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

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Datp 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 Datp Analogue, PDB code: 6crb 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) 19.97 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.763, 78.772, 54.472, 90.00, 108.78, 90.00
R / Rfree (%) 21.8 / 27.5

Other elements in 6crb:

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

Fluorine binding site 1 out of 2 in 6crb

Go back to Fluorine Binding Sites List in 6crb
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 Datp 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 Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:41.7
occ:1.00
F1B A:VA6401 0.0 41.7 1.0
C3B A:VA6401 1.3 42.7 1.0
F2B A:VA6401 2.2 50.8 1.0
PG A:VA6401 2.5 44.7 1.0
PB A:VA6401 2.6 45.0 1.0
O3G A:VA6401 2.7 45.6 1.0
O2B A:VA6401 2.8 40.9 1.0
O2G A:VA6401 3.2 45.7 1.0
NH2 A:ARG183 3.4 43.9 1.0
O1B A:VA6401 3.5 43.0 1.0
CB A:SER180 3.5 38.0 1.0
OG A:SER180 3.7 40.1 1.0
O1G A:VA6401 3.8 40.3 1.0
O3A A:VA6401 3.8 38.8 1.0
CZ A:ARG183 4.4 44.2 1.0
NH1 A:ARG183 4.5 45.8 1.0
O A:HOH610 4.5 40.1 1.0
N A:SER180 4.5 38.0 1.0
CA A:SER180 4.5 38.8 1.0
O A:HOH567 4.9 45.5 1.0
O A:HOH541 4.9 32.9 1.0
NH1 A:ARG149 5.0 45.6 1.0
MG A:MG402 5.0 40.9 1.0

Fluorine binding site 2 out of 2 in 6crb

Go back to Fluorine Binding Sites List in 6crb
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 Datp 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 Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:50.8
occ:1.00
F2B A:VA6401 0.0 50.8 1.0
C3B A:VA6401 1.4 42.7 1.0
F1B A:VA6401 2.2 41.7 1.0
PG A:VA6401 2.6 44.7 1.0
PB A:VA6401 2.6 45.0 1.0
O2G A:VA6401 2.8 45.7 1.0
O3A A:VA6401 2.9 38.8 1.0
O A:HOH567 3.1 45.5 1.0
O1G A:VA6401 3.4 40.3 1.0
O2B A:VA6401 3.6 40.9 1.0
O1B A:VA6401 3.8 43.0 1.0
PA A:VA6401 3.8 44.4 1.0
O3G A:VA6401 3.9 45.6 1.0
O2A A:VA6401 3.9 44.0 1.0
O1A A:VA6401 4.4 46.2 1.0
MG A:MG402 4.7 40.9 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: Sun Dec 13 12:46:52 2020

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