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Chlorine in PDB 3jpt: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro 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-Fluoro Chloro Methylene Triphosphate, PDB code: 3jpt 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) 23.89 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.660, 80.120, 55.450, 90.00, 108.05, 90.00
R / Rfree (%) 19.4 / 25.4

Other elements in 3jpt:

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

Fluorine (F) 1 atom
Magnesium (Mg) 1 atom
Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate (pdb code 3jpt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate, PDB code: 3jpt:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3jpt

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Chlorine binding site 1 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl338

b:21.3
occ:1.00
 CL3B A:GFC338 0.0 21.3 1.0
C3B A:GFC338 1.8 17.5 1.0
F3B A:GFC338 2.5 19.4 1.0
PG A:GFC338 2.9 18.9 1.0
PB A:GFC338 2.9 13.9 1.0
O3A A:GFC338 3.0 15.7 1.0
O2G A:GFC338 3.1 22.0 1.0
O A:HOH597 3.2 43.7 1.0
O A:HOH407 3.2 25.6 1.0
O1G A:GFC338 3.6 15.2 1.0
O A:HOH336 3.6 10.0 1.0
O1B A:GFC338 3.6 16.5 1.0
O2A A:GFC338 3.7 14.5 1.0
PA A:GFC338 3.8 14.9 1.0
O A:HOH556 4.0 30.2 1.0
O2B A:GFC338 4.1 12.4 1.0
O3G A:GFC338 4.2 17.4 1.0
O A:HOH416 4.3 33.0 1.0
O1A A:GFC338 4.3 13.7 1.0
O A:HOH495 4.4 26.1 1.0
O A:HOH534 4.5 35.6 1.0
O A:HOH511 4.7 36.7 1.0
MG A:MG339 4.8 12.9 1.0
O A:HOH572 4.9 44.9 1.0

Chlorine binding site 2 out of 4 in 3jpt

Go back to Chlorine Binding Sites List in 3jpt
Chlorine binding site 2 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl343

b:33.3
occ:1.00
 N A:HIS34 3.3 26.5 1.0
C A:ALA32 3.5 24.9 1.0
CB A:HIS34 3.5 27.8 1.0
CA A:ALA32 3.5 25.1 1.0
N A:LYS35 3.6 24.8 1.0
CB A:ALA32 3.6 21.8 1.0
CA A:HIS34 3.8 26.9 1.0
O A:ALA32 3.8 25.2 1.0
N A:ILE33 3.8 25.3 1.0
C A:HIS34 4.1 27.1 1.0
CG A:HIS34 4.1 30.1 1.0
CD2 A:HIS34 4.2 30.8 1.0
CG A:LYS35 4.3 25.3 1.0
C A:ILE33 4.3 26.1 1.0
CB A:LYS35 4.5 22.9 1.0
O A:HOH426 4.6 25.5 1.0
CA A:ILE33 4.6 26.5 1.0
CA A:LYS35 4.6 22.8 1.0
O6 D:DG1 4.8 29.4 1.0
CG2 A:ILE33 4.9 29.4 1.0
N A:ALA32 5.0 24.1 1.0

Chlorine binding site 3 out of 4 in 3jpt

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Chlorine binding site 3 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl344

b:34.6
occ:1.00
 O A:HOH430 3.2 26.3 1.0
N A:CYS267 3.3 19.1 1.0
CB A:TYR266 3.6 23.3 1.0
N A:TYR266 3.6 18.9 1.0
CG1 A:VAL313 3.6 26.5 1.0
CA A:GLN264 3.6 22.8 1.0
C A:GLN264 3.7 21.8 1.0
CB A:VAL313 3.8 25.7 1.0
SG A:CYS267 3.8 21.1 1.0
O A:GLN264 3.9 23.5 1.0
CA A:TYR266 3.9 19.8 1.0
O A:ASP263 4.0 23.9 1.0
CB A:CYS267 4.0 20.3 1.0
C A:TYR266 4.0 20.2 1.0
N A:TYR265 4.1 21.4 1.0
CA A:CYS267 4.2 18.0 1.0
CD2 A:TYR266 4.3 26.1 1.0
CG A:TYR266 4.5 24.6 1.0
O A:VAL313 4.5 27.4 1.0
C A:TYR265 4.5 20.3 1.0
O A:TYR296 4.5 20.9 1.0
CG2 A:VAL313 4.6 25.3 1.0
CB A:GLN264 4.6 23.8 1.0
N A:GLN264 4.6 23.1 1.0
C A:ASP263 4.7 23.4 1.0
C A:VAL313 4.8 28.1 1.0
CA A:TYR265 4.9 20.5 1.0
CA A:VAL313 4.9 27.2 1.0

Chlorine binding site 4 out of 4 in 3jpt

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Chlorine binding site 4 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl345

b:33.4
occ:1.00
 NH2 A:ARG299 3.0 28.2 1.0
ND2 A:ASN294 3.2 19.4 1.0
OG1 A:THR297 3.2 27.1 1.0
NE A:ARG299 3.3 25.6 1.0
O A:HOH507 3.4 33.0 1.0
CZ A:ARG299 3.5 29.2 1.0
O T:HOH372 3.9 48.0 1.0
CG A:ASN294 4.0 20.8 1.0
CB A:TYR296 4.1 21.0 1.0
OD1 A:ASN294 4.1 20.4 1.0
CD2 A:TYR296 4.2 19.0 1.0
CB A:THR297 4.5 25.7 1.0
CD A:ARG299 4.6 24.8 1.0
CG A:TYR296 4.6 18.5 1.0
O A:HOH413 4.6 17.6 1.0
N A:THR297 4.7 20.8 1.0
NH1 A:ARG299 4.7 29.8 1.0
O T:HOH186 4.7 31.4 1.0
CG2 A:THR297 4.9 27.9 1.0

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: Sat Dec 12 09:49:25 2020

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