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Sodium in PDB 3rji: Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp)

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp)

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp):
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp), PDB code: 3rji 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) 23.38 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.760, 80.180, 55.790, 90.00, 107.96, 90.00
R / Rfree (%) 20.7 / 26.6

Other elements in 3rji:

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp) also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp) (pdb code 3rji). 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 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp), PDB code: 3rji:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3rji

Go back to Sodium Binding Sites List in 3rji
Sodium binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp)


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 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:22.6
occ:1.00
O A:THR101 2.3 22.6 1.0
O A:HOH551 2.4 42.4 1.0
O A:HOH605 2.5 23.1 1.0
O A:VAL103 2.5 19.3 1.0
OP1 P:DG9 2.6 26.3 1.0
O A:ILE106 2.6 19.1 1.0
C A:THR101 3.3 20.8 1.0
C A:VAL103 3.4 18.8 1.0
P P:DG9 3.5 29.2 1.0
OP2 P:DG9 3.5 27.9 1.0
C A:ILE106 3.6 19.7 1.0
O A:HOH719 3.7 45.7 1.0
N A:ILE106 3.8 19.8 1.0
CA A:THR101 3.9 21.9 1.0
CA A:SER104 4.0 18.7 1.0
N A:GLY105 4.0 18.8 1.0
N A:VAL103 4.1 19.3 1.0
N A:SER104 4.1 17.5 1.0
CA A:ILE106 4.2 18.9 1.0
O3' P:DC8 4.3 26.3 1.0
C A:SER104 4.3 18.3 1.0
N A:ARG102 4.3 18.9 1.0
C A:ARG102 4.3 19.9 1.0
O P:HOH115 4.4 30.2 1.0
CA A:VAL103 4.4 18.5 1.0
N A:GLY107 4.5 18.6 1.0
CB A:THR101 4.5 22.9 1.0
CB A:ILE106 4.6 19.4 1.0
CA A:ARG102 4.6 19.1 1.0
C A:GLY105 4.7 19.9 1.0
CA A:GLY107 4.8 20.2 1.0
O5' P:DG9 4.8 28.3 1.0
O A:LEU100 4.8 16.4 1.0
O A:ARG102 4.9 18.6 1.0
CA A:GLY105 5.0 19.2 1.0

Sodium binding site 2 out of 2 in 3rji

Go back to Sodium Binding Sites List in 3rji
Sodium binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp)


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 8ODG at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:39.0
occ:1.00
OP1 D:DC3 2.5 41.5 1.0
O A:HOH586 2.5 34.9 1.0
O A:LYS60 2.6 41.6 1.0
O A:VAL65 2.6 35.7 1.0
O A:LEU62 2.6 38.6 1.0
O D:HOH101 2.8 35.4 1.0
P D:DC3 3.5 43.0 1.0
C A:LEU62 3.5 39.4 1.0
OP2 D:DC3 3.5 40.3 1.0
C A:VAL65 3.6 35.5 1.0
CA A:PRO63 3.7 39.0 1.0
C A:LYS60 3.7 41.3 1.0
N A:VAL65 3.8 35.1 1.0
N A:PRO63 3.9 39.5 1.0
N A:GLY64 3.9 37.7 1.0
O A:LYS61 4.0 43.4 1.0
CA A:VAL65 4.2 35.0 1.0
C A:PRO63 4.2 39.0 1.0
C A:LYS61 4.2 42.4 1.0
CA A:LYS60 4.5 40.4 1.0
CG A:LYS60 4.5 39.6 1.0
CB A:VAL65 4.5 35.8 1.0
O3' D:DT2 4.5 42.3 1.0
N A:LEU62 4.5 40.7 1.0
CA A:LEU62 4.7 39.2 1.0
N A:GLY66 4.7 34.9 1.0
O5' D:DC3 4.7 43.9 1.0
N A:LYS61 4.7 42.0 1.0
C A:GLY64 4.8 36.9 1.0
CA A:LYS61 4.9 43.4 1.0
CB A:PRO63 4.9 40.2 1.0
CA A:GLY66 5.0 34.1 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 06:23:51 2020

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