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Chlorine in PDB 6cr3: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Datp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Datp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, 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 CBR2, Beta, Gamma Datp Analogue, PDB code: 6cr3 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) 23.18 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.874, 79.669, 55.784, 90.00, 107.72, 90.00
R / Rfree (%) 17.5 / 22.7

Other elements in 6cr3:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Datp Analogue also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Bromine (Br) 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 A Dideoxy Terminated Primer with CBR2, Beta, Gamma Datp Analogue (pdb code 6cr3). 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 CBR2, Beta, Gamma Datp Analogue, PDB code: 6cr3:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6cr3

Go back to Chlorine Binding Sites List in 6cr3
Chlorine binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, 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 CBR2, Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:35.9
occ:1.00
N A:HIS34 3.3 23.2 1.0
O A:HOH848 3.3 40.4 1.0
CB A:HIS34 3.5 28.5 1.0
C A:ALA32 3.5 27.0 1.0
CB A:ALA32 3.5 24.8 1.0
CA A:ALA32 3.6 29.3 1.0
N A:LYS35 3.6 22.6 1.0
N A:ILE33 3.7 23.7 1.0
CA A:HIS34 3.8 25.2 1.0
O A:ALA32 3.8 23.0 1.0
CD2 A:HIS34 3.9 36.9 1.0
CG A:HIS34 4.0 30.3 1.0
C A:HIS34 4.2 23.2 1.0
CG A:LYS35 4.2 22.3 1.0
C A:ILE33 4.3 24.3 1.0
O A:HOH604 4.6 29.9 1.0
CB A:LYS35 4.6 20.7 1.0
CA A:ILE33 4.6 26.4 1.0
O T:HOH154 4.6 46.6 1.0
CA A:LYS35 4.7 22.3 1.0
O6 D:DG1 4.7 25.9 1.0
CD A:LYS35 4.9 25.6 1.0

Chlorine binding site 2 out of 2 in 6cr3

Go back to Chlorine Binding Sites List in 6cr3
Chlorine binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, 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 CBR2, Beta, Gamma Datp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:38.7
occ:1.00
OG1 A:THR297 3.0 22.2 1.0
ND2 A:ASN294 3.3 21.4 1.0
O A:HOH837 3.5 34.4 1.0
O A:HOH760 3.5 35.3 1.0
O T:HOH156 3.7 36.5 1.0
OD1 A:ASN294 3.9 19.1 1.0
CG2 A:THR297 3.9 24.2 1.0
CB A:TYR296 3.9 20.6 1.0
CZ A:ARG299 3.9 34.2 1.0
NE A:ARG299 4.0 30.2 1.0
CG A:ASN294 4.0 22.5 1.0
CB A:THR297 4.0 23.0 1.0
CD2 A:TYR296 4.1 25.4 1.0
NH2 A:ARG299 4.1 29.5 1.0
NH1 A:ARG299 4.2 36.3 1.0
CG A:TYR296 4.4 25.2 1.0
CD A:ARG299 4.5 30.5 1.0
O A:HOH651 4.6 19.2 1.0
N A:THR297 4.6 19.5 1.0
O T:HOH102 4.8 31.6 1.0
CA A:THR297 4.9 22.4 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 Jul 12 12:31:10 2025

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