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Chlorine in PDB 6ctu: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl, Beta, Gamma Dctp Analogue

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Cfcl, Beta, Gamma Dctp 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 Cfcl, Beta, Gamma Dctp Analogue, PDB code: 6ctu 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) 23.72 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.810, 79.636, 55.483, 90.00, 107.78, 90.00
R / Rfree (%) 17.1 / 20.6

Other elements in 6ctu:

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

Fluorine (F) 1 atom
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 A Dideoxy Terminated Primer with Cfcl, Beta, Gamma Dctp Analogue (pdb code 6ctu). 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 Cfcl, Beta, Gamma Dctp Analogue, PDB code: 6ctu:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6ctu

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

b:34.4
occ:1.00
O A:HOH801 3.1 38.9 1.0
OG1 A:THR297 3.2 23.9 1.0
ND2 A:ASN294 3.4 25.0 1.0
O A:HOH843 3.5 38.5 1.0
O A:HOH901 3.6 44.2 1.0
CG2 A:THR297 3.9 21.3 1.0
CB A:TYR296 3.9 20.5 1.0
OD1 A:ASN294 4.0 21.3 1.0
NE A:ARG299 4.1 32.2 1.0
CB A:THR297 4.1 20.9 1.0
NH2 A:ARG299 4.1 35.6 1.0
CZ A:ARG299 4.1 40.0 1.0
CG A:ASN294 4.2 17.7 1.0
CD2 A:TYR296 4.2 21.6 1.0
CG A:TYR296 4.4 21.9 1.0
O A:HOH820 4.6 37.8 1.0
N A:THR297 4.6 18.8 1.0
NH1 A:ARG299 4.7 45.4 1.0
O A:HOH665 4.8 21.5 1.0
CD A:ARG299 4.8 31.1 1.0
O T:HOH219 4.9 34.5 1.0
O T:HOH227 5.0 37.3 1.0

Chlorine binding site 2 out of 2 in 6ctu

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

b:23.8
occ:1.00
CL1 A:VC6404 0.0 23.8 1.0
C3B A:VC6404 1.8 21.6 1.0
F4B A:VC6404 2.5 20.9 1.0
PB A:VC6404 2.9 16.2 1.0
PG A:VC6404 2.9 24.4 1.0
O3A A:VC6404 3.0 15.9 1.0
O1G A:VC6404 3.1 30.6 1.0
O A:HOH740 3.4 23.9 1.0
O2G A:VC6404 3.5 16.9 1.0
O A:HOH681 3.6 16.2 1.0
O2B A:VC6404 3.7 14.6 1.0
O A:HOH834 3.8 24.9 1.0
O2A A:VC6404 3.9 15.0 1.0
PA A:VC6404 3.9 16.1 1.0
O1B A:VC6404 4.1 14.0 1.0
O3G A:VC6404 4.2 21.9 1.0
O1A A:VC6404 4.4 12.3 1.0
O A:HOH581 4.4 32.0 1.0
MG A:MG402 4.9 14.9 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 Jul 12 12:34:31 2025

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