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

Enzymatic activity of Ternary Complex Crystal Structure 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 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 Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp, PDB code: 6nkv 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) 23.73 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.636, 79.707, 55.412, 90.00, 107.63, 90.00
R / Rfree (%) 16.4 / 20.3

Other elements in 6nkv:

The structure of Ternary Complex Crystal Structure 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) 2 atoms
Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp (pdb code 6nkv). 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 Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp, PDB code: 6nkv:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6nkv

Go back to Chlorine Binding Sites List in 6nkv
Chlorine binding site 1 out of 3 in the Ternary Complex Crystal Structure 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 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:27.2
occ:1.00
 N A:HIS34 3.3 20.6 1.0
O A:HOH905 3.4 35.0 1.0
CB A:HIS34 3.5 26.8 1.0
C A:ALA32 3.5 21.3 1.0
CB A:ALA32 3.5 20.1 1.0
CA A:ALA32 3.6 22.3 1.0
N A:LYS35 3.6 19.6 1.0
N A:ILE33 3.7 17.8 1.0
CD2 A:HIS34 3.7 27.7 1.0
CA A:HIS34 3.8 23.2 1.0
CG A:HIS34 3.9 23.4 1.0
O A:ALA32 3.9 19.5 1.0
C A:HIS34 4.2 21.2 1.0
CG A:LYS35 4.3 21.9 1.0
C A:ILE33 4.3 21.7 1.0
CA A:ILE33 4.6 22.0 1.0
CB A:LYS35 4.7 17.8 1.0
O A:HOH745 4.7 29.9 1.0
O4 D:DT1 4.7 21.2 1.0
CA A:LYS35 4.7 16.1 1.0
O D:HOH124 4.8 42.1 1.0
CG2 A:ILE33 4.9 26.0 1.0
NE2 A:HIS34 5.0 26.2 1.0

Chlorine binding site 2 out of 3 in 6nkv

Go back to Chlorine Binding Sites List in 6nkv
Chlorine binding site 2 out of 3 in the Ternary Complex Crystal Structure 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 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:40.8
occ:1.00
 NH1 A:ARG89 3.0 40.1 1.0
O A:HOH642 3.3 37.9 1.0
N A:LEU82 3.4 19.8 1.0
O A:HOH840 3.4 30.8 1.0
CA A:LYS81 3.7 24.0 1.0
CB A:LYS81 3.9 30.5 1.0
OE1 A:GLU86 4.0 48.9 1.0
C A:LYS81 4.0 23.3 1.0
CZ A:ARG89 4.1 42.8 1.0
CD1 A:LEU85 4.1 20.2 1.0
CB A:LEU85 4.2 22.4 1.0
O A:LEU82 4.3 21.1 1.0
NH2 A:ARG89 4.3 42.4 1.0
CB A:LEU82 4.3 22.9 1.0
CA A:LEU82 4.3 24.1 1.0
C A:LEU82 4.8 25.1 1.0
CE1 A:PHE76 4.8 23.9 1.0
CG A:LEU85 4.8 23.0 1.0
O A:GLY80 4.9 24.7 1.0
CD1 A:PHE76 5.0 25.1 1.0
CD A:GLU86 5.0 48.1 1.0
O A:HOH682 5.0 24.1 1.0

Chlorine binding site 3 out of 3 in 6nkv

Go back to Chlorine Binding Sites List in 6nkv
Chlorine binding site 3 out of 3 in the Ternary Complex Crystal Structure 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 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:28.9
occ:1.00
 NH2 A:ARG299 3.1 36.4 0.9
OG1 A:THR297 3.2 19.8 1.0
O A:HOH823 3.2 28.8 1.0
ND2 A:ASN294 3.3 16.6 1.0
NE A:ARG299 3.5 38.3 0.9
O A:HOH937 3.5 28.0 1.0
CZ A:ARG299 3.7 36.2 0.9
CG2 A:THR297 3.9 19.8 1.0
OD1 A:ASN294 3.9 17.6 1.0
CB A:TYR296 4.0 18.9 1.0
CG A:ASN294 4.1 16.8 1.0
CB A:THR297 4.1 20.9 1.0
CD2 A:TYR296 4.2 16.9 1.0
CG A:TYR296 4.5 17.7 1.0
CD A:ARG299 4.7 23.4 0.9
N A:THR297 4.7 16.2 1.0
O A:HOH700 4.8 18.7 1.0
O A:HOH865 4.8 36.5 1.0
O T:HOH220 4.8 32.4 1.0
NH1 A:ARG299 5.0 37.9 0.9

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure To Be Published.
Page generated: Mon Jul 29 12:06:20 2024

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