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Chlorine in PDB 4do9: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer:
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-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer, PDB code: 4do9 was solved by V.K.Batra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.28 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.693, 79.914, 55.607, 90.00, 107.66, 90.00
R / Rfree (%) 18.8 / 24.3

Other elements in 4do9:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer 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-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer (pdb code 4do9). 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-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer, PDB code: 4do9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4do9

Go back to Chlorine Binding Sites List in 4do9
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-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer


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-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:35.3
occ:1.00
 O A:HOH509 2.9 19.6 1.0
N A:CYS267 3.3 22.0 1.0
CA A:GLN264 3.4 22.1 1.0
C A:GLN264 3.5 23.2 1.0
N A:TYR266 3.6 22.7 1.0
CG1 A:VAL313 3.6 24.7 1.0
O A:GLN264 3.8 23.0 1.0
O A:ASP263 3.8 23.4 1.0
CB A:VAL313 3.8 25.7 1.0
CB A:TYR266 3.8 24.2 1.0
SG A:CYS267 3.8 20.7 1.0
CB A:CYS267 3.9 21.3 1.0
N A:TYR265 4.0 22.8 1.0
CA A:TYR266 4.0 22.1 1.0
C A:TYR266 4.1 20.9 1.0
CA A:CYS267 4.2 18.7 1.0
O A:TYR296 4.2 20.1 1.0
CB A:GLN264 4.3 20.1 1.0
C A:TYR265 4.5 22.7 1.0
N A:GLN264 4.5 22.0 1.0
CD2 A:TYR266 4.5 31.1 1.0
O A:VAL313 4.5 28.4 1.0
C A:ASP263 4.5 25.2 1.0
CG2 A:VAL313 4.6 22.8 1.0
CG A:TYR266 4.7 26.6 1.0
CA A:TYR265 4.8 23.8 1.0
CG A:GLN264 4.9 26.0 1.0
CA A:VAL313 5.0 26.3 1.0
C A:VAL313 5.0 28.1 1.0

Chlorine binding site 2 out of 5 in 4do9

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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-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer


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-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:34.6
occ:1.00
 N A:HIS34 3.3 29.2 1.0
C A:ALA32 3.4 26.2 1.0
CB A:ALA32 3.4 24.6 1.0
CA A:ALA32 3.5 32.0 1.0
CB A:HIS34 3.6 34.1 1.0
N A:LYS35 3.6 26.4 1.0
O A:ALA32 3.6 27.5 1.0
N A:ILE33 3.7 24.2 1.0
CA A:HIS34 3.9 28.0 1.0
CD2 A:HIS34 4.0 40.4 1.0
CG A:HIS34 4.1 36.6 1.0
CG A:LYS35 4.1 30.8 1.0
C A:HIS34 4.2 27.6 1.0
C A:ILE33 4.4 28.9 1.0
CB A:LYS35 4.5 26.0 1.0
CA A:ILE33 4.6 32.4 1.0
CA A:LYS35 4.7 25.6 1.0
O A:HOH693 4.7 40.6 1.0
O6 D:DG1 4.9 37.3 1.0
N A:ALA32 5.0 26.3 1.0

Chlorine binding site 3 out of 5 in 4do9

Go back to Chlorine Binding Sites List in 4do9
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-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer


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-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:48.2
occ:1.00
 NH2 A:ARG89 3.0 49.6 1.0
N A:LEU82 3.3 27.2 1.0
NH1 A:ARG89 3.5 45.2 1.0
O A:HOH615 3.6 31.0 1.0
CA A:LYS81 3.6 24.4 1.0
CZ A:ARG89 3.7 47.2 1.0
CB A:LYS81 3.7 34.5 1.0
OE2 A:GLU86 3.9 52.7 1.0
C A:LYS81 3.9 29.7 1.0
CB A:LEU82 4.2 29.8 1.0
O A:LEU82 4.2 31.4 1.0
CA A:LEU82 4.2 28.5 1.0
CB A:LEU85 4.3 28.4 1.0
CD1 A:LEU85 4.4 27.4 1.0
C A:LEU82 4.7 31.8 1.0
O A:GLY80 4.8 36.7 1.0
CE1 A:PHE76 4.9 25.4 1.0
N A:LYS81 4.9 26.2 1.0
CG A:LEU85 4.9 25.1 1.0
CD A:GLU86 5.0 62.9 1.0
CG A:LYS81 5.0 38.2 1.0
NE A:ARG89 5.0 33.1 1.0

Chlorine binding site 4 out of 5 in 4do9

Go back to Chlorine Binding Sites List in 4do9
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-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer


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-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:34.3
occ:1.00
 OG1 A:THR297 3.0 21.7 1.0
O A:HOH731 3.1 36.6 1.0
NH2 A:ARG299 3.1 30.6 1.0
ND2 A:ASN294 3.2 24.0 1.0
NE A:ARG299 3.3 27.6 0.7
CZ A:ARG299 3.6 30.7 0.1
CG2 A:THR297 3.6 20.0 1.0
CB A:THR297 3.9 22.7 1.0
CB A:TYR296 3.9 27.8 1.0
OD1 A:ASN294 4.0 22.7 1.0
CG A:ASN294 4.0 21.8 1.0
CD2 A:TYR296 4.2 24.5 1.0
CD A:ARG299 4.5 30.1 1.0
CG A:TYR296 4.5 20.8 1.0
N A:THR297 4.6 17.9 1.0
O T:HOH137 4.7 35.3 1.0
O A:HOH513 4.7 20.5 1.0
NH1 A:ARG299 4.7 36.7 1.0
CA A:THR297 4.9 22.7 1.0

Chlorine binding site 5 out of 5 in 4do9

Go back to Chlorine Binding Sites List in 4do9
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-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer


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-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:47.0
occ:1.00
 N A:LYS331 3.1 24.0 1.0
CD A:PRO330 3.3 23.2 1.0
CB A:PRO330 3.5 18.0 1.0
N A:PRO330 3.5 20.4 1.0
CB A:LYS331 3.5 24.0 1.0
CG A:LYS331 3.6 32.6 1.0
CB A:GLU329 3.6 29.2 1.0
CG A:PRO330 3.7 24.2 1.0
CD A:LYS331 3.7 44.1 1.0
CA A:LYS331 3.9 23.2 1.0
CA A:PRO330 3.9 21.3 1.0
C A:PRO330 4.0 19.4 1.0
OE1 A:GLU329 4.0 41.8 1.0
C A:GLU329 4.0 22.4 1.0
CA A:GLU329 4.3 27.1 1.0
CE A:LYS331 4.5 50.8 1.0
O A:ARG182 4.5 18.9 1.0
CG A:GLU329 4.5 37.6 1.0
CD A:GLU329 4.7 43.9 1.0
O A:GLU329 4.7 19.8 1.0

Reference:

Y.Wu, V.M.Zakharova, B.A.Kashemirov, M.F.Goodman, V.K.Batra, S.H.Wilson, C.E.Mckenna. Beta,Gamma-Chf- and Beta,Gamma-Chcl-Dgtp Diastereomers: Synthesis, Discrete (31)P uc(Nmr) Signatures, and Absolute Configurations of New Stereochemical Probes For Dna Polymerases J.Am.Chem.Soc. V. 134 8734 2012.
ISSN: ISSN 0002-7863
PubMed: 22397499
DOI: 10.1021/JA300218X
Page generated: Fri Jul 11 14:28:24 2025

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