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Sodium in PDB 5bpc: Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog

Enzymatic activity of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog

All present enzymatic activity of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog, PDB code: 5bpc was solved by B.D.Freudenthal, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.83 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.654, 78.635, 55.077, 90.00, 113.22, 90.00
R / Rfree (%) 21 / 25.9

Other elements in 5bpc:

The structure of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog (pdb code 5bpc). 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 Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog, PDB code: 5bpc:

Sodium binding site 1 out of 1 in 5bpc

Go back to Sodium Binding Sites List in 5bpc
Sodium binding site 1 out of 1 in the Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Datp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:30.0
occ:1.00
 O A:HOH608 2.4 35.4 1.0
O A:THR101 2.4 21.9 1.0
O A:VAL103 2.4 20.3 1.0
O A:ILE106 2.5 23.8 1.0
O P:HOH107 2.5 27.1 1.0
OP1 P:DG9 2.6 31.0 1.0
C A:THR101 3.3 25.5 1.0
C A:VAL103 3.4 22.9 1.0
C A:ILE106 3.4 18.9 1.0
P P:DG9 3.6 25.6 1.0
O A:HOH578 3.6 38.8 1.0
OP2 P:DG9 3.7 27.1 1.0
N A:ILE106 3.8 21.0 1.0
CA A:THR101 3.9 27.0 1.0
N A:GLY105 4.0 24.5 1.0
CA A:SER104 4.0 23.4 1.0
CA A:ILE106 4.1 23.3 1.0
N A:SER104 4.1 19.0 1.0
N A:VAL103 4.1 21.9 1.0
N A:ARG102 4.3 24.1 1.0
C A:ARG102 4.4 25.6 1.0
CA A:VAL103 4.4 25.2 1.0
C A:SER104 4.4 25.0 1.0
N A:GLY107 4.4 15.9 1.0
CB A:THR101 4.4 24.6 1.0
CB A:ILE106 4.5 20.3 1.0
O3' P:DC8 4.6 22.9 1.0
CA A:GLY107 4.6 22.2 1.0
CA A:ARG102 4.6 27.1 1.0
C A:GLY105 4.7 23.3 1.0
O5' P:DG9 4.7 26.3 1.0
O A:LEU100 4.8 23.4 1.0
CA A:GLY105 4.9 21.0 1.0
O A:ARG102 4.9 25.5 1.0

Reference:

B.I.Fedeles, B.D.Freudenthal, E.Yau, V.Singh, S.C.Chang, D.Li, J.C.Delaney, S.H.Wilson, J.M.Essigmann. Intrinsic Mutagenic Properties of 5-Chlorocytosine: A Mechanistic Connection Between Chronic Inflammation and Cancer. Proc.Natl.Acad.Sci.Usa V. 112 E4571 2015.
ISSN: ESSN 1091-6490
PubMed: 26243878
DOI: 10.1073/PNAS.1507709112
Page generated: Mon Oct 7 20:08:20 2024

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