Fluorine in PDB 6nl0: Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma CF2 Analogue of Dgtp

Enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma CF2 Analogue of Dgtp

All present enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma CF2 Analogue of Dgtp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma CF2 Analogue of Dgtp, PDB code: 6nl0 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) 21.23 / 1.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.317, 79.933, 55.119, 90.00, 107.97, 90.00
R / Rfree (%) 19.3 / 23.7

Other elements in 6nl0:

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma CF2 Analogue of Dgtp also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma CF2 Analogue of Dgtp (pdb code 6nl0). 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 K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma CF2 Analogue of Dgtp, PDB code: 6nl0:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6nl0

Go back to Fluorine Binding Sites List in 6nl0
Fluorine binding site 1 out of 2 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma CF2 Analogue of Dgtp


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 K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma CF2 Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:34.1
occ:1.00
 F1B A:GFF405 0.0 34.1 1.0
C3B A:GFF405 1.4 31.2 1.0
F2B A:GFF405 2.2 30.4 1.0
P3 A:GFF405 2.6 33.0 1.0
P2 A:GFF405 2.7 26.7 1.0
O3G A:GFF405 2.9 32.3 1.0
O1B A:GFF405 2.9 29.5 1.0
NH2 A:ARG183 3.2 28.8 1.0
O2G A:GFF405 3.3 35.8 1.0
CB A:SER180 3.4 30.4 1.0
O A:HOH661 3.4 42.9 1.0
O2B A:GFF405 3.5 25.0 1.0
O1G A:GFF405 3.8 31.1 1.0
O3A A:GFF405 3.9 29.9 1.0
OG A:SER180 3.9 35.8 1.0
O A:HOH622 4.1 24.9 1.0
CZ A:ARG183 4.2 33.0 1.0
N A:SER180 4.3 28.3 1.0
CA A:SER180 4.3 28.7 1.0
NH1 A:ARG183 4.3 26.3 1.0
O A:HOH631 4.4 43.3 1.0
MG A:MG401 4.9 27.4 1.0

Fluorine binding site 2 out of 2 in 6nl0

Go back to Fluorine Binding Sites List in 6nl0
Fluorine binding site 2 out of 2 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma CF2 Analogue of Dgtp


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 K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma CF2 Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:30.4
occ:1.00
 F2B A:GFF405 0.0 30.4 1.0
C3B A:GFF405 1.4 31.2 1.0
F1B A:GFF405 2.2 34.1 1.0
P3 A:GFF405 2.6 33.0 1.0
P2 A:GFF405 2.7 26.7 1.0
O3A A:GFF405 2.8 29.9 1.0
O2G A:GFF405 2.8 35.8 1.0
O1G A:GFF405 3.4 31.1 1.0
O A:HOH622 3.4 24.9 1.0
O A:HOH605 3.4 33.2 1.0
O1B A:GFF405 3.4 29.5 1.0
O A:HOH661 3.8 42.9 1.0
O3G A:GFF405 3.8 32.3 1.0
O2B A:GFF405 3.8 25.0 1.0
P1 A:GFF405 3.9 29.9 1.0
O2A A:GFF405 4.0 31.6 1.0
O A:HOH620 4.3 32.5 1.0
O1A A:GFF405 4.4 27.4 1.0
O A:HOH617 4.6 49.0 1.0
MG A:MG401 4.7 27.4 1.0

Reference:

V.K.Batra, S.H.Wilson. Crystal Structure of A Ternary Complex To Be Published.
Page generated: Sun Dec 13 13:00:55 2020

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