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Chlorine in PDB 6cr7: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf, Beta, Gamma Datp Analogue

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf, Beta, Gamma Datp 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 Chf, Beta, Gamma Datp Analogue, PDB code: 6cr7 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) 19.80 / 2.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.174, 79.060, 55.611, 90.00, 107.05, 90.00
R / Rfree (%) 17.4 / 24

Other elements in 6cr7:

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

Fluorine (F) 1 atom
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 Chf, Beta, Gamma Datp Analogue (pdb code 6cr7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf, Beta, Gamma Datp Analogue, PDB code: 6cr7:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6cr7

Go back to Chlorine Binding Sites List in 6cr7
Chlorine binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf, Beta, Gamma Datp 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 Chf, Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:46.8
occ:1.00
 N A:HIS34 3.3 38.6 1.0
CB A:HIS34 3.4 41.8 1.0
CB A:ALA32 3.5 34.1 1.0
C A:ALA32 3.5 35.6 1.0
N A:LYS35 3.5 34.1 1.0
CA A:ALA32 3.6 34.6 1.0
CD2 A:HIS34 3.7 39.6 1.0
N A:ILE33 3.8 39.1 1.0
CA A:HIS34 3.8 38.2 1.0
O A:ALA32 3.8 36.1 1.0
CG A:HIS34 3.9 44.7 1.0
CG A:LYS35 4.0 41.0 1.0
C A:HIS34 4.1 38.1 1.0
C A:ILE33 4.4 38.9 1.0
CB A:LYS35 4.6 37.5 1.0
CA A:LYS35 4.7 34.9 1.0
CA A:ILE33 4.7 38.1 1.0
O6 D:DG1 4.9 42.9 1.0

Chlorine binding site 2 out of 3 in 6cr7

Go back to Chlorine Binding Sites List in 6cr7
Chlorine binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf, Beta, Gamma Datp 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 Chf, Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:55.3
occ:1.00
 N A:TYR266 3.3 35.2 1.0
O A:ASP263 3.4 41.7 1.0
CA A:GLN264 3.4 34.2 1.0
C A:GLN264 3.5 35.9 1.0
O A:HOH534 3.5 36.7 1.0
N A:CYS267 3.5 32.1 1.0
CB A:TYR266 3.7 33.7 1.0
CG1 A:VAL313 3.8 42.1 1.0
N A:TYR265 3.8 31.9 1.0
O A:GLN264 3.9 32.5 1.0
CA A:TYR266 3.9 35.5 1.0
CB A:VAL313 3.9 41.6 1.0
O A:VAL313 4.1 42.7 1.0
CD2 A:TYR266 4.1 47.5 1.0
C A:ASP263 4.2 38.7 1.0
C A:TYR266 4.2 32.4 1.0
N A:GLN264 4.2 40.7 1.0
SG A:CYS267 4.3 34.8 1.0
C A:TYR265 4.3 35.3 1.0
CB A:CYS267 4.4 31.3 1.0
CG A:TYR266 4.4 39.1 1.0
CB A:GLN264 4.5 34.1 1.0
CA A:CYS267 4.6 29.0 1.0
CA A:TYR265 4.7 30.6 1.0
O A:TYR296 4.7 30.2 1.0
C A:VAL313 4.8 40.2 1.0
O A:HOH596 4.8 38.1 1.0
CG2 A:VAL313 4.9 38.0 1.0
CA A:VAL313 4.9 40.4 1.0

Chlorine binding site 3 out of 3 in 6cr7

Go back to Chlorine Binding Sites List in 6cr7
Chlorine binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chf, Beta, Gamma Datp Analogue


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 A Dideoxy Terminated Primer with Chf, Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:44.0
occ:1.00
 OG1 A:THR297 3.1 31.7 1.0
ND2 A:ASN294 3.3 22.8 1.0
O A:HOH591 3.7 35.3 1.0
CG2 A:THR297 3.9 31.7 1.0
CZ A:ARG299 3.9 45.5 1.0
OD1 A:ASN294 3.9 33.4 1.0
NH1 A:ARG299 3.9 47.3 1.0
CG A:ASN294 4.1 31.5 1.0
CB A:TYR296 4.1 33.2 1.0
CB A:THR297 4.1 32.6 1.0
NH2 A:ARG299 4.2 37.9 1.0
CD2 A:TYR296 4.2 33.7 1.0
NE A:ARG299 4.2 41.6 1.0
CG A:TYR296 4.6 30.9 1.0
CD A:ARG299 4.7 35.6 1.0
N A:THR297 4.7 33.1 1.0
O A:HOH549 4.7 30.9 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 12:51:09 2020

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