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

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochloromethylene 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-Monochloromethylene Triphosphate, PDB code: 3jpo 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) 22.30 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.460, 79.990, 55.430, 90.00, 107.91, 90.00
R / Rfree (%) 19.4 / 24.7

Other elements in 3jpo:

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

Chlorine binding site 1 out of 5 in 3jpo

Go back to Chlorine Binding Sites List in 3jpo
Chlorine binding site 1 out of 5 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochloromethylene 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-Monochloromethylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl338

b:23.1
occ:0.50
 CL3B A:G1C338 0.0 23.1 0.5
C3B A:G1C338 1.5 20.7 0.5
C3B A:G1C338 1.8 20.2 0.5
CL3B A:G1C338 2.3 22.9 0.5
PG A:G1C338 2.8 23.0 0.5
PB A:G1C338 2.9 17.7 0.5
PG A:G1C338 2.9 22.7 0.5
PB A:G1C338 2.9 17.5 0.5
O3A A:G1C338 3.0 17.1 0.5
O2G A:G1C338 3.1 23.4 0.5
O2G A:G1C338 3.1 23.4 0.5
O3A A:G1C338 3.2 18.7 0.5
O A:HOH479 3.3 28.1 1.0
O A:HOH645 3.4 16.6 1.0
O1B A:G1C338 3.5 18.2 0.5
O2A A:G1C338 3.6 19.7 0.5
O1B A:G1C338 3.6 19.0 0.5
O1G A:G1C338 3.6 21.0 0.5
O1G A:G1C338 3.7 21.9 0.5
PA A:G1C338 3.8 20.3 0.5
O A:HOH597 3.9 34.2 1.0
O2A A:G1C338 3.9 15.3 0.5
PA A:G1C338 3.9 17.9 0.5
O3G A:G1C338 4.0 21.8 0.5
O2B A:G1C338 4.0 15.9 0.5
O A:HOH472 4.1 41.4 1.0
O2B A:G1C338 4.1 17.2 0.5
O3G A:G1C338 4.2 21.6 0.5
O A:HOH488 4.3 30.3 1.0
O1A A:G1C338 4.4 18.9 0.5
O A:HOH540 4.4 41.1 1.0
O1A A:G1C338 4.5 15.3 0.5
O A:HOH651 4.7 48.2 1.0
MG A:MG339 4.9 17.5 1.0

Chlorine binding site 2 out of 5 in 3jpo

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Chlorine binding site 2 out of 5 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochloromethylene 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-Monochloromethylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl338

b:22.9
occ:0.50
 CL3B A:G1C338 0.0 22.9 0.5
C3B A:G1C338 1.7 20.2 0.5
C3B A:G1C338 1.8 20.7 0.5
CL3B A:G1C338 2.3 23.1 0.5
PG A:G1C338 2.9 23.0 0.5
PG A:G1C338 3.0 22.7 0.5
PB A:G1C338 3.0 17.7 0.5
O A:HOH651 3.0 48.2 1.0
O1B A:G1C338 3.0 18.2 0.5
O3G A:G1C338 3.1 21.8 0.5
PB A:G1C338 3.1 17.5 0.5
O A:HOH597 3.1 34.2 1.0
O1B A:G1C338 3.3 19.0 0.5
O2G A:G1C338 3.3 23.4 0.5
NH2 A:ARG183 3.3 19.8 1.0
O3G A:G1C338 3.4 21.6 0.5
O2G A:G1C338 3.4 23.4 0.5
CB A:SER180 3.8 18.7 1.0
O A:HOH645 3.9 16.6 1.0
O2B A:G1C338 3.9 15.9 0.5
O3A A:G1C338 4.1 17.1 0.5
O2B A:G1C338 4.1 17.2 0.5
O3A A:G1C338 4.1 18.7 0.5
O1G A:G1C338 4.2 21.9 0.5
O1G A:G1C338 4.2 21.0 0.5
OG A:SER180 4.3 21.0 1.0
CZ A:ARG183 4.5 20.5 1.0
O A:HOH507 4.5 38.6 1.0
NH1 A:ARG183 4.8 13.6 1.0
CA A:SER180 4.8 19.2 1.0
N A:SER180 4.9 19.3 1.0

Chlorine binding site 3 out of 5 in 3jpo

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

b:32.7
occ:1.00
 NH2 A:ARG299 3.0 32.0 1.0
ND2 A:ASN294 3.2 19.1 1.0
OG1 A:THR297 3.2 28.9 1.0
O A:HOH435 3.4 36.8 1.0
NE A:ARG299 3.5 33.6 1.0
CZ A:ARG299 3.7 34.9 1.0
OD1 A:ASN294 3.9 24.1 1.0
CB A:TYR296 4.0 25.1 1.0
CG A:ASN294 4.0 20.4 1.0
CD2 A:TYR296 4.2 25.8 1.0
CB A:THR297 4.4 27.9 1.0
CG2 A:THR297 4.5 29.0 1.0
O T:HOH150 4.5 36.9 1.0
CG A:TYR296 4.5 24.1 1.0
N A:THR297 4.6 22.1 1.0
CD A:ARG299 4.8 31.1 1.0
O A:HOH443 4.8 17.4 1.0
NH1 A:ARG299 4.9 33.6 1.0

Chlorine binding site 4 out of 5 in 3jpo

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Chlorine binding site 4 out of 5 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochloromethylene 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-Monochloromethylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl344

b:38.0
occ:1.00
 N A:HIS34 3.2 28.5 1.0
C A:ALA32 3.4 25.9 1.0
CB A:HIS34 3.4 30.9 1.0
CA A:ALA32 3.4 26.4 1.0
CB A:ALA32 3.5 23.4 1.0
N A:LYS35 3.6 27.0 1.0
N A:ILE33 3.7 26.8 1.0
CA A:HIS34 3.7 29.5 1.0
CD2 A:HIS34 3.7 35.2 1.0
O A:ALA32 3.7 24.1 1.0
CG A:HIS34 3.9 35.5 1.0
C A:HIS34 4.1 29.1 1.0
C A:ILE33 4.2 28.4 1.0
O A:HOH404 4.3 24.6 1.0
CG A:LYS35 4.3 30.2 1.0
CA A:ILE33 4.4 28.7 1.0
CB A:LYS35 4.6 25.9 1.0
CA A:LYS35 4.7 25.6 1.0
CG2 A:ILE33 4.7 31.7 1.0
N A:ALA32 4.9 23.9 1.0
O6 D:DG1 4.9 32.0 1.0
NE2 A:HIS34 5.0 38.0 1.0

Chlorine binding site 5 out of 5 in 3jpo

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


Mono view


Stereo pair view

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

b:37.2
occ:1.00
 O A:HOH469 3.0 28.0 1.0
N A:CYS267 3.3 21.9 1.0
N A:TYR266 3.5 21.9 1.0
CB A:TYR266 3.5 26.4 1.0
CG1 A:VAL313 3.6 26.0 1.0
CA A:GLN264 3.6 24.1 1.0
C A:GLN264 3.6 24.8 1.0
CB A:VAL313 3.7 27.8 1.0
CA A:TYR266 3.8 23.2 1.0
O A:ASP263 3.9 24.9 1.0
O A:GLN264 3.9 25.6 1.0
SG A:CYS267 3.9 23.2 1.0
C A:TYR266 4.0 23.1 1.0
N A:TYR265 4.0 23.9 1.0
CB A:CYS267 4.1 24.2 1.0
CD2 A:TYR266 4.2 30.9 1.0
CA A:CYS267 4.3 22.7 1.0
O A:VAL313 4.3 28.4 1.0
CG A:TYR266 4.4 28.5 1.0
C A:TYR265 4.4 23.9 1.0
O A:TYR296 4.5 21.2 1.0
N A:GLN264 4.5 24.7 1.0
CB A:GLN264 4.6 24.8 1.0
C A:ASP263 4.6 25.5 1.0
CG2 A:VAL313 4.6 24.4 1.0
CA A:TYR265 4.8 24.1 1.0
C A:VAL313 4.8 28.7 1.0
CA A:VAL313 4.9 29.0 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 22:04:21 2024

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