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Fluorine 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:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 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 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 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 at Template Position Paired with Non-Hydrolyzable Dctp Analog (Dcmp(CF2)Pp), PDB code: 3rji:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3rji

Go back to Fluorine Binding Sites List in 3rji
Fluorine 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 Fluorine with other atoms in the F 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:F401

b:15.8
occ:1.00
 F1A A:6CF401 0.0 15.8 1.0
C3A A:6CF401 1.3 17.2 1.0
F2A A:6CF401 2.2 15.7 1.0
P1 A:6CF401 2.5 13.8 1.0
P2 A:6CF401 2.6 15.8 1.0
O1B A:6CF401 2.8 17.0 1.0
O5' A:6CF401 3.0 14.6 1.0
O2A A:6CF401 3.0 15.7 1.0
O A:HOH503 3.1 15.6 1.0
C3' A:6CF401 3.5 17.9 1.0
O3B A:6CF401 3.5 14.0 1.0
C5' A:6CF401 3.6 17.5 1.0
O2B A:6CF401 3.7 14.6 1.0
C6 A:6CF401 3.7 15.0 1.0
O1A A:6CF401 3.8 10.4 1.0
O3' A:6CF401 4.0 14.9 1.0
C4' A:6CF401 4.1 15.9 1.0
O A:HOH704 4.1 27.1 1.0
C5 A:6CF401 4.1 11.3 1.0
OD2 A:ASP276 4.4 27.8 1.0
O3G A:6CF401 4.5 14.6 1.0
CB A:ASP276 4.5 21.1 1.0
CG A:ASP276 4.6 24.6 1.0
O4' A:6CF401 4.6 13.6 1.0
P3 A:6CF401 4.6 18.9 1.0
N1 A:6CF401 4.6 14.4 1.0
C2' A:6CF401 4.6 15.5 1.0
N A:ASP276 4.8 21.5 1.0
MG A:MG402 4.8 15.7 1.0
C1' A:6CF401 4.9 15.3 1.0
O1G A:6CF401 5.0 19.6 1.0

Fluorine binding site 2 out of 2 in 3rji

Go back to Fluorine Binding Sites List in 3rji
Fluorine 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 Fluorine with other atoms in the F 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:F401

b:15.7
occ:1.00
 F2A A:6CF401 0.0 15.7 1.0
C3A A:6CF401 1.3 17.2 1.0
F1A A:6CF401 2.2 15.8 1.0
P1 A:6CF401 2.5 13.8 1.0
P2 A:6CF401 2.6 15.8 1.0
O3B A:6CF401 2.7 14.0 1.0
O3G A:6CF401 2.9 14.6 1.0
O2A A:6CF401 2.9 15.7 1.0
P3 A:6CF401 3.1 18.9 1.0
O1G A:6CF401 3.1 19.6 1.0
O1A A:6CF401 3.2 10.4 1.0
O A:HOH592 3.4 21.1 1.0
O A:HOH659 3.5 31.6 1.0
O2B A:6CF401 3.5 14.6 1.0
O1B A:6CF401 3.5 17.0 1.0
O5' A:6CF401 3.9 14.6 1.0
MG A:MG402 3.9 15.7 1.0
O A:HOH704 4.3 27.1 1.0
O A:HOH503 4.4 15.6 1.0
O2G A:6CF401 4.5 17.9 1.0
O P:HOH101 4.6 26.6 1.0
C5' A:6CF401 4.7 17.5 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: Wed Jul 31 22:20:04 2024

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