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Sodium in PDB 6wid: Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate

Enzymatic activity of Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate

All present enzymatic activity of Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate:
2.7.7.7;

Protein crystallography data

The structure of Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate, PDB code: 6wid was solved by A.M.Kaminski, T.A.Kunkel, L.C.Pedersen, K.Bebenek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.02 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.186, 62.040, 118.320, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 17.7

Other elements in 6wid:

The structure of Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate (pdb code 6wid). 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 Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate, PDB code: 6wid:

Sodium binding site 1 out of 1 in 6wid

Go back to Sodium Binding Sites List in 6wid
Sodium binding site 1 out of 1 in the Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Nucleotide Incorporation Intermediate Into Quaternary Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na705

b:11.1
occ:1.00
 O A:HOH1015 2.4 31.4 1.0
O P:HOH119 2.4 21.9 1.0
O A:VAL246 2.4 11.8 1.0
O A:THR241 2.5 15.3 1.0
O A:ILE243 2.5 12.4 0.4
O A:ILE243 2.7 11.8 0.6
OP1 P:DT3 2.8 11.8 1.0
O P:HOH118 3.5 23.3 1.0
C A:VAL246 3.5 10.3 1.0
C A:ILE243 3.5 12.4 0.4
C A:THR241 3.6 12.2 1.0
C A:ILE243 3.6 12.3 0.6
N A:VAL246 3.8 10.7 1.0
P P:DT3 3.8 10.3 1.0
O A:HOH913 3.9 40.2 1.0
OP2 P:DT3 4.0 11.1 1.0
N A:ILE243 4.2 12.8 0.4
CA A:VAL246 4.2 9.8 1.0
N A:ILE243 4.2 12.3 0.6
C A:GLN242 4.2 16.1 1.0
N A:GLY245 4.3 10.4 1.0
CA A:THR241 4.3 11.9 1.0
N A:PHE244 4.3 10.4 1.0
CA A:PHE244 4.3 10.6 1.0
O A:HOH1032 4.5 29.9 1.0
N A:GLN242 4.5 13.8 1.0
CA A:ILE243 4.5 12.3 0.4
CA A:ILE243 4.5 11.6 0.6
CA A:GLN242 4.5 15.8 1.0
N A:GLY247 4.6 9.6 1.0
O A:GLN242 4.6 19.8 1.0
CB A:VAL246 4.6 10.0 1.0
O P:HOH101 4.6 32.4 1.0
C A:PHE244 4.7 10.0 1.0
O3' P:DG2 4.8 10.1 1.0
C A:GLY245 4.9 11.2 1.0
CA A:GLY247 4.9 9.4 1.0
CB A:THR241 4.9 12.3 1.0
O A:PHE240 5.0 13.3 1.0

Reference:

A.M.Kaminski, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, L.C.Pedersen, K.Bebenek. Structural Snapshots of Human Dna Polymerase Mu Engaged on A Dna Double-Strand Break. Nat Commun V. 11 4784 2020.
ISSN: ESSN 2041-1723
PubMed: 32963245
DOI: 10.1038/S41467-020-18506-5
Page generated: Tue Oct 8 14:36:53 2024

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