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

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

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

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Dgtp, PDB code: 6nku 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) 23.29 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.630, 79.764, 55.378, 90.00, 107.69, 90.00
R / Rfree (%) 17.4 / 21.1

Other elements in 6nku:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with 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 Dgtp (pdb code 6nku). 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 Dgtp, PDB code: 6nku:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6nku

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

b:34.6
occ:1.00
 O A:HOH568 3.0 28.1 1.0
N A:CYS267 3.2 21.2 1.0
N A:TYR266 3.5 22.3 1.0
CG1 A:VAL313 3.5 26.0 1.0
CA A:GLN264 3.6 22.6 1.0
C A:GLN264 3.6 25.2 1.0
CB A:TYR266 3.7 23.6 1.0
O A:GLN264 3.8 24.9 1.0
CB A:VAL313 3.8 27.4 1.0
SG A:CYS267 3.8 25.4 1.0
CA A:TYR266 3.9 23.8 1.0
O A:HOH646 3.9 38.3 1.0
O A:ASP263 3.9 29.4 1.0
CB A:CYS267 3.9 22.6 1.0
C A:TYR266 4.0 22.5 1.0
N A:TYR265 4.1 24.4 1.0
CA A:CYS267 4.1 21.6 1.0
CD2 A:TYR266 4.4 33.0 1.0
C A:TYR265 4.4 25.5 1.0
CB A:GLN264 4.4 26.8 1.0
O A:VAL313 4.5 37.3 1.0
O A:TYR296 4.5 24.7 1.0
CG A:TYR266 4.5 29.4 1.0
N A:GLN264 4.6 23.1 1.0
CG2 A:VAL313 4.6 25.6 1.0
C A:ASP263 4.7 29.3 1.0
CA A:TYR265 4.9 28.1 1.0
CG A:GLN264 4.9 26.3 1.0
C A:VAL313 4.9 35.3 1.0
CA A:VAL313 5.0 31.7 1.0

Chlorine binding site 2 out of 4 in 6nku

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

b:37.5
occ:1.00
 N A:HIS34 3.3 28.9 1.0
O A:HOH791 3.3 46.0 1.0
C A:ALA32 3.5 25.4 1.0
CB A:HIS34 3.5 32.4 1.0
CA A:ALA32 3.6 30.0 1.0
N A:LYS35 3.6 26.2 1.0
N A:ILE33 3.6 26.4 1.0
CB A:ALA32 3.7 27.0 1.0
CD2 A:HIS34 3.8 32.5 1.0
CA A:HIS34 3.8 32.4 1.0
O A:ALA32 3.9 27.6 1.0
CG A:HIS34 4.0 33.9 1.0
CG A:LYS35 4.2 28.3 1.0
C A:HIS34 4.2 28.6 1.0
C A:ILE33 4.3 27.9 1.0
CA A:ILE33 4.6 31.8 1.0
CB A:LYS35 4.6 25.2 1.0
O A:HOH630 4.6 34.3 1.0
O4 D:DT1 4.6 32.3 1.0
CA A:LYS35 4.7 26.5 1.0
O A:HOH780 4.9 55.5 1.0
C7 D:DT1 4.9 27.4 1.0
C4 D:DT1 5.0 31.3 1.0
CD A:LYS35 5.0 26.5 1.0

Chlorine binding site 3 out of 4 in 6nku

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

b:54.1
occ:1.00
 NH1 A:ARG89 3.1 50.8 1.0
N A:LEU82 3.3 28.6 1.0
NH2 A:ARG89 3.6 52.4 1.0
O A:HOH766 3.7 38.4 1.0
CZ A:ARG89 3.8 49.2 1.0
CA A:LYS81 3.8 32.9 1.0
C A:LYS81 4.0 35.6 1.0
O A:LEU82 4.0 29.6 1.0
CB A:LEU85 4.0 32.9 1.0
CA A:LEU82 4.2 31.6 1.0
CB A:LEU82 4.3 31.2 1.0
CD1 A:LEU85 4.3 30.6 1.0
CB A:LYS81 4.3 41.1 1.0
CG A:LYS81 4.5 40.4 1.0
C A:LEU82 4.5 36.0 1.0
CG A:GLU86 4.6 47.3 1.0
CG A:LEU85 4.8 31.3 1.0
N A:GLU86 4.9 33.3 1.0
O A:GLY80 4.9 33.9 1.0

Chlorine binding site 4 out of 4 in 6nku

Go back to Chlorine Binding Sites List in 6nku
Chlorine binding site 4 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with 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 Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:35.1
occ:1.00
 NH2 A:ARG299 2.9 24.0 0.5
O A:HOH724 3.1 35.8 1.0
OG1 A:THR297 3.2 27.7 1.0
NE A:ARG299 3.3 31.4 0.5
ND2 A:ASN294 3.3 24.9 1.0
O A:HOH812 3.5 41.6 1.0
CZ A:ARG299 3.5 30.1 0.5
CG2 A:THR297 3.8 24.2 1.0
CB A:TYR296 3.9 25.8 1.0
OD1 A:ASN294 4.0 24.5 1.0
CB A:THR297 4.1 27.2 1.0
CG A:ASN294 4.1 24.7 1.0
CD2 A:TYR296 4.2 23.5 1.0
CZ A:ARG299 4.2 30.3 0.5
NE A:ARG299 4.2 29.2 0.5
NH2 A:ARG299 4.4 25.4 0.5
CG A:TYR296 4.5 25.4 1.0
NH1 A:ARG299 4.5 29.2 0.5
CD A:ARG299 4.6 29.3 0.5
N A:THR297 4.7 27.1 1.0
CD A:ARG299 4.7 29.6 0.5
NH1 A:ARG299 4.8 30.6 0.5
O T:HOH232 4.8 36.9 1.0
O A:HOH628 4.8 24.7 1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot-Spot Sequence" with Dgtp To Be Published.
Page generated: Mon Jul 29 12:06:20 2024

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