Chlorine in PDB 6cto: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, 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 CF2, Beta, Gamma Dttp Analogue, PDB code: 6cto 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) 19.79 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.784, 79.168, 55.494, 90.00, 107.10, 90.00
R / Rfree (%) 17.9 / 23.2

Other elements in 6cto:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, Beta, Gamma Dttp Analogue also contains other interesting chemical elements:

Fluorine (F) 2 atoms
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 CF2, Beta, Gamma Dttp Analogue (pdb code 6cto). 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 CF2, Beta, Gamma Dttp Analogue, PDB code: 6cto:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6cto

Go back to Chlorine Binding Sites List in 6cto
Chlorine binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, 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 CF2, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:39.4
occ:1.00
N A:HIS34 3.3 28.3 1.0
CB A:ALA32 3.4 26.3 1.0
CB A:HIS34 3.4 33.5 1.0
C A:ALA32 3.4 25.7 1.0
CA A:ALA32 3.5 30.2 1.0
N A:LYS35 3.5 29.9 1.0
N A:ILE33 3.7 26.6 1.0
CA A:HIS34 3.8 34.7 1.0
O A:ALA32 3.8 25.7 1.0
CD2 A:HIS34 3.9 36.9 1.0
CG A:HIS34 4.0 37.5 1.0
CG A:LYS35 4.0 29.5 1.0
C A:HIS34 4.1 30.3 1.0
C A:ILE33 4.4 28.8 1.0
CB A:LYS35 4.6 25.0 1.0
CA A:LYS35 4.6 27.6 1.0
CA A:ILE33 4.7 28.1 1.0
O A:HOH641 4.8 37.5 1.0
CD A:LYS35 4.9 24.4 1.0
O6 D:DG1 4.9 30.7 1.0
N A:ALA32 5.0 29.2 1.0

Chlorine binding site 2 out of 2 in 6cto

Go back to Chlorine Binding Sites List in 6cto
Chlorine binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CF2, 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 CF2, Beta, Gamma Dttp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:44.2
occ:1.00
O A:HOH552 3.0 26.7 1.0
N A:CYS267 3.2 19.6 1.0
N A:TYR266 3.4 26.3 1.0
CA A:GLN264 3.4 27.2 1.0
C A:GLN264 3.4 26.6 1.0
O A:GLN264 3.6 24.7 1.0
O A:ASP263 3.7 26.8 1.0
CG1 A:VAL313 3.8 28.0 1.0
CB A:TYR266 3.8 26.8 1.0
CA A:TYR266 3.9 27.1 1.0
SG A:CYS267 3.9 23.1 1.0
CB A:VAL313 3.9 25.6 1.0
CB A:CYS267 3.9 25.9 1.0
N A:TYR265 3.9 26.5 1.0
C A:TYR266 3.9 23.6 1.0
CA A:CYS267 4.1 21.4 1.0
CB A:GLN264 4.3 25.0 1.0
O A:TYR296 4.3 25.2 1.0
C A:TYR265 4.3 27.8 1.0
N A:GLN264 4.4 25.4 1.0
C A:ASP263 4.5 25.8 1.0
CD2 A:TYR266 4.5 37.2 1.0
O A:VAL313 4.6 31.7 1.0
CG A:TYR266 4.7 32.0 1.0
CG2 A:VAL313 4.7 22.8 1.0
CA A:TYR265 4.7 25.2 1.0
CG A:GLN264 5.0 28.4 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: Sat Dec 12 12:51:23 2020

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