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Bromine in PDB 3jpq: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene Triphosphate

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene Triphosphate

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene Triphosphate:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene Triphosphate, PDB code: 3jpq was solved by V.K.Batra, J.Upton, B.Kashmerov, W.A.Beard, S.H.Wilson, M.F.Goodman, C.E.Mckenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.23 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.680, 80.180, 55.560, 90.00, 107.82, 90.00
R / Rfree (%) 19.3 / 23.4

Other elements in 3jpq:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene Triphosphate also contains other interesting chemical elements:

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

Bromine Binding Sites:

The binding sites of Bromine atom in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene Triphosphate (pdb code 3jpq). 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 of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene Triphosphate, PDB code: 3jpq:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 3jpq

Go back to Bromine Binding Sites List in 3jpq
Bromine binding site 1 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene Triphosphate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br338

b:27.3
occ:0.65
 BRB A:GBR338 0.0 27.3 0.7
C3B A:GBR338 1.8 12.1 0.3
C3B A:GBR338 2.0 17.1 0.7
BRB A:GBR338 2.1 16.1 0.3
O A:HOH699 2.8 35.9 1.0
O A:HOH636 3.0 33.7 1.0
PG A:GBR338 3.1 12.6 0.3
PG A:GBR338 3.1 19.3 0.7
O1B A:GBR338 3.1 14.3 0.7
PB A:GBR338 3.2 14.4 0.7
O2G A:GBR338 3.2 15.5 0.3
PB A:GBR338 3.2 10.8 0.3
O3G A:GBR338 3.3 15.6 0.7
O1B A:GBR338 3.4 11.1 0.3
O2G A:GBR338 3.5 18.8 0.7
NH2 A:ARG183 3.6 10.3 1.0
O3G A:GBR338 3.7 13.4 0.3
O A:HOH346 3.9 10.7 1.0
O3A A:GBR338 4.1 9.4 0.3
CB A:SER180 4.1 15.0 1.0
O2B A:GBR338 4.1 11.1 0.7
O3A A:GBR338 4.2 11.3 0.7
O1G A:GBR338 4.3 12.0 0.3
O2B A:GBR338 4.3 10.5 0.3
O1G A:GBR338 4.4 17.2 0.7
OG A:SER180 4.5 18.6 1.0
CZ A:ARG183 4.7 13.8 1.0
O A:HOH534 4.7 32.4 1.0
NH1 A:ARG183 4.9 9.9 1.0

Bromine binding site 2 out of 2 in 3jpq

Go back to Bromine Binding Sites List in 3jpq
Bromine binding site 2 out of 2 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene Triphosphate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monobromo Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br338

b:16.1
occ:0.35
 BRB A:GBR338 0.0 16.1 0.3
C3B A:GBR338 1.6 17.1 0.7
C3B A:GBR338 2.0 12.1 0.3
BRB A:GBR338 2.1 27.3 0.7
PG A:GBR338 2.9 19.3 0.7
PB A:GBR338 3.0 14.4 0.7
O2G A:GBR338 3.0 18.8 0.7
PG A:GBR338 3.1 12.6 0.3
O3A A:GBR338 3.1 9.4 0.3
PB A:GBR338 3.1 10.8 0.3
O2G A:GBR338 3.2 15.5 0.3
O3A A:GBR338 3.4 11.3 0.7
O A:HOH346 3.5 10.7 1.0
O1B A:GBR338 3.5 14.3 0.7
O A:HOH485 3.6 20.8 1.0
O A:HOH636 3.7 33.7 1.0
O1G A:GBR338 3.7 12.0 0.3
O1B A:GBR338 3.7 11.1 0.3
O1G A:GBR338 3.9 17.2 0.7
O3G A:GBR338 3.9 15.6 0.7
O2A A:GBR338 3.9 13.1 0.7
O2A A:GBR338 4.1 11.6 0.3
PA A:GBR338 4.1 12.0 0.3
PA A:GBR338 4.1 13.5 0.7
O2B A:GBR338 4.2 11.1 0.7
O2B A:GBR338 4.3 10.5 0.3
O A:HOH577 4.3 37.0 1.0
O3G A:GBR338 4.4 13.4 0.3
O A:HOH546 4.4 29.1 1.0
O1A A:GBR338 4.6 11.0 0.3
O A:HOH699 4.6 35.9 1.0
O1A A:GBR338 4.7 11.1 0.7

Reference:

V.K.Batra, L.C.Pedersen, W.A.Beard, S.H.Wilson, B.A.Kashemirov, T.G.Upton, M.F.Goodman, C.E.Mckenna. Halogenated Beta,Gamma-Methylene- and Ethylidene-Dgtp-Dna Ternary Complexes with Dna Polymerase Beta: Structural Evidence For Stereospecific Binding of the Fluoromethylene Analogues. J.Am.Chem.Soc. V. 132 7617 2010.
ISSN: ISSN 0002-7863
PubMed: 20465217
DOI: 10.1021/JA909370K
Page generated: Wed Jul 10 19:45:33 2024

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