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Chlorine in PDB 6bem: Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp, PDB code: 6bem 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) 24.64 / 1.88
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.806, 79.995, 55.521, 90.00, 107.68, 90.00
R / Rfree (%) 18.7 / 22.6

Other elements in 6bem:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp 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 S-Isomer of Beta-Gamma-Chcl-Dctp (pdb code 6bem). 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 S-Isomer of Beta-Gamma-Chcl-Dctp, PDB code: 6bem:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6bem

Go back to Chlorine Binding Sites List in 6bem
Chlorine binding site 1 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp


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 S-Isomer of Beta-Gamma-Chcl-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:35.6
occ:1.00
 O D:HOH212 2.6 39.7 1.0
N A:HIS34 3.3 23.6 1.0
CB A:ALA32 3.4 26.5 1.0
CA A:ALA32 3.5 25.9 1.0
C A:ALA32 3.6 26.6 1.0
CB A:HIS34 3.6 25.8 1.0
N A:LYS35 3.7 22.8 1.0
N A:ILE33 3.8 25.1 1.0
CA A:HIS34 3.9 24.3 1.0
CD2 A:HIS34 4.0 29.5 1.0
O A:ALA32 4.0 27.8 1.0
CG A:HIS34 4.1 28.6 1.0
CG A:LYS35 4.1 26.6 1.0
C A:HIS34 4.2 21.8 1.0
C A:ILE33 4.4 26.8 1.0
CB A:LYS35 4.7 19.9 1.0
O6 D:DG1 4.7 26.7 1.0
CA A:ILE33 4.7 26.1 1.0
O A:HOH878 4.8 31.0 1.0
CA A:LYS35 4.8 21.9 1.0
O A:HOH762 4.9 26.7 1.0
N A:ALA32 5.0 26.8 1.0

Chlorine binding site 2 out of 4 in 6bem

Go back to Chlorine Binding Sites List in 6bem
Chlorine binding site 2 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp


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 S-Isomer of Beta-Gamma-Chcl-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:50.0
occ:1.00
 O A:HOH807 2.9 36.6 1.0
OE1 A:GLU86 3.3 47.4 1.0
N A:LEU82 3.4 25.4 1.0
CA A:LYS81 3.9 28.3 1.0
NH2 A:ARG89 3.9 44.9 1.0
C A:LYS81 4.1 28.9 1.0
CD1 A:LEU85 4.1 23.0 1.0
O A:LEU82 4.2 25.9 1.0
CB A:LEU85 4.2 29.3 1.0
CB A:LYS81 4.3 32.3 1.0
CA A:LEU82 4.3 29.2 1.0
CD A:GLU86 4.3 45.8 1.0
CB A:LEU82 4.3 27.8 1.0
CZ A:ARG89 4.4 42.1 1.0
C A:LEU82 4.7 27.7 1.0
CG A:GLU86 4.7 36.2 1.0
CG A:LYS81 4.8 35.4 1.0
NH1 A:ARG89 4.8 42.7 1.0
O A:GLY80 4.8 29.1 1.0
CG A:LEU85 4.8 27.1 1.0
NE A:ARG89 4.8 36.2 1.0

Chlorine binding site 3 out of 4 in 6bem

Go back to Chlorine Binding Sites List in 6bem
Chlorine binding site 3 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp


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 S-Isomer of Beta-Gamma-Chcl-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:35.7
occ:1.00
 O A:HOH806 3.0 37.3 1.0
OG1 A:THR297 3.1 22.2 1.0
ND2 A:ASN294 3.4 22.6 1.0
CG2 A:THR297 3.6 22.3 1.0
OD1 A:ASN294 3.9 19.7 1.0
NE A:ARG299 4.0 32.1 1.0
CB A:THR297 4.0 21.7 1.0
CB A:TYR296 4.0 21.0 1.0
CZ A:ARG299 4.0 36.9 1.0
O T:HOH153 4.1 33.0 1.0
CG A:ASN294 4.1 18.3 1.0
NH2 A:ARG299 4.1 33.5 1.0
CD2 A:TYR296 4.3 21.0 1.0
CG A:TYR296 4.6 20.5 1.0
CD A:ARG299 4.6 26.9 1.0
N A:THR297 4.6 19.1 1.0
NH1 A:ARG299 4.6 31.6 1.0
O A:HOH831 4.7 37.8 1.0
O A:HOH668 4.7 21.1 1.0
O A:HOH536 4.8 33.5 1.0
O T:HOH109 4.9 30.4 1.0
CA A:THR297 4.9 16.2 1.0

Chlorine binding site 4 out of 4 in 6bem

Go back to Chlorine Binding Sites List in 6bem
Chlorine binding site 4 out of 4 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with S-Isomer of Beta-Gamma-Chcl-Dctp


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 S-Isomer of Beta-Gamma-Chcl-Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:24.9
occ:1.00
 CL1 A:DJJ408 0.0 24.9 1.0
C3B A:DJJ408 1.8 16.1 1.0
PB A:DJJ408 2.9 14.0 1.0
O3A A:DJJ408 2.9 16.6 1.0
PG A:DJJ408 2.9 18.5 1.0
O2G A:DJJ408 3.0 20.0 1.0
O1G A:DJJ408 3.6 13.7 1.0
O A:HOH725 3.6 14.9 1.0
O2B A:DJJ408 3.6 14.1 1.0
O A:HOH749 3.7 23.6 1.0
O A:HOH895 3.7 36.3 1.0
PA A:DJJ408 4.0 13.6 1.0
O2A A:DJJ408 4.0 17.0 1.0
O A:HOH648 4.1 31.4 1.0
O3G A:DJJ408 4.2 21.0 1.0
O1B A:DJJ408 4.2 13.3 1.0
O A:HOH766 4.4 36.2 1.0
O A:HOH573 4.4 24.4 1.0
O1A A:DJJ408 4.6 13.5 1.0
O A:HOH846 4.9 47.1 1.0

Reference:

V.K.Batra, K.Oertell, W.A.Beard, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson. Mapping Functional Substrate-Enzyme Interactions in the Pol Beta Active Site Through Chemical Biology: Structural Responses to Acidity Modification of Incoming Dntps. Biochemistry V. 57 3934 2018.
ISSN: ISSN 1520-4995
PubMed: 29874056
DOI: 10.1021/ACS.BIOCHEM.8B00418
Page generated: Fri Jul 26 22:46:41 2024

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