 4.2 8.7 1.0
N A:GLY245 4.3 8.3 1.0
CA A:PHE244 4.3 10.1 1.0
CA A:ILE243 4.4 9.9 1.0
N A:GLN242 4.4 10.3 1.0
N A:GLY247 4.5 6.8 1.0
CB A:VAL246 4.5 9.2 1.0
O A:HOH871 4.5 26.0 1.0
CA A:GLN242 4.5 14.4 1.0
O A:GLN242 4.6 12.5 1.0
C A:PHE244 4.7 8.9 1.0
O3' P:DG2 4.7 7.2 1.0
O P:HOH219 4.8 46.6 1.0
CA A:GLY247 4.8 6.7 1.0
C A:GLY245 4.8 8.1 1.0
CB A:THR241 4.8 8.6 1.0
O A:PHE240 4.8 10.4 1.0
O5' P:DT3 5.0 8.5 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: Tue Oct 8 17:29:00 2024

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