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Sodium in PDB 6w2m: Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da

Enzymatic activity of Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da

All present enzymatic activity of Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da:
2.7.7.7;

Protein crystallography data

The structure of Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da, PDB code: 6w2m was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.93 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.751, 80.462, 55.612, 90.00, 107.75, 90.00
R / Rfree (%) 19.3 / 23.8

Other elements in 6w2m:

The structure of Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da (pdb code 6w2m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da, PDB code: 6w2m:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6w2m

Go back to Sodium Binding Sites List in 6w2m
Sodium binding site 1 out of 2 in the Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:20.6
occ:1.00
O P:HOH106 2.4 18.4 1.0
O A:THR101 2.5 13.5 1.0
O A:VAL103 2.6 12.7 1.0
OP1 P:DG9 2.6 16.4 1.0
O A:ILE106 2.8 12.6 1.0
O P:HOH101 3.1 21.5 1.0
C A:VAL103 3.3 15.2 1.0
O A:HOH760 3.4 35.2 1.0
C A:THR101 3.4 14.1 1.0
O P:HOH121 3.5 33.5 1.0
P P:DG9 3.6 16.0 1.0
OP2 P:DG9 3.7 18.4 1.0
CA A:SER104 3.8 11.0 1.0
C A:ILE106 3.8 13.8 1.0
N A:GLY105 3.8 13.8 1.0
N A:SER104 3.8 9.8 1.0
N A:ILE106 3.9 12.9 1.0
N A:VAL103 4.0 12.9 1.0
C A:ARG102 4.1 13.2 1.0
CA A:THR101 4.2 14.4 1.0
C A:SER104 4.2 13.7 1.0
O P:HOH124 4.3 19.0 1.0
CA A:VAL103 4.3 14.5 1.0
N A:ARG102 4.3 13.2 1.0
CA A:ILE106 4.4 13.4 1.0
CA A:ARG102 4.5 16.2 1.0
O A:ARG102 4.6 13.0 1.0
O5' P:DG9 4.7 15.8 1.0
C A:GLY105 4.7 14.8 1.0
N A:GLY107 4.7 14.5 1.0
CB A:ILE106 4.8 12.4 1.0
O3' P:DC8 4.8 15.4 1.0
CA A:GLY105 4.8 14.7 1.0
CB A:THR101 4.8 12.4 1.0
O A:LEU100 4.9 12.8 1.0

Sodium binding site 2 out of 2 in 6w2m

Go back to Sodium Binding Sites List in 6w2m
Sodium binding site 2 out of 2 in the Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Abortive Ternary Complex Crystal Structure of Dna Polymerase Beta with 8OG-Dc Base Pair at the Primer Terminus and Flipped Out Da within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:25.4
occ:1.00
O A:HOH756 2.3 27.0 1.0
O A:LEU62 2.4 26.4 1.0
O A:VAL65 2.4 20.8 1.0
O A:LYS60 2.5 25.9 1.0
O D:HOH103 2.6 34.1 1.0
OP1 D:DC3 2.7 26.6 1.0
C A:LEU62 3.3 26.5 1.0
C A:LYS60 3.5 22.4 1.0
C A:VAL65 3.5 27.4 1.0
P D:DC3 3.8 23.4 1.0
N A:VAL65 3.8 20.7 1.0
OP2 D:DC3 3.9 21.5 1.0
N A:LEU62 4.0 24.6 1.0
CA A:PRO63 4.0 24.3 1.0
C A:LYS61 4.0 26.7 1.0
N A:PRO63 4.0 23.4 1.0
CA A:VAL65 4.1 21.7 1.0
N A:GLY64 4.1 23.9 1.0
CA A:LYS60 4.2 22.1 1.0
O A:LYS61 4.2 28.2 1.0
CA A:LEU62 4.3 22.0 1.0
CB A:VAL65 4.4 22.5 1.0
N A:LYS61 4.4 19.5 1.0
CG A:LYS60 4.4 28.2 1.0
C A:PRO63 4.4 26.1 1.0
CA A:LYS61 4.5 26.6 1.0
N A:GLY66 4.6 18.8 1.0
O A:ALA59 4.7 17.5 1.0
O3' D:DT2 4.7 26.2 1.0
C A:GLY64 4.7 21.0 1.0
CA A:GLY66 4.9 24.9 1.0
CB A:LYS60 4.9 26.0 1.0
NZ A:LYS60 4.9 36.6 1.0
O5' D:DC3 5.0 31.3 1.0

Reference:

V.K.Batra, S.H.Wilson. Structure of A Dna Polymerase Abortive Complex with the 8OG:Da Base Pair at the Primer Terminus. Commun Biol V. 3 348 2020.
ISSN: ESSN 2399-3642
PubMed: 32620932
DOI: 10.1038/S42003-020-1080-4
Page generated: Tue Oct 8 14:31:24 2024

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