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

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Non-Interactive Binding of S-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: Non-Interactive Binding of S-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: Non-Interactive Binding of S-Isomer, PDB code: 4doa 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) 20.27 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.638, 79.933, 55.519, 90.00, 107.70, 90.00
R / Rfree (%) 19.1 / 24.3

Other elements in 4doa:

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

Chlorine binding site 1 out of 5 in 4doa

Go back to Chlorine Binding Sites List in 4doa
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: Non-Interactive Binding of S-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: Non-Interactive Binding of S-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:32.4
occ:1.00
 O A:HOH551 3.0 23.7 1.0
N A:CYS267 3.2 23.2 1.0
N A:TYR266 3.4 20.7 1.0
C A:GLN264 3.5 17.8 1.0
CA A:GLN264 3.6 21.8 1.0
CG1 A:VAL313 3.6 24.9 1.0
CB A:TYR266 3.7 25.4 1.0
O A:GLN264 3.8 26.7 1.0
SG A:CYS267 3.8 24.2 1.0
CB A:VAL313 3.8 26.7 1.0
CA A:TYR266 3.9 23.6 1.0
O A:ASP263 3.9 29.1 1.0
CB A:CYS267 3.9 21.2 1.0
N A:TYR265 3.9 25.0 1.0
C A:TYR266 4.0 26.5 1.0
CA A:CYS267 4.2 16.7 1.0
CD2 A:TYR266 4.3 33.3 1.0
C A:TYR265 4.3 26.4 1.0
O A:VAL313 4.4 25.9 1.0
O A:TYR296 4.4 17.7 1.0
CB A:GLN264 4.5 18.9 1.0
CG A:TYR266 4.5 31.7 1.0
N A:GLN264 4.6 27.4 1.0
CG2 A:VAL313 4.6 21.8 1.0
C A:ASP263 4.6 29.5 1.0
CA A:TYR265 4.7 23.1 1.0
C A:VAL313 5.0 29.9 1.0

Chlorine binding site 2 out of 5 in 4doa

Go back to Chlorine Binding Sites List in 4doa
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: Non-Interactive Binding of S-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: Non-Interactive Binding of S-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:38.3
occ:1.00
 N A:HIS34 3.3 35.7 1.0
CB A:HIS34 3.4 38.9 1.0
C A:ALA32 3.5 35.4 1.0
N A:LYS35 3.5 28.7 1.0
CB A:ALA32 3.6 24.5 1.0
CA A:ALA32 3.6 36.3 1.0
CA A:HIS34 3.7 34.4 1.0
O A:ALA32 3.7 29.7 1.0
N A:ILE33 3.8 28.7 1.0
CD2 A:HIS34 3.9 47.0 1.0
CG A:HIS34 4.0 47.5 1.0
C A:HIS34 4.1 31.1 1.0
CG A:LYS35 4.2 29.8 1.0
C A:ILE33 4.4 34.7 1.0
CB A:LYS35 4.5 25.5 1.0
CA A:LYS35 4.6 25.1 1.0
O6 D:DG1 4.7 40.3 1.0
CA A:ILE33 4.7 40.6 1.0
O A:HOH719 4.8 36.7 1.0

Chlorine binding site 3 out of 5 in 4doa

Go back to Chlorine Binding Sites List in 4doa
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: Non-Interactive Binding of S-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: Non-Interactive Binding of S-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:44.4
occ:1.00
 NH2 A:ARG89 3.0 59.5 1.0
O A:HOH678 3.1 42.0 1.0
N A:LEU82 3.3 28.4 1.0
NH1 A:ARG89 3.4 47.8 1.0
CZ A:ARG89 3.7 54.8 1.0
CA A:LYS81 3.7 29.2 1.0
CB A:LYS81 3.8 49.2 1.0
C A:LYS81 4.0 39.1 1.0
CD1 A:LEU85 4.0 30.3 1.0
CB A:LEU85 4.1 32.2 1.0
CB A:LEU82 4.1 37.3 1.0
O A:LEU82 4.2 29.9 1.0
CA A:LEU82 4.2 33.1 1.0
CG A:LEU85 4.7 25.8 1.0
C A:LEU82 4.7 37.3 1.0
CE1 A:PHE76 4.7 32.5 1.0
OE2 A:GLU86 4.8 74.5 1.0
O A:GLY80 4.9 38.5 1.0
CD1 A:PHE76 4.9 28.0 1.0
NE A:ARG89 5.0 43.4 1.0

Chlorine binding site 4 out of 5 in 4doa

Go back to Chlorine Binding Sites List in 4doa
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: Non-Interactive Binding of S-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: Non-Interactive Binding of S-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:32.0
occ:1.00
 NH2 A:ARG299 3.1 19.3 0.6
OG1 A:THR297 3.2 24.7 1.0
ND2 A:ASN294 3.2 20.2 1.0
NE A:ARG299 3.5 22.6 0.6
CZ A:ARG299 3.6 26.1 0.6
CG2 A:THR297 3.8 25.3 1.0
CB A:TYR296 3.9 36.4 1.0
OD1 A:ASN294 3.9 25.2 1.0
CG A:ASN294 4.0 22.2 1.0
CZ A:ARG299 4.0 27.9 0.4
CD2 A:TYR296 4.1 20.8 1.0
CB A:THR297 4.1 26.2 1.0
NE A:ARG299 4.2 31.3 0.4
NH1 A:ARG299 4.2 33.7 0.4
NH2 A:ARG299 4.3 26.3 0.4
O T:HOH116 4.3 33.7 1.0
CG A:TYR296 4.4 23.8 1.0
CD A:ARG299 4.6 27.4 0.6
CD A:ARG299 4.6 27.1 0.4
O A:HOH510 4.8 22.0 1.0
NH1 A:ARG299 4.8 22.7 0.6
N A:THR297 4.8 22.2 1.0

Chlorine binding site 5 out of 5 in 4doa

Go back to Chlorine Binding Sites List in 4doa
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: Non-Interactive Binding of S-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: Non-Interactive Binding of S-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:38.0
occ:1.00
 N A:LYS331 3.2 25.6 1.0
CD A:PRO330 3.5 22.0 1.0
CB A:LYS331 3.5 25.3 1.0
CG A:LYS331 3.7 37.7 1.0
CB A:PRO330 3.8 22.9 1.0
N A:PRO330 3.8 28.0 1.0
CG A:PRO330 3.9 24.1 1.0
CB A:GLU329 3.9 33.3 1.0
CA A:LYS331 4.0 28.0 1.0
CD A:LYS331 4.1 52.2 1.0
C A:PRO330 4.1 24.7 1.0
CA A:PRO330 4.1 23.8 1.0
OE1 A:GLU329 4.2 41.5 1.0
C A:GLU329 4.3 23.9 1.0
O A:ARG182 4.5 21.6 1.0
CA A:GLU329 4.6 28.8 1.0
CE A:LYS331 4.7 50.1 1.0
CG A:GLU329 4.9 33.0 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 14:28:39 2025

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