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

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Dichloro 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-Dichloro Methylene Triphosphate, PDB code: 3jpn 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) 22.33 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.650, 80.110, 55.480, 90.00, 107.93, 90.00
R / Rfree (%) 19 / 24.2

Other elements in 3jpn:

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

Magnesium (Mg) 1 atom

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-Dichloro Methylene Triphosphate (pdb code 3jpn). 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-Dichloro Methylene Triphosphate, PDB code: 3jpn:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3jpn

Go back to Chlorine Binding Sites List in 3jpn
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-Dichloro 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-Dichloro Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl338

b:24.9
occ:1.00
 CL1B A:G2C338 0.0 24.9 1.0
C3B A:G2C338 1.8 19.3 1.0
CL2B A:G2C338 2.9 25.0 1.0
PG A:G2C338 2.9 22.0 1.0
PB A:G2C338 3.0 14.8 1.0
O1B A:G2C338 3.1 16.0 1.0
O3G A:G2C338 3.1 15.6 1.0
O A:HOH382 3.2 41.8 1.0
NH2 A:ARG183 3.3 17.3 1.0
O A:HOH560 3.3 36.5 1.0
O2G A:G2C338 3.4 22.8 1.0
O A:HOH562 3.6 24.8 1.0
CB A:SER180 3.8 12.5 1.0
O2B A:G2C338 3.9 10.2 1.0
O A:HOH365 4.0 11.2 1.0
O A:HOH505 4.0 26.2 1.0
O3A A:G2C338 4.1 12.2 1.0
O1G A:G2C338 4.2 15.7 1.0
OG A:SER180 4.3 15.4 1.0
O A:HOH460 4.3 33.3 1.0
CZ A:ARG183 4.4 17.1 1.0
NH1 A:ARG183 4.7 12.6 1.0
CA A:SER180 4.8 13.0 1.0
N A:SER180 4.8 14.0 1.0

Chlorine binding site 2 out of 4 in 3jpn

Go back to Chlorine Binding Sites List in 3jpn
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-Dichloro 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-Dichloro Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl338

b:25.0
occ:1.00
 CL2B A:G2C338 0.0 25.0 1.0
C3B A:G2C338 1.8 19.3 1.0
CL1B A:G2C338 2.9 24.9 1.0
PG A:G2C338 2.9 22.0 1.0
PB A:G2C338 3.0 14.8 1.0
O3A A:G2C338 3.0 12.2 1.0
O2G A:G2C338 3.2 22.8 1.0
O A:HOH448 3.4 22.7 1.0
O2A A:G2C338 3.4 12.2 1.0
O1G A:G2C338 3.5 15.7 1.0
O A:HOH365 3.6 11.2 1.0
PA A:G2C338 3.6 13.3 1.0
O A:HOH562 3.7 24.8 1.0
O1B A:G2C338 3.7 16.0 1.0
O A:HOH462 3.9 37.0 1.0
O2B A:G2C338 4.1 10.2 1.0
O1A A:G2C338 4.1 10.1 1.0
O A:HOH616 4.2 27.4 1.0
O3G A:G2C338 4.2 15.6 1.0
O A:HOH369 4.2 46.0 1.0
O A:HOH470 4.3 39.1 1.0
O A:HOH560 4.8 36.5 1.0
MG A:MG339 4.8 10.1 1.0

Chlorine binding site 3 out of 4 in 3jpn

Go back to Chlorine Binding Sites List in 3jpn
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-Dichloro 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-Dichloro Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl343

b:28.5
occ:1.00
 NH2 A:ARG299 2.9 32.6 1.0
ND2 A:ASN294 3.2 18.5 1.0
OG1 A:THR297 3.2 27.6 1.0
O A:HOH621 3.3 37.6 1.0
NE A:ARG299 3.3 31.8 1.0
CZ A:ARG299 3.6 33.7 1.0
CB A:TYR296 3.9 20.6 1.0
OD1 A:ASN294 4.0 21.9 1.0
CG A:ASN294 4.0 20.7 1.0
CD2 A:TYR296 4.2 21.2 1.0
O A:HOH435 4.5 25.4 1.0
CG A:TYR296 4.5 20.5 1.0
CB A:THR297 4.5 26.2 1.0
CD A:ARG299 4.6 29.2 1.0
N A:THR297 4.7 19.5 1.0
O T:HOH301 4.8 34.8 1.0
O T:HOH133 4.8 35.9 1.0
CG2 A:THR297 4.8 25.9 1.0
NH1 A:ARG299 4.9 35.3 1.0

Chlorine binding site 4 out of 4 in 3jpn

Go back to Chlorine Binding Sites List in 3jpn
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-Dichloro 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-Dichloro Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl344

b:33.0
occ:1.00
 N A:HIS34 3.3 24.9 1.0
CB A:HIS34 3.4 26.6 1.0
C A:ALA32 3.5 23.3 1.0
CB A:ALA32 3.5 20.5 1.0
CA A:ALA32 3.6 23.3 1.0
N A:LYS35 3.6 23.7 1.0
O A:ALA32 3.8 23.1 1.0
CA A:HIS34 3.8 25.9 1.0
CD2 A:HIS34 3.8 29.7 1.0
N A:ILE33 3.9 24.1 1.0
CG A:HIS34 4.0 30.0 1.0
C A:HIS34 4.1 25.3 1.0
CG A:LYS35 4.2 27.7 1.0
C A:ILE33 4.3 25.1 1.0
CB A:LYS35 4.5 22.8 1.0
CA A:ILE33 4.6 26.3 1.0
CA A:LYS35 4.6 22.3 1.0
O A:HOH468 4.8 34.6 1.0
O6 D:DG1 4.8 28.7 1.0
CG2 A:ILE33 4.9 29.3 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: Fri Jul 11 06:39:38 2025

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