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

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene 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-Methylene Dgtp, PDB code: 6nkw 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) 31.16 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.441, 79.186, 55.352, 90.00, 107.60, 90.00
R / Rfree (%) 17.4 / 21.7

Other elements in 6nkw:

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

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-Methylene Dgtp (pdb code 6nkw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp, PDB code: 6nkw:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6nkw

Go back to Chlorine Binding Sites List in 6nkw
Chlorine binding site 1 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene 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-Methylene Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:37.8
occ:1.00
 O A:HOH595 3.0 24.9 1.0
N A:CYS267 3.1 18.9 1.0
N A:TYR266 3.4 20.8 1.0
CA A:GLN264 3.5 21.8 1.0
C A:GLN264 3.5 25.0 1.0
CG1 A:VAL313 3.6 26.4 1.0
CB A:TYR266 3.7 24.8 1.0
O A:GLN264 3.8 22.2 1.0
SG A:CYS267 3.8 20.8 1.0
CB A:CYS267 3.8 20.9 1.0
O A:HOH604 3.9 34.9 1.0
CA A:TYR266 3.9 19.6 1.0
O A:ASP263 3.9 25.4 1.0
C A:TYR266 3.9 19.9 1.0
N A:TYR265 4.0 22.9 1.0
CB A:VAL313 4.0 26.6 1.0
CA A:CYS267 4.1 17.9 1.0
CB A:GLN264 4.3 21.4 1.0
O A:TYR296 4.3 20.9 1.0
C A:TYR265 4.4 22.5 1.0
N A:GLN264 4.5 20.4 1.0
CD2 A:TYR266 4.5 31.1 1.0
O A:VAL313 4.6 30.3 1.0
CG A:TYR266 4.6 27.8 1.0
C A:ASP263 4.6 24.4 1.0
CA A:TYR265 4.8 23.4 1.0
CG A:GLN264 4.8 23.2 1.0
CG2 A:VAL313 4.8 27.7 1.0

Chlorine binding site 2 out of 4 in 6nkw

Go back to Chlorine Binding Sites List in 6nkw
Chlorine binding site 2 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene 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-Methylene Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:31.1
occ:1.00
 N A:HIS34 3.3 25.4 1.0
CB A:ALA32 3.4 21.0 1.0
C A:ALA32 3.4 24.3 1.0
CB A:HIS34 3.5 24.8 1.0
CA A:ALA32 3.5 25.8 1.0
N A:LYS35 3.6 22.7 1.0
N A:ILE33 3.7 21.0 1.0
CD2 A:HIS34 3.8 28.6 1.0
CA A:HIS34 3.8 27.6 1.0
O A:ALA32 3.9 23.8 1.0
CG A:HIS34 4.0 28.0 1.0
CG A:LYS35 4.2 26.0 1.0
C A:HIS34 4.2 24.6 1.0
C A:ILE33 4.3 25.0 1.0
O A:HOH641 4.6 25.4 1.0
CA A:ILE33 4.6 25.0 1.0
CB A:LYS35 4.6 21.2 1.0
CA A:LYS35 4.7 21.5 1.0
O4 D:DT1 4.7 24.7 1.0
N A:ALA32 5.0 22.7 1.0

Chlorine binding site 3 out of 4 in 6nkw

Go back to Chlorine Binding Sites List in 6nkw
Chlorine binding site 3 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene 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-Methylene Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:42.0
occ:1.00
 NH1 A:ARG89 3.0 42.3 1.0
N A:LEU82 3.2 23.5 1.0
CA A:LYS81 3.7 30.2 1.0
C A:LYS81 3.9 27.6 1.0
CZ A:ARG89 4.0 45.8 1.0
O A:LEU82 4.0 29.1 1.0
CB A:LYS81 4.1 33.9 1.0
CB A:LEU85 4.1 31.2 1.0
NH2 A:ARG89 4.1 44.2 1.0
CA A:LEU82 4.2 27.0 1.0
CD1 A:LEU85 4.3 25.0 1.0
CB A:LEU82 4.3 26.5 1.0
CG A:LYS81 4.5 39.7 1.0
C A:LEU82 4.6 30.0 1.0
O A:GLY80 4.7 28.7 1.0
CG A:GLU86 4.8 38.8 1.0
CG A:LEU85 4.8 26.8 1.0
CE1 A:PHE76 4.9 25.5 1.0
N A:LYS81 4.9 26.2 1.0
N A:GLU86 5.0 33.5 1.0

Chlorine binding site 4 out of 4 in 6nkw

Go back to Chlorine Binding Sites List in 6nkw
Chlorine binding site 4 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:30.4
occ:1.00
 NH2 A:ARG299 3.0 27.3 0.6
OG1 A:THR297 3.2 22.5 1.0
O A:HOH711 3.2 30.5 1.0
ND2 A:ASN294 3.3 20.2 1.0
NE A:ARG299 3.3 28.1 0.6
O A:HOH832 3.4 37.3 1.0
CZ A:ARG299 3.6 29.0 0.6
CG2 A:THR297 3.8 23.9 1.0
OD1 A:ASN294 3.9 20.5 1.0
CB A:TYR296 3.9 22.9 1.0
CG A:ASN294 4.0 19.1 1.0
CB A:THR297 4.1 24.0 1.0
NH1 A:ARG299 4.1 31.2 0.4
O A:HOH819 4.1 46.2 1.0
CZ A:ARG299 4.2 27.8 0.4
CD2 A:TYR296 4.2 22.8 1.0
NE A:ARG299 4.3 27.3 0.4
CD A:ARG299 4.5 26.4 0.4
CG A:TYR296 4.5 23.0 1.0
CD A:ARG299 4.5 26.9 0.6
O A:HOH531 4.7 23.7 1.0
NH2 A:ARG299 4.7 25.3 0.4
N A:THR297 4.7 19.5 1.0
NH1 A:ARG299 4.8 29.1 0.6
O T:HOH219 4.9 35.0 1.0

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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