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Fluorine in PDB 6ctk: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf-R/S Isomers, Beta, Gamma Dttp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf-R/S Isomers, Beta, Gamma Dttp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf-R/S Isomers, Beta, Gamma Dttp Analogue:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf-R/S Isomers, Beta, Gamma Dttp Analogue, PDB code: 6ctk 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) 21.24 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.640, 79.240, 55.382, 90.00, 107.08, 90.00
R / Rfree (%) 17.9 / 24.4

Other elements in 6ctk:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf-R/S Isomers, Beta, Gamma Dttp Analogue also contains other interesting chemical elements:

Magnesium (Mg) 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 A Dideoxy Terminated Primer with Chf-R/S Isomers, Beta, Gamma Dttp Analogue (pdb code 6ctk). 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 A Dideoxy Terminated Primer with Chf-R/S Isomers, Beta, Gamma Dttp Analogue, PDB code: 6ctk:

Fluorine binding site 1 out of 1 in 6ctk

Go back to Fluorine Binding Sites List in 6ctk
Fluorine binding site 1 out of 1 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf-R/S Isomers, Beta, Gamma Dttp Analogue


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 A Dideoxy Terminated Primer with Chf-R/S Isomers, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:29.2
occ:1.00
 F2B A:FDY401 0.0 29.2 1.0
C3B A:FDY401 1.3 30.2 1.0
PG A:FDY401 2.6 30.5 1.0
PB A:FDY401 2.6 25.0 1.0
O2B A:FDY401 2.8 26.9 1.0
O3G A:FDY401 3.0 30.6 1.0
NH2 A:ARG183 3.1 25.4 1.0
O2G A:FDY401 3.2 28.1 1.0
CB A:SER180 3.3 27.1 1.0
O A:HOH671 3.4 29.9 1.0
O1B A:FDY401 3.5 23.3 1.0
OG A:SER180 3.6 32.6 1.0
O3A A:FDY401 3.7 30.1 1.0
O1G A:FDY401 3.8 29.5 1.0
O A:HOH565 3.9 27.9 1.0
CZ A:ARG183 4.0 26.3 1.0
N A:SER180 4.0 26.6 1.0
NH1 A:ARG183 4.0 24.6 1.0
CA A:SER180 4.1 26.9 1.0
O A:HOH609 4.3 35.8 1.0
O A:HOH573 4.4 35.6 1.0
O A:HOH632 5.0 29.9 1.0
MG A:MG402 5.0 28.2 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 10:29:08 2025

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