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

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, 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 CF2, Beta, Gamma Dttp Analogue, PDB code: 6cto 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) 19.79 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.784, 79.168, 55.494, 90.00, 107.10, 90.00
R / Rfree (%) 17.9 / 23.2

Other elements in 6cto:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 2 atoms
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 Dttp Analogue (pdb code 6cto). 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 Dttp Analogue, PDB code: 6cto:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6cto

Go back to Fluorine Binding Sites List in 6cto
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 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 CF2, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:20.0
occ:1.00
F2B A:VT7405 0.0 20.0 1.0
C3B A:VT7405 1.4 29.4 1.0
F3B A:VT7405 2.2 23.7 1.0
PB A:VT7405 2.6 21.1 1.0
PG A:VT7405 2.7 26.8 1.0
O3A A:VT7405 2.9 26.0 1.0
O2G A:VT7405 3.1 26.6 1.0
O1G A:VT7405 3.3 21.8 1.0
O2B A:VT7405 3.4 24.8 1.0
O A:HOH659 3.4 34.3 1.0
O A:HOH643 3.7 25.5 1.0
O3G A:VT7405 3.9 24.7 1.0
O1B A:VT7405 3.9 18.7 1.0
PA A:VT7405 4.1 26.8 1.0
O2A A:VT7405 4.1 23.6 1.0
O A:HOH710 4.3 26.7 1.0
O1A A:VT7405 4.5 20.5 1.0
O A:HOH656 4.7 26.2 1.0
MG A:MG401 4.7 20.2 1.0

Fluorine binding site 2 out of 2 in 6cto

Go back to Fluorine Binding Sites List in 6cto
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 Dttp 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 Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:23.7
occ:1.00
F3B A:VT7405 0.0 23.7 1.0
C3B A:VT7405 1.3 29.4 1.0
F2B A:VT7405 2.2 20.0 1.0
PG A:VT7405 2.6 26.8 1.0
PB A:VT7405 2.6 21.1 1.0
O2B A:VT7405 2.9 24.8 1.0
O3G A:VT7405 2.9 24.7 1.0
O2G A:VT7405 3.2 26.6 1.0
NH2 A:ARG183 3.3 22.6 1.0
O1B A:VT7405 3.5 18.7 1.0
CB A:SER180 3.5 23.3 1.0
OG A:SER180 3.7 25.2 1.0
O1G A:VT7405 3.8 21.8 1.0
O A:HOH710 3.8 26.7 1.0
O3A A:VT7405 3.9 26.0 1.0
O A:HOH643 4.1 25.5 1.0
CZ A:ARG183 4.3 24.3 1.0
N A:SER180 4.4 21.6 1.0
O A:HOH634 4.4 34.9 1.0
NH1 A:ARG183 4.5 21.0 1.0
CA A:SER180 4.5 21.5 1.0
O A:HOH594 4.5 36.6 1.0
MG A:MG401 4.8 20.2 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: Sun Dec 13 12:46:56 2020

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