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Chlorine in PDB 6ctt: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R &Amp; S Isomers, Beta, Gamma Dctp Analogue

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R &Amp; S Isomers, Beta, Gamma Dctp Analogue

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R &Amp; S Isomers, 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 Chcl (R &Amp; S Isomers, Beta, Gamma Dctp Analogue, PDB code: 6ctt 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) 25.48 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.825, 79.508, 55.524, 90.00, 107.67, 90.00
R / Rfree (%) 17.6 / 22.2

Other elements in 6ctt:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R &Amp; S Isomers, Beta, Gamma Dctp Analogue also contains other interesting chemical elements:

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 Chcl (R &Amp; S Isomers, Beta, Gamma Dctp Analogue (pdb code 6ctt). 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 Chcl (R &Amp; S Isomers, Beta, Gamma Dctp Analogue, PDB code: 6ctt:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6ctt

Go back to Chlorine Binding Sites List in 6ctt
Chlorine binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R &Amp; S Isomers, 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 Chcl (R &Amp; S Isomers, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:30.1
occ:0.60
 CL A:FF7401 0.0 30.1 0.6
C3B A:FF7401 1.8 23.5 0.6
C3B A:DJJ402 1.8 23.4 0.4
CL1 A:DJJ402 2.9 24.8 0.4
PG A:FF7401 2.9 25.6 0.6
PG A:DJJ402 2.9 25.5 0.4
PB A:FF7401 3.0 16.6 0.6
PB A:DJJ402 3.0 16.6 0.4
O1B A:FF7401 3.0 17.1 0.6
O2B A:DJJ402 3.0 17.1 0.4
O3G A:FF7401 3.1 21.9 0.6
O3G A:DJJ402 3.1 21.8 0.4
O A:HOH824 3.1 27.2 1.0
NH2 A:ARG183 3.1 17.3 1.0
O1G A:FF7401 3.5 31.1 0.6
O2G A:DJJ402 3.5 31.1 0.4
CB A:SER180 3.7 17.4 1.0
O2B A:FF7401 3.9 16.0 0.6
O1B A:DJJ402 3.9 15.9 0.4
O A:HOH684 4.0 15.9 1.0
OG A:SER180 4.1 19.7 1.0
O A:HOH688 4.1 31.9 1.0
O2G A:FF7401 4.2 22.2 0.6
O1G A:DJJ402 4.2 22.2 0.4
O3A A:FF7401 4.2 18.0 0.6
O3A A:DJJ402 4.2 17.9 0.4
CZ A:ARG183 4.3 18.1 1.0
O A:HOH732 4.3 33.0 1.0
NH1 A:ARG183 4.6 13.4 1.0
CA A:SER180 4.7 16.8 1.0
N A:SER180 4.8 16.1 1.0

Chlorine binding site 2 out of 3 in 6ctt

Go back to Chlorine Binding Sites List in 6ctt
Chlorine binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R &Amp; S Isomers, 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 Chcl (R &Amp; S Isomers, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:24.8
occ:0.40
 CL1 A:DJJ402 0.0 24.8 0.4
C3B A:FF7401 1.8 23.5 0.6
C3B A:DJJ402 1.8 23.4 0.4
CL A:FF7401 2.9 30.1 0.6
PG A:FF7401 2.9 25.6 0.6
PG A:DJJ402 2.9 25.5 0.4
O3A A:FF7401 3.0 18.0 0.6
O3A A:DJJ402 3.0 17.9 0.4
PB A:FF7401 3.0 16.6 0.6
PB A:DJJ402 3.0 16.6 0.4
O1G A:FF7401 3.0 31.1 0.6
O2G A:DJJ402 3.0 31.1 0.4
O A:HOH753 3.1 23.3 1.0
O A:HOH684 3.5 15.9 1.0
O2G A:FF7401 3.6 22.2 0.6
O1G A:DJJ402 3.6 22.2 0.4
O2A A:FF7401 3.6 17.6 0.6
O2A A:DJJ402 3.6 17.5 0.4
O A:HOH824 3.8 27.2 1.0
O1B A:FF7401 3.8 17.1 0.6
O2B A:DJJ402 3.8 17.1 0.4
PA A:FF7401 3.8 15.2 0.6
PA A:DJJ402 3.8 15.2 0.4
O A:HOH699 3.9 34.6 1.0
O A:HOH678 3.9 24.2 1.0
O3G A:FF7401 4.2 21.9 0.6
O3G A:DJJ402 4.2 21.8 0.4
O2B A:FF7401 4.2 16.0 0.6
O1B A:DJJ402 4.2 15.9 0.4
O1A A:FF7401 4.4 15.9 0.6
O1A A:DJJ402 4.4 15.9 0.4
O A:HOH660 4.4 26.6 1.0
MG A:MG405 5.0 14.5 1.0

Chlorine binding site 3 out of 3 in 6ctt

Go back to Chlorine Binding Sites List in 6ctt
Chlorine binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with Chcl (R &Amp; S Isomers, Beta, Gamma Dctp 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 Chcl (R &Amp; S Isomers, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:31.4
occ:1.00
 OG1 A:THR297 3.0 20.9 1.0
O A:HOH796 3.1 29.4 1.0
ND2 A:ASN294 3.4 22.7 1.0
CG2 A:THR297 3.7 19.0 1.0
OD1 A:ASN294 3.9 19.6 1.0
CB A:TYR296 3.9 20.6 1.0
CB A:THR297 3.9 19.8 1.0
O T:HOH249 4.0 40.4 1.0
CG A:ASN294 4.1 19.4 1.0
CZ A:ARG299 4.1 42.4 1.0
NE A:ARG299 4.2 35.3 1.0
CD2 A:TYR296 4.2 22.1 1.0
NH2 A:ARG299 4.3 32.4 1.0
NH1 A:ARG299 4.4 40.7 1.0
CG A:TYR296 4.5 21.7 1.0
N A:THR297 4.6 17.4 1.0
O A:HOH644 4.7 20.6 1.0
CD A:ARG299 4.7 24.5 1.0
O A:HOH746 4.9 45.8 1.0
O A:HOH826 4.9 42.4 1.0
O T:HOH206 4.9 35.5 1.0
CA A:THR297 4.9 18.8 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 12:34:25 2025

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