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Fluorine in PDB 6bel: Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp, PDB code: 6bel 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) 23.70 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.709, 79.533, 55.458, 90.00, 107.66, 90.00
R / Rfree (%) 16.8 / 20.2

Other elements in 6bel:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom
Sodium (Na) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp (pdb code 6bel). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp, PDB code: 6bel:

Fluorine binding site 1 out of 1 in 6bel

Go back to Fluorine Binding Sites List in 6bel
Fluorine binding site 1 out of 1 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with R-Isomer of Beta-Gamma-Chf-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:22.4
occ:1.00
 F4B A:F3C406 0.0 22.4 1.0
C3B A:F3C406 1.3 20.2 1.0
PG A:F3C406 2.6 23.8 1.0
PB A:F3C406 2.7 16.2 1.0
O2B A:F3C406 2.9 15.0 1.0
O3G A:F3C406 2.9 20.1 1.0
NH2 A:ARG183 3.1 18.3 1.0
O A:HOH845 3.1 28.8 1.0
O A:HOH642 3.3 35.3 1.0
O2G A:F3C406 3.4 28.9 1.0
CB A:SER180 3.4 17.1 1.0
O1B A:F3C406 3.5 16.5 1.0
OG A:SER180 3.7 20.0 1.0
O1G A:F3C406 3.8 17.0 1.0
O3A A:F3C406 3.8 19.1 1.0
O A:HOH731 4.0 17.5 1.0
CZ A:ARG183 4.1 18.4 1.0
NH1 A:ARG183 4.3 16.1 1.0
CA A:SER180 4.3 18.7 1.0
N A:SER180 4.3 18.6 1.0
O A:HOH717 4.5 33.3 1.0
O A:HOH781 4.5 32.8 1.0
MG A:MG402 5.0 14.9 1.0

Reference:

V.K.Batra, K.Oertell, W.A.Beard, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson. Mapping Functional Substrate-Enzyme Interactions in the Pol Beta Active Site Through Chemical Biology: Structural Responses to Acidity Modification of Incoming Dntps. Biochemistry V. 57 3934 2018.
ISSN: ISSN 1520-4995
PubMed: 29874056
DOI: 10.1021/ACS.BIOCHEM.8B00418
Page generated: Tue Jul 15 10:03:55 2025

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