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Sodium in PDB 7cod: Post Insertion Complex of Dna Polymerase Mu (K438A/Q441A) with 1-Nt Gapped Dna

Enzymatic activity of Post Insertion Complex of Dna Polymerase Mu (K438A/Q441A) with 1-Nt Gapped Dna

All present enzymatic activity of Post Insertion Complex of Dna Polymerase Mu (K438A/Q441A) with 1-Nt Gapped Dna:
2.7.7.7;

Protein crystallography data

The structure of Post Insertion Complex of Dna Polymerase Mu (K438A/Q441A) with 1-Nt Gapped Dna, PDB code: 7cod was solved by M.Guo, Y.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.77 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.18, 68.52, 111.91, 90, 90, 90
R / Rfree (%) 18.6 / 21.1

Other elements in 7cod:

The structure of Post Insertion Complex of Dna Polymerase Mu (K438A/Q441A) with 1-Nt Gapped Dna also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Post Insertion Complex of Dna Polymerase Mu (K438A/Q441A) with 1-Nt Gapped Dna (pdb code 7cod). 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 Post Insertion Complex of Dna Polymerase Mu (K438A/Q441A) with 1-Nt Gapped Dna, PDB code: 7cod:

Sodium binding site 1 out of 1 in 7cod

Go back to Sodium Binding Sites List in 7cod
Sodium binding site 1 out of 1 in the Post Insertion Complex of Dna Polymerase Mu (K438A/Q441A) with 1-Nt Gapped Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Post Insertion Complex of Dna Polymerase Mu (K438A/Q441A) with 1-Nt Gapped Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:13.9
occ:1.00
 OP1 P:DG5 2.3 32.5 1.0
O A:VAL246 2.4 23.9 1.0
O A:THR241 2.4 24.2 1.0
OP1 P:DT3 2.4 21.3 1.0
O P:HOH205 2.5 27.5 1.0
O A:ILE243 2.5 23.7 1.0
C A:VAL246 3.4 23.8 1.0
C A:ILE243 3.5 25.5 1.0
C A:THR241 3.5 24.1 1.0
P P:DT3 3.6 21.7 1.0
P P:DG5 3.7 34.3 1.0
N A:VAL246 3.8 24.1 1.0
OP2 P:DT3 4.0 19.3 1.0
C5' P:DG5 4.1 34.8 1.0
CA A:VAL246 4.1 22.8 1.0
N A:ILE243 4.2 24.9 1.0
N A:GLY245 4.2 23.6 1.0
C A:GLN242 4.2 25.7 1.0
CA A:THR241 4.3 23.2 1.0
N A:PHE244 4.3 23.8 1.0
CA A:PHE244 4.4 22.2 1.0
O5' P:DG5 4.4 35.3 1.0
N A:GLY247 4.4 24.4 1.0
C3' P:DA4 4.4 31.2 1.0
CA A:ILE243 4.5 25.5 1.0
O A:GLN242 4.5 25.7 1.0
N A:GLN242 4.5 21.3 1.0
O A:HOH829 4.6 40.7 1.0
OP2 P:DA4 4.6 26.5 1.0
O3' P:DA4 4.6 34.6 1.0
O3' P:DG2 4.6 22.1 1.0
CB A:VAL246 4.6 24.6 1.0
CA A:GLY247 4.7 24.1 1.0
C A:PHE244 4.7 24.2 1.0
CA A:GLN242 4.7 26.4 1.0
OP2 P:DG5 4.7 35.3 1.0
O5' P:DT3 4.7 22.9 1.0
C A:GLY245 4.8 25.2 1.0
O A:PHE240 4.9 23.1 1.0
CB A:THR241 4.9 22.7 1.0

Reference:

M.Guo, Y.Wang, Y.Tang, Z.Chen, J.Hou, J.Dai, Y.Wang, L.Wang, H.Xu, B.Tian, Y.Hua, Y.Zhao. Mechanism of Genome Instability Mediated By Human Dna Polymerase Mu Misincorporation. Nat Commun V. 12 3759 2021.
ISSN: ESSN 2041-1723
PubMed: 34145298
DOI: 10.1038/S41467-021-24096-7
Page generated: Tue Oct 8 16:23:57 2024

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