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Chlorine in PDB 6nky: Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp

Enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf 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 Chf 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 Chf Analogue of Dgtp, PDB code: 6nky 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) 21.98 / 2.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.643, 80.158, 55.251, 90.00, 107.89, 90.00
R / Rfree (%) 19.9 / 25.6

Other elements in 6nky:

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

Fluorine (F) 1 atom
Magnesium (Mg) 1 atom
Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp (pdb code 6nky). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp, PDB code: 6nky:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6nky

Go back to Chlorine Binding Sites List in 6nky
Chlorine binding site 1 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:46.0
occ:1.00
 CB A:ALA32 3.4 34.7 1.0
N A:HIS34 3.4 36.5 1.0
C A:ALA32 3.5 34.1 1.0
CA A:ALA32 3.5 34.8 1.0
CB A:HIS34 3.5 35.0 1.0
N A:LYS35 3.6 32.2 1.0
O A:ALA32 3.8 33.3 1.0
N A:ILE33 3.8 34.4 1.0
CA A:HIS34 3.9 38.5 1.0
CD2 A:HIS34 4.0 42.5 1.0
CG A:LYS35 4.1 34.3 1.0
CG A:HIS34 4.1 37.5 1.0
C A:HIS34 4.2 35.8 1.0
C A:ILE33 4.4 35.3 1.0
O A:HOH574 4.5 38.1 1.0
CB A:LYS35 4.6 33.0 1.0
O4 D:DT1 4.6 37.9 1.0
CA A:LYS35 4.7 31.0 1.0
C7 D:DT1 4.7 29.9 1.0
CA A:ILE33 4.8 39.6 1.0
CD A:LYS35 4.9 32.5 1.0
C4 D:DT1 5.0 34.8 1.0
N A:ALA32 5.0 33.6 1.0

Chlorine binding site 2 out of 3 in 6nky

Go back to Chlorine Binding Sites List in 6nky
Chlorine binding site 2 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:54.3
occ:1.00
 N A:LEU82 3.1 34.7 1.0
NH1 A:ARG89 3.6 49.5 1.0
CA A:LYS81 3.7 44.1 1.0
C A:LYS81 3.8 42.4 1.0
NH2 A:ARG89 3.8 52.9 1.0
CD1 A:LEU85 4.0 35.6 1.0
CB A:LEU82 4.0 38.7 1.0
CA A:LEU82 4.0 42.1 1.0
O A:LEU82 4.0 39.6 1.0
CB A:LEU85 4.2 40.0 1.0
CB A:LYS81 4.2 47.0 1.0
CZ A:ARG89 4.2 53.0 1.0
C A:LEU82 4.5 43.1 1.0
CG A:LEU85 4.7 39.0 1.0
CG A:GLU86 4.7 52.6 1.0
O A:GLY80 4.8 43.2 1.0
CE1 A:PHE76 4.8 36.7 1.0
O A:LYS81 4.9 39.6 1.0
CD1 A:PHE76 4.9 38.0 1.0
N A:LYS81 4.9 40.4 1.0

Chlorine binding site 3 out of 3 in 6nky

Go back to Chlorine Binding Sites List in 6nky
Chlorine binding site 3 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:47.2
occ:1.00
 NH2 A:ARG299 2.9 43.7 1.0
OG1 A:THR297 3.3 39.4 1.0
ND2 A:ASN294 3.4 30.5 1.0
NE A:ARG299 3.5 45.5 1.0
CZ A:ARG299 3.6 52.0 1.0
CG2 A:THR297 3.7 31.4 1.0
CB A:TYR296 4.0 32.0 1.0
OD1 A:ASN294 4.1 36.6 1.0
CB A:THR297 4.1 39.7 1.0
CG A:ASN294 4.2 33.6 1.0
CD2 A:TYR296 4.3 30.8 1.0
CG A:TYR296 4.5 32.4 1.0
O A:HOH555 4.7 37.4 1.0
N A:THR297 4.7 31.3 1.0
CD A:ARG299 4.8 37.9 1.0
NH1 A:ARG299 4.8 57.4 1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp To Be Published.
Page generated: Sat Jul 12 17:21:45 2025

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