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Fluorine 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:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 3 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 2 in 3rjk

Go back to Fluorine Binding Sites List in 3rjk
Fluorine binding site 1 out of 2 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 Fluorine with other atoms in the F 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:F338

b:11.8
occ:1.00
F1A A:6CF338 0.0 11.8 1.0
C3A A:6CF338 1.3 12.6 1.0
F2A A:6CF338 2.1 13.8 1.0
P1 A:6CF338 2.5 11.6 1.0
P2 A:6CF338 2.5 11.0 1.0
O1B A:6CF338 2.7 9.4 1.0
O A:HOH361 3.0 16.0 1.0
O2A A:6CF338 3.0 14.3 1.0
O5' A:6CF338 3.0 12.4 1.0
O3B A:6CF338 3.4 11.8 1.0
C3' A:6CF338 3.5 11.7 1.0
O2B A:6CF338 3.7 10.4 1.0
C5' A:6CF338 3.7 12.3 1.0
O1A A:6CF338 3.8 7.8 1.0
C6 A:6CF338 3.9 9.3 1.0
O A:HOH563 4.0 28.1 1.0
O3' A:6CF338 4.1 9.9 1.0
C4' A:6CF338 4.1 11.3 1.0
C5 A:6CF338 4.3 10.2 1.0
O3G A:6CF338 4.4 12.8 1.0
P3 A:6CF338 4.5 17.2 1.0
CB A:ASP276 4.6 15.7 1.0
O4' A:6CF338 4.6 10.0 1.0
C2' A:6CF338 4.6 11.1 1.0
MG A:MG339 4.7 16.4 1.0
N1 A:6CF338 4.8 9.5 1.0
CG A:ASP276 4.8 21.0 1.0
N A:ASP276 4.8 12.4 1.0
O1G A:6CF338 4.9 18.2 1.0
OD1 A:ASP276 4.9 22.1 1.0
C1' A:6CF338 5.0 10.2 1.0

Fluorine binding site 2 out of 2 in 3rjk

Go back to Fluorine Binding Sites List in 3rjk
Fluorine binding site 2 out of 2 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 Fluorine with other atoms in the F 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:F338

b:13.8
occ:1.00
F2A A:6CF338 0.0 13.8 1.0
C3A A:6CF338 1.3 12.6 1.0
F1A A:6CF338 2.1 11.8 1.0
P2 A:6CF338 2.5 11.0 1.0
P1 A:6CF338 2.5 11.6 1.0
O3B A:6CF338 2.6 11.8 1.0
O3G A:6CF338 2.8 12.8 1.0
O2A A:6CF338 2.9 14.3 1.0
P3 A:6CF338 3.0 17.2 1.0
O1G A:6CF338 3.1 18.2 1.0
O1A A:6CF338 3.2 7.8 1.0
O A:HOH399 3.3 16.3 1.0
O A:HOH540 3.5 34.9 1.0
O2B A:6CF338 3.5 10.4 1.0
O1B A:6CF338 3.5 9.4 1.0
MG A:MG339 3.9 16.4 1.0
O5' A:6CF338 3.9 12.4 1.0
O A:HOH563 4.1 28.1 1.0
O A:HOH361 4.4 16.0 1.0
O A:HOH477 4.4 39.8 1.0
O2G A:6CF338 4.5 14.4 1.0
O A:HOH373 4.6 16.1 1.0
C5' A:6CF338 4.7 12.3 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: Mon Jul 14 19:08:36 2025

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