Fluorine in PDB 6nkt: Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro Analogue of Dgtp

Enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro Analogue of Dgtp

All present enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro 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 Beta-Gamma Difluoro Analogue of Dgtp, PDB code: 6nkt 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) 31.86 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.330, 79.669, 54.673, 90.00, 106.36, 90.00
R / Rfree (%) 19.9 / 30.3

Other elements in 6nkt:

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

Sodium (Na) 2 atoms

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 2 in 6nkt

Go back to Fluorine Binding Sites List in 6nkt
Fluorine binding site 1 out of 2 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro 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 Beta-Gamma Difluoro Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
T:F101

b:97.8
occ:1.00
F1B T:GFF101 0.0 97.8 1.0
C3B T:GFF101 1.4 1.0 1.0
F2B T:GFF101 2.2 0.7 1.0
P3 T:GFF101 2.7 94.2 1.0
P2 T:GFF101 2.7 0.5 1.0
O1B T:GFF101 2.9 97.3 1.0
O3G T:GFF101 3.0 79.5 1.0
O2G T:GFF101 3.3 77.9 1.0
O2B T:GFF101 3.6 91.6 1.0
O3A T:GFF101 3.9 95.4 1.0
CB A:SER180 3.9 66.3 1.0
O1G T:GFF101 3.9 72.3 1.0
NH2 A:ARG183 4.5 73.9 1.0
N A:SER180 4.8 61.5 1.0
OG A:SER180 4.8 64.4 1.0
CA A:SER180 5.0 59.0 1.0

Fluorine binding site 2 out of 2 in 6nkt

Go back to Fluorine Binding Sites List in 6nkt
Fluorine binding site 2 out of 2 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro 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 Beta-Gamma Difluoro Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
T:F101

b:0.7
occ:1.00
F2B T:GFF101 0.0 0.7 1.0
C3B T:GFF101 1.4 1.0 1.0
F1B T:GFF101 2.2 97.8 1.0
P2 T:GFF101 2.6 0.5 1.0
P3 T:GFF101 2.7 94.2 1.0
O3A T:GFF101 2.8 95.4 1.0
O2G T:GFF101 2.9 77.9 1.0
O1G T:GFF101 3.4 72.3 1.0
O1B T:GFF101 3.5 97.3 1.0
O2B T:GFF101 3.8 91.6 1.0
O3G T:GFF101 3.9 79.5 1.0
O2A T:GFF101 4.0 76.5 1.0
P1 T:GFF101 4.0 99.5 1.0
O1A T:GFF101 4.7 71.8 1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure To Be Published.
Page generated: Sun Dec 13 13:00:53 2020

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