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Chlorine in PDB 3rjk: Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site, PDB code: 3rjk 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) 22.32 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.650, 79.970, 55.510, 90.00, 107.75, 90.00
R / Rfree (%) 20 / 25.8

Other elements in 3rjk:

The structure of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Magnesium (Mg) 2 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site (pdb code 3rjk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site, PDB code: 3rjk:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 3rjk

Go back to Chlorine Binding Sites List in 3rjk
Chlorine binding site 1 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl343

b:30.1
occ:1.00
 N A:HIS34 3.2 21.8 1.0
CB A:HIS34 3.3 20.4 1.0
C A:ALA32 3.5 24.2 1.0
N A:LYS35 3.5 18.9 1.0
CB A:ALA32 3.5 22.9 1.0
CA A:ALA32 3.6 24.8 1.0
CA A:HIS34 3.6 21.1 1.0
O A:ALA32 3.7 24.5 1.0
N A:ILE33 3.9 23.7 1.0
CD2 A:HIS34 4.0 22.1 1.0
CG A:HIS34 4.0 24.4 1.0
C A:HIS34 4.0 19.7 1.0
O A:HOH606 4.1 26.2 1.0
CG A:LYS35 4.2 16.8 1.0
C A:ILE33 4.2 24.4 1.0
CB A:LYS35 4.5 16.4 1.0
CA A:LYS35 4.6 17.0 1.0
CA A:ILE33 4.6 24.2 1.0
O6 D:DG1 4.9 19.4 1.0

Chlorine binding site 2 out of 3 in 3rjk

Go back to Chlorine Binding Sites List in 3rjk
Chlorine binding site 2 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl344

b:34.6
occ:1.00
 O A:HOH636 2.8 33.6 1.0
O A:HOH367 3.1 16.6 1.0
N A:CYS267 3.3 14.3 1.0
CA A:GLN264 3.4 16.8 1.0
C A:GLN264 3.5 16.6 1.0
N A:TYR266 3.6 17.7 1.0
SG A:CYS267 3.7 17.4 1.0
CG1 A:VAL313 3.7 19.5 1.0
CB A:TYR266 3.8 20.0 1.0
O A:GLN264 3.8 17.4 1.0
O A:ASP263 3.9 19.7 1.0
CB A:CYS267 3.9 14.1 1.0
CB A:VAL313 3.9 20.6 1.0
CA A:TYR266 4.0 17.2 1.0
N A:TYR265 4.0 17.8 1.0
C A:TYR266 4.1 17.0 1.0
CA A:CYS267 4.2 13.1 1.0
CB A:GLN264 4.2 17.6 1.0
O A:TYR296 4.3 14.1 1.0
CD2 A:TYR266 4.5 23.2 1.0
C A:TYR265 4.5 18.5 1.0
N A:GLN264 4.5 17.3 1.0
O A:VAL313 4.6 23.9 1.0
CG A:TYR266 4.6 21.6 1.0
C A:ASP263 4.6 19.4 1.0
CG2 A:VAL313 4.7 18.6 1.0
CA A:TYR265 4.8 19.3 1.0
CG A:GLN264 4.9 16.9 1.0

Chlorine binding site 3 out of 3 in 3rjk

Go back to Chlorine Binding Sites List in 3rjk
Chlorine binding site 3 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ternary Complex of Dna Polymerase Beta with A Gapped Dna Containing 8ODG:Dc Base Pair at Primer Terminus and Dg:Dcmp(CF2)Pp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl345

b:26.1
occ:1.00
 NH2 A:ARG299 3.1 31.7 1.0
ND2 A:ASN294 3.2 16.6 1.0
O A:HOH541 3.3 23.5 1.0
OG1 A:THR297 3.3 17.8 1.0
NE A:ARG299 3.3 29.5 1.0
CZ A:ARG299 3.6 33.1 1.0
CG2 A:THR297 3.9 15.8 1.0
O A:HOH402 3.9 38.3 1.0
OD1 A:ASN294 4.0 16.7 1.0
CG A:ASN294 4.0 15.4 1.0
CB A:TYR296 4.1 19.1 1.0
CB A:THR297 4.2 18.2 1.0
CD2 A:TYR296 4.3 16.7 1.0
CD A:ARG299 4.5 22.7 1.0
O A:HOH398 4.6 21.9 1.0
CG A:TYR296 4.7 17.9 1.0
N A:THR297 4.7 16.4 1.0
O T:HOH321 4.7 43.0 1.0
NH1 A:ARG299 5.0 35.5 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: Sat Dec 12 10:07:20 2020

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