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Sodium in PDB 3rjf: Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp)

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp)

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp):
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp), PDB code: 3rjf was solved by V.K.Batra, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.17 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.550, 79.810, 55.690, 90.00, 107.88, 90.00
R / Rfree (%) 19.3 / 25.6

Other elements in 3rjf:

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp) (pdb code 3rjf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp), PDB code: 3rjf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3rjf

Go back to Sodium Binding Sites List in 3rjf
Sodium binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:30.9
occ:1.00
O A:THR101 2.3 25.8 1.0
O P:HOH71 2.4 34.0 1.0
OP1 P:DG9 2.5 25.2 1.0
O A:HOH499 2.5 39.0 1.0
O A:VAL103 2.6 24.3 1.0
O A:ILE106 2.6 28.1 1.0
C A:THR101 3.3 27.0 1.0
P P:DG9 3.5 26.1 1.0
C A:VAL103 3.5 24.3 1.0
OP2 P:DG9 3.6 27.4 1.0
C A:ILE106 3.7 28.3 1.0
N A:ILE106 3.8 27.7 1.0
CA A:SER104 3.9 26.2 1.0
N A:GLY105 3.9 26.0 1.0
CA A:THR101 4.0 26.0 1.0
N A:SER104 4.1 25.4 1.0
N A:VAL103 4.1 25.7 1.0
C A:ARG102 4.2 25.0 1.0
CA A:ILE106 4.3 26.5 1.0
N A:ARG102 4.3 25.9 1.0
C A:SER104 4.3 26.5 1.0
O3' P:DC8 4.4 24.6 1.0
CA A:ARG102 4.5 25.7 1.0
CA A:VAL103 4.5 24.4 1.0
O A:ARG102 4.6 26.0 1.0
CB A:ILE106 4.6 25.1 1.0
O5' P:DG9 4.7 28.1 1.0
CB A:THR101 4.7 25.2 1.0
C A:GLY105 4.7 27.2 1.0
N A:GLY107 4.8 26.8 1.0
O A:LEU100 4.8 25.9 1.0
O A:HOH490 4.9 30.3 1.0
CA A:GLY105 4.9 27.9 1.0

Sodium binding site 2 out of 2 in 3rjf

Go back to Sodium Binding Sites List in 3rjf
Sodium binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing (Syn)8ODG at Template Position Paired with Non-Hydrolyzable Datp Analog (Dapcpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:44.9
occ:1.00
O A:LEU62 2.0 43.9 1.0
O A:LYS60 2.1 42.2 1.0
O A:VAL65 2.6 36.3 1.0
OP1 D:DC3 2.8 44.4 1.0
O A:HOH437 2.8 34.7 1.0
C A:LEU62 3.1 41.5 1.0
C A:LYS60 3.2 43.0 1.0
C A:VAL65 3.4 35.1 1.0
N A:VAL65 3.6 33.4 1.0
N A:LEU62 3.8 44.0 1.0
CA A:PRO63 3.8 38.0 1.0
N A:PRO63 3.8 39.2 1.0
CA A:LYS60 3.9 42.1 1.0
CA A:VAL65 3.9 33.0 1.0
N A:GLY64 3.9 36.1 1.0
C A:LYS61 4.0 45.1 1.0
P D:DC3 4.0 43.9 1.0
CB A:VAL65 4.1 31.4 1.0
CA A:LEU62 4.1 42.5 1.0
N A:LYS61 4.2 43.9 1.0
C A:PRO63 4.3 36.2 1.0
OP2 D:DC3 4.3 46.4 1.0
O A:LYS61 4.3 45.2 1.0
O A:ALA59 4.3 35.3 1.0
CG A:LYS60 4.3 41.5 1.0
CA A:LYS61 4.4 45.5 1.0
N A:GLY66 4.5 36.4 1.0
C A:GLY64 4.6 33.8 1.0
CB A:LYS60 4.7 41.0 1.0
O3' D:DT2 4.8 42.8 1.0
CA A:GLY66 4.9 37.8 1.0
CA A:GLY64 4.9 34.4 1.0
CG1 A:VAL65 5.0 26.9 1.0
CB A:LEU62 5.0 42.3 1.0

Reference:

V.K.Batra, D.D.Shock, W.A.Beard, C.E.Mckenna, S.H.Wilson. Binary Complex Crystal Structure of Dna Polymerase Beta Reveals Multiple Conformations of the Templating 8-Oxoguanine Lesion Proc.Natl.Acad.Sci.Usa V. 109 113 2012.
ISSN: ISSN 0027-8424
PubMed: 22178760
DOI: 10.1073/PNAS.1112235108
Page generated: Tue Dec 15 06:23:48 2020

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