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Chlorine in PDB 6ctl: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl-R/S Isomers, Beta, Gamma Dttp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl-R/S Isomers, Beta, Gamma Dttp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl-R/S Isomers, Beta, Gamma Dttp Analogue:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl-R/S Isomers, Beta, Gamma Dttp Analogue, PDB code: 6ctl 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) 22.20 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.862, 79.699, 55.119, 90.00, 107.66, 90.00
R / Rfree (%) 17.9 / 22.5

Other elements in 6ctl:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl-R/S Isomers, Beta, Gamma Dttp Analogue also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl-R/S Isomers, Beta, Gamma Dttp Analogue (pdb code 6ctl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl-R/S Isomers, Beta, Gamma Dttp Analogue, PDB code: 6ctl:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6ctl

Go back to Chlorine Binding Sites List in 6ctl
Chlorine binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl-R/S Isomers, Beta, Gamma Dttp Analogue


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 A Dideoxy Terminated Primer with Chcl-R/S Isomers, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:41.4
occ:1.00
 N A:HIS34 3.2 32.5 1.0
C A:ALA32 3.3 35.1 1.0
CB A:HIS34 3.3 37.3 1.0
CB A:ALA32 3.5 32.3 1.0
CA A:ALA32 3.5 37.3 1.0
N A:LYS35 3.6 27.8 1.0
N A:ILE33 3.6 36.1 1.0
O A:ALA32 3.7 35.0 1.0
CA A:HIS34 3.7 34.4 1.0
CD2 A:HIS34 3.7 35.0 1.0
CG A:HIS34 3.8 37.5 1.0
C A:HIS34 4.1 29.1 1.0
C A:ILE33 4.2 33.2 1.0
CG A:LYS35 4.3 34.1 1.0
O A:HOH648 4.5 41.8 1.0
CA A:ILE33 4.5 32.9 1.0
CB A:LYS35 4.6 33.0 1.0
CA A:LYS35 4.7 28.5 1.0
N A:ALA32 4.9 31.2 1.0
NE2 A:HIS34 5.0 39.9 1.0

Chlorine binding site 2 out of 2 in 6ctl

Go back to Chlorine Binding Sites List in 6ctl
Chlorine binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl-R/S Isomers, Beta, Gamma Dttp Analogue


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 A Dideoxy Terminated Primer with Chcl-R/S Isomers, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:36.9
occ:0.63
 CL1 A:FDJ406 0.0 36.9 0.6
C3B A:FDJ406 1.8 26.1 1.0
PG A:FDJ406 2.9 27.2 1.0
O A:HOH704 3.0 39.6 1.0
PB A:FDJ406 3.0 26.5 1.0
O2B A:FDJ406 3.1 24.2 1.0
O3G A:FDJ406 3.2 24.6 1.0
NH2 A:ARG183 3.3 27.4 1.0
O2G A:FDJ406 3.5 25.8 1.0
O A:HOH548 3.5 36.6 1.0
O A:HOH608 3.7 23.9 1.0
O1B A:FDJ406 3.9 22.9 1.0
CB A:SER180 4.0 27.3 1.0
O3A A:FDJ406 4.1 26.9 1.0
O1G A:FDJ406 4.2 24.2 1.0
OG A:SER180 4.3 31.9 1.0
CZ A:ARG183 4.4 28.5 1.0
O A:HOH660 4.5 38.5 1.0
NH1 A:ARG183 4.6 24.7 1.0
CA A:SER180 4.9 25.3 1.0
N A:SER180 5.0 26.7 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 23:43:40 2024

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