Chlorine 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
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6w2m

Go back to Chlorine Binding Sites List in 6w2m
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl405

b:31.9
occ:1.00
N A:HIS34 3.3 22.0 1.0
C A:ALA32 3.5 20.2 1.0
CB A:HIS34 3.5 21.8 1.0
CA A:ALA32 3.5 23.7 1.0
CB A:ALA32 3.5 19.8 1.0
N A:LYS35 3.6 20.2 1.0
N A:ILE33 3.7 19.7 1.0
CA A:HIS34 3.8 20.8 1.0
CD2 A:HIS34 3.9 28.5 1.0
O A:ALA32 3.9 17.7 1.0
CG A:HIS34 4.0 29.0 1.0
O A:HOH569 4.2 27.9 1.0
C A:HIS34 4.2 15.8 1.0
C A:ILE33 4.3 23.8 1.0
CG A:LYS35 4.3 17.4 1.0
CA A:ILE33 4.6 23.2 1.0
CB A:LYS35 4.7 18.1 1.0
CA A:LYS35 4.7 16.5 1.0
O6 D:DG1 4.9 29.4 1.0
CG1 A:ILE33 5.0 26.5 1.0
N A:ALA32 5.0 19.9 1.0

Chlorine binding site 2 out of 2 in 6w2m

Go back to Chlorine Binding Sites List in 6w2m
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl406

b:27.3
occ:1.00
NH2 A:ARG299 2.8 34.8 1.0
OG1 A:THR297 3.1 21.9 1.0
ND2 A:ASN294 3.2 17.4 1.0
O A:HOH690 3.3 44.7 1.0
NE A:ARG299 3.3 29.1 1.0
CZ A:ARG299 3.5 35.6 1.0
CG2 A:THR297 3.6 19.4 1.0
OD1 A:ASN294 3.9 17.5 1.0
CB A:THR297 4.0 19.9 1.0
CG A:ASN294 4.0 14.6 1.0
CB A:TYR296 4.0 21.9 1.0
O A:HOH793 4.2 37.1 1.0
O T:HOH145 4.2 40.0 1.0
CD2 A:TYR296 4.3 20.0 1.0
CG A:TYR296 4.6 18.7 1.0
CD A:ARG299 4.6 27.0 1.0
N A:THR297 4.6 17.4 1.0
O A:HOH662 4.7 19.2 1.0
NH1 A:ARG299 4.7 37.2 1.0
O T:HOH116 4.8 25.0 1.0
CA A:THR297 4.9 19.3 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: Sat Dec 12 14:26:35 2020

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