Bromine in PDB 6ctx: Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp Analogue

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, 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 CBR2, Beta, Gamma Dctp Analogue, PDB code: 6ctx 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) 31.79 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.815, 79.565, 55.502, 90.00, 107.78, 90.00
R / Rfree (%) 17.7 / 22.9

Other elements in 6ctx:

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

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom
Sodium (Na) 3 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp Analogue (pdb code 6ctx). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp Analogue, PDB code: 6ctx:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 6ctx

Go back to Bromine Binding Sites List in 6ctx
Bromine 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 Dctp Analogue


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br404

b:24.8
occ:0.62
 BR1 A:VC9404 0.0 24.8 0.6
C3B A:VC9404 1.9 21.1 1.0
BR2 A:VC9404 2.9 29.9 0.8
PG A:VC9404 3.0 24.9 1.0
O3A A:VC9404 3.1 17.9 1.0
O1G A:VC9404 3.1 26.0 1.0
PB A:VC9404 3.1 19.3 1.0
O A:HOH726 3.5 27.1 1.0
O2G A:VC9404 3.5 17.4 1.0
O A:HOH505 3.6 32.0 1.0
O A:HOH688 3.7 18.9 1.0
O2A A:VC9404 3.7 19.0 1.0
O A:HOH796 3.9 30.8 1.0
PA A:VC9404 3.9 17.9 1.0
O A:HOH780 4.0 32.3 1.0
O2B A:VC9404 4.0 17.0 1.0
O3G A:VC9404 4.3 19.0 1.0
O1B A:VC9404 4.3 19.0 1.0
O1A A:VC9404 4.4 15.4 1.0
O A:HOH741 4.4 35.5 1.0
O A:HOH509 4.5 34.6 1.0

Bromine binding site 2 out of 2 in 6ctx

Go back to Bromine Binding Sites List in 6ctx
Bromine 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 Dctp Analogue


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with A Dideoxy Terminated Primer with CBR2, Beta, Gamma Dctp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br404

b:29.9
occ:0.76
 BR2 A:VC9404 0.0 29.9 0.8
C3B A:VC9404 1.9 21.1 1.0
BR1 A:VC9404 2.9 24.8 0.6
PG A:VC9404 3.1 24.9 1.0
PB A:VC9404 3.2 19.3 1.0
O2B A:VC9404 3.2 17.0 1.0
NH2 A:ARG183 3.3 16.7 1.0
O3G A:VC9404 3.3 19.0 1.0
O A:HOH509 3.4 34.6 1.0
O1G A:VC9404 3.5 26.0 1.0
O A:HOH796 3.6 30.8 1.0
CB A:SER180 3.8 20.4 1.0
O A:HOH688 4.1 18.9 1.0
O A:HOH643 4.1 28.6 1.0
O1B A:VC9404 4.1 19.0 1.0
OG A:SER180 4.2 19.2 1.0
O3A A:VC9404 4.3 17.9 1.0
O2G A:VC9404 4.4 17.4 1.0
CZ A:ARG183 4.4 19.5 1.0
NH1 A:ARG183 4.8 16.6 1.0
CA A:SER180 4.9 16.8 1.0
N A:SER180 5.0 19.1 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 02:32:45 2020

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