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Sodium in PDB 6p1q: Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp

Enzymatic activity of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp

All present enzymatic activity of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp:
2.7.7.7;

Protein crystallography data

The structure of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp, PDB code: 6p1q was solved by L.C.Pedersen, A.M.Kaminski, K.Bebenek, K.K.Chiruvella, D.A.Ramsden, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.07 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.768, 68.740, 110.479, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.6

Other elements in 6p1q:

The structure of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp (pdb code 6p1q). 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-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp, PDB code: 6p1q:

Sodium binding site 1 out of 1 in 6p1q

Go back to Sodium Binding Sites List in 6p1q
Sodium binding site 1 out of 1 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:18.4
occ:1.00
 O P:HOH114 2.3 25.8 1.0
O A:VAL246 2.3 22.9 1.0
O A:THR241 2.4 23.4 1.0
O P:HOH115 2.4 31.3 1.0
O A:ILE243 2.5 21.6 1.0
OP1 P:DT3 2.5 20.4 1.0
C A:VAL246 3.4 22.9 1.0
C A:ILE243 3.5 24.2 1.0
C A:THR241 3.5 24.9 1.0
P P:DT3 3.6 21.1 1.0
N A:VAL246 3.7 25.4 1.0
OP2 P:DT3 3.8 17.4 1.0
CA A:VAL246 4.1 22.6 1.0
N A:ILE243 4.2 23.4 1.0
N A:GLY245 4.2 20.8 1.0
CA A:THR241 4.2 22.9 1.0
C A:GLN242 4.3 23.7 1.0
N A:PHE244 4.3 20.2 1.0
CA A:PHE244 4.3 22.8 1.0
O A:HOH830 4.4 39.4 1.0
N A:GLY247 4.4 22.9 1.0
CA A:ILE243 4.5 22.4 1.0
O3' P:DG2 4.5 20.4 1.0
CB A:VAL246 4.5 20.8 1.0
N A:GLN242 4.5 21.1 1.0
O A:GLN242 4.6 24.8 1.0
CA A:GLN242 4.6 23.7 1.0
C A:PHE244 4.7 22.2 1.0
CA A:GLY247 4.7 23.7 1.0
C A:GLY245 4.8 23.8 1.0
O5' P:DT3 4.8 18.3 1.0
O A:PHE240 4.9 19.2 1.0
CB A:THR241 4.9 23.2 1.0

Reference:

A.M.Kaminski, K.K.Chiruvella, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Unexpected Behavior of Dna Polymerase Mu Opposite Template 8-Oxo-7,8-Dihydro-2'-Guanosine. Nucleic Acids Res. V. 47 9410 2019.
ISSN: ESSN 1362-4962
PubMed: 31435651
DOI: 10.1093/NAR/GKZ680
Page generated: Tue Oct 8 12:39:37 2024

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