Fluorine in PDB 6ctv: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp 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 CF2, Beta, Gamma Dctp Analogue, PDB code: 6ctv 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) 23.62 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.666, 79.251, 55.337, 90.00, 107.75, 90.00
R / Rfree (%) 18 / 22

Other elements in 6ctv:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue 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 A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue (pdb code 6ctv). 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 Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue, PDB code: 6ctv:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6ctv

Go back to Fluorine Binding Sites List in 6ctv
Fluorine binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp 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 CF2, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:21.2
occ:1.00
 F3B A:FFJ406 0.0 21.2 1.0
C3B A:FFJ406 1.4 23.2 1.0
F4B A:FFJ406 2.3 24.2 1.0
PB A:FFJ406 2.6 20.7 1.0
PG A:FFJ406 2.6 26.3 1.0
O3A A:FFJ406 2.7 24.4 1.0
O1G A:FFJ406 2.8 25.5 1.0
O A:HOH807 3.2 40.6 1.0
O2G A:FFJ406 3.3 23.2 1.0
O A:HOH657 3.3 22.1 1.0
O A:HOH735 3.4 29.2 1.0
O2B A:FFJ406 3.4 19.0 1.0
O A:HOH760 3.5 31.0 1.0
O A:HOH799 3.6 43.5 1.0
O1B A:FFJ406 3.9 20.0 1.0
O3G A:FFJ406 3.9 24.7 1.0
PA A:FFJ406 3.9 20.4 1.0
O2A A:FFJ406 4.0 21.3 1.0
O A:HOH742 4.2 34.4 1.0
O A:HOH628 4.2 36.4 1.0
O1A A:FFJ406 4.4 16.8 1.0
O A:HOH748 4.7 39.6 1.0
MG A:MG402 4.7 19.1 1.0
NH2 A:ARG183 4.9 20.4 1.0

Fluorine binding site 2 out of 2 in 6ctv

Go back to Fluorine Binding Sites List in 6ctv
Fluorine binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:24.2
occ:1.00
 F4B A:FFJ406 0.0 24.2 1.0
C3B A:FFJ406 1.4 23.2 1.0
F3B A:FFJ406 2.3 21.2 1.0
PB A:FFJ406 2.6 20.7 1.0
PG A:FFJ406 2.7 26.3 1.0
O2B A:FFJ406 2.9 19.0 1.0
O3G A:FFJ406 2.9 24.7 1.0
NH2 A:ARG183 3.1 20.4 1.0
O A:HOH628 3.1 36.4 1.0
O A:HOH760 3.2 31.0 1.0
O1G A:FFJ406 3.3 25.5 1.0
CB A:SER180 3.4 23.5 1.0
O A:HOH799 3.4 43.5 1.0
O1B A:FFJ406 3.5 20.0 1.0
OG A:SER180 3.8 27.5 1.0
O3A A:FFJ406 3.8 24.4 1.0
O2G A:FFJ406 3.9 23.2 1.0
O A:HOH657 4.0 22.1 1.0
CZ A:ARG183 4.1 19.5 1.0
NH1 A:ARG183 4.2 15.6 1.0
N A:SER180 4.2 20.8 1.0
CA A:SER180 4.3 18.9 1.0
O A:HOH682 4.5 31.8 1.0
O A:HOH515 4.5 33.7 1.0
MG A:MG402 4.9 19.1 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: Sun Dec 13 12:47:04 2020

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