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

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Dimethyl 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-Dimethyl Methylene Triphosphate, PDB code: 3jpr 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) 25.46 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.630, 80.100, 55.330, 90.00, 108.07, 90.00
R / Rfree (%) 20.1 / 25.3

Other elements in 3jpr:

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

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-Dimethyl Methylene Triphosphate (pdb code 3jpr). 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 of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Dimethyl Methylene Triphosphate, PDB code: 3jpr:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 3jpr

Go back to Chlorine Binding Sites List in 3jpr
Chlorine binding site 1 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Dimethyl 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-Dimethyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl343

b:32.9
occ:1.00
 N A:HIS34 3.4 29.1 1.0
C A:ALA32 3.6 27.8 1.0
CB A:HIS34 3.6 31.6 1.0
CA A:ALA32 3.7 27.9 1.0
CB A:ALA32 3.7 24.9 1.0
N A:LYS35 3.7 27.7 1.0
N A:ILE33 3.9 27.2 1.0
CA A:HIS34 3.9 30.4 1.0
CD2 A:HIS34 3.9 36.5 1.0
O A:ALA32 4.0 27.0 1.0
CG A:HIS34 4.0 36.4 1.0
C A:HIS34 4.3 29.5 1.0
O D:HOH311 4.3 51.7 1.0
CG A:LYS35 4.3 27.3 1.0
O A:HOH422 4.3 40.0 1.0
C A:ILE33 4.4 28.8 1.0
CG2 A:ILE33 4.6 32.2 1.0
CA A:ILE33 4.6 29.1 1.0
CB A:LYS35 4.6 26.3 1.0
CA A:LYS35 4.7 25.9 1.0
O6 D:DG1 4.8 34.4 1.0
O D:HOH319 4.9 31.8 1.0

Chlorine binding site 2 out of 3 in 3jpr

Go back to Chlorine Binding Sites List in 3jpr
Chlorine binding site 2 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Dimethyl 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-Dimethyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl344

b:33.3
occ:1.00
 O A:HOH363 2.9 30.3 1.0
N A:CYS267 3.3 26.7 1.0
CA A:GLN264 3.6 24.5 1.0
C A:GLN264 3.6 25.3 1.0
N A:TYR266 3.7 27.5 1.0
CB A:TYR266 3.7 32.7 1.0
O A:ASP263 3.8 25.8 1.0
SG A:CYS267 3.8 27.7 1.0
CB A:VAL313 3.9 32.3 1.0
CG1 A:VAL313 3.9 31.9 1.0
O A:GLN264 3.9 25.1 1.0
CB A:CYS267 4.0 27.1 1.0
CA A:TYR266 4.0 29.0 1.0
N A:TYR265 4.1 26.2 1.0
C A:TYR266 4.1 29.1 1.0
CA A:CYS267 4.2 25.4 1.0
CD2 A:TYR266 4.4 36.3 1.0
CB A:GLN264 4.4 25.4 1.0
O A:TYR296 4.4 25.5 1.0
C A:TYR265 4.5 26.4 1.0
CG A:TYR266 4.5 33.5 1.0
N A:GLN264 4.5 24.1 1.0
O A:VAL313 4.6 32.9 1.0
CG2 A:VAL313 4.6 32.2 1.0
C A:ASP263 4.6 25.4 1.0
CG A:GLN264 4.8 26.0 1.0
CA A:TYR265 4.9 25.7 1.0
C A:VAL313 5.0 33.2 1.0

Chlorine binding site 3 out of 3 in 3jpr

Go back to Chlorine Binding Sites List in 3jpr
Chlorine binding site 3 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Dimethyl 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-Dimethyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl345

b:29.7
occ:1.00
 NH2 A:ARG299 2.8 37.4 1.0
OG1 A:THR297 3.1 30.2 1.0
ND2 A:ASN294 3.2 23.8 1.0
NE A:ARG299 3.3 37.8 1.0
CZ A:ARG299 3.5 40.4 1.0
OD1 A:ASN294 4.1 23.6 1.0
CG A:ASN294 4.1 24.0 1.0
CB A:TYR296 4.1 28.5 1.0
CD2 A:TYR296 4.3 28.7 1.0
O A:HOH388 4.4 28.1 1.0
CB A:THR297 4.4 29.4 1.0
CG2 A:THR297 4.5 28.6 1.0
CD A:ARG299 4.6 34.5 1.0
CG A:TYR296 4.7 29.2 1.0
N A:THR297 4.7 26.3 1.0
NH1 A:ARG299 4.8 42.3 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 Jul 20 22:06:00 2024

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