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Chlorine in PDB 4dob: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene 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-Monochlororomethylene 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-Monochlororomethylene 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-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer, PDB code: 4dob 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) 21.36 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.601, 80.403, 55.634, 90.00, 107.72, 90.00
R / Rfree (%) 20.5 / 26.3

Other elements in 4dob:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer 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-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer (pdb code 4dob). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 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-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer, PDB code: 4dob:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4dob

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Chlorine binding site 1 out of 6 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene 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-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:37.4
occ:1.00
 O A:HOH523 3.1 26.5 1.0
N A:CYS267 3.3 22.6 1.0
N A:TYR266 3.5 19.9 1.0
C A:GLN264 3.5 22.1 1.0
CA A:GLN264 3.5 22.4 1.0
O A:GLN264 3.7 24.8 1.0
CG1 A:VAL313 3.7 31.3 1.0
CB A:TYR266 3.8 27.3 1.0
O A:ASP263 3.8 32.1 1.0
SG A:CYS267 3.8 25.2 1.0
CB A:VAL313 3.9 32.4 1.0
CB A:CYS267 3.9 21.5 1.0
CA A:TYR266 3.9 22.9 1.0
N A:TYR265 4.1 24.7 1.0
C A:TYR266 4.1 22.9 1.0
CA A:CYS267 4.2 18.9 1.0
O A:TYR296 4.3 18.1 1.0
C A:TYR265 4.3 24.8 1.0
CD2 A:TYR266 4.4 33.9 1.0
CB A:GLN264 4.4 21.2 1.0
CG2 A:VAL313 4.5 24.4 1.0
CG A:TYR266 4.6 32.2 1.0
N A:GLN264 4.6 22.9 1.0
C A:ASP263 4.6 28.4 1.0
O A:VAL313 4.6 24.8 1.0
CA A:TYR265 4.8 23.0 1.0
CG A:GLN264 4.9 32.2 1.0

Chlorine binding site 2 out of 6 in 4dob

Go back to Chlorine Binding Sites List in 4dob
Chlorine binding site 2 out of 6 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene 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-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:42.0
occ:1.00
 N A:HIS34 3.4 31.8 1.0
CB A:ALA32 3.4 29.6 1.0
C A:ALA32 3.5 31.0 1.0
CB A:HIS34 3.5 38.3 1.0
CA A:ALA32 3.6 33.0 1.0
N A:LYS35 3.6 26.8 1.0
O A:ALA32 3.8 30.6 1.0
N A:ILE33 3.8 34.6 1.0
CA A:HIS34 3.9 31.3 1.0
CD2 A:HIS34 3.9 39.6 1.0
CG A:LYS35 4.0 37.4 1.0
CG A:HIS34 4.1 42.7 1.0
C A:HIS34 4.2 32.8 1.0
CD A:LYS35 4.4 39.0 1.0
C A:ILE33 4.4 33.8 1.0
CB A:LYS35 4.5 27.4 1.0
O6 D:DG1 4.7 43.9 1.0
CA A:ILE33 4.7 38.4 1.0
CA A:LYS35 4.7 28.6 1.0

Chlorine binding site 3 out of 6 in 4dob

Go back to Chlorine Binding Sites List in 4dob
Chlorine binding site 3 out of 6 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene 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-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:49.7
occ:1.00
 O A:HOH587 3.0 40.8 1.0
NH2 A:ARG89 3.1 49.0 1.0
N A:LEU82 3.3 29.5 1.0
NH1 A:ARG89 3.4 43.9 1.0
CZ A:ARG89 3.7 48.0 1.0
CA A:LYS81 3.7 32.3 1.0
CB A:LYS81 3.9 39.5 1.0
C A:LYS81 4.0 36.6 1.0
CB A:LEU82 4.1 32.7 1.0
CD1 A:LEU85 4.1 32.4 1.0
CB A:LEU85 4.2 26.4 1.0
O A:LEU82 4.2 29.7 1.0
CA A:LEU82 4.2 31.9 1.0
C A:LEU82 4.7 32.7 1.0
O A:GLY80 4.8 38.5 1.0
CG A:LEU85 4.8 30.1 1.0
CG A:LYS81 4.9 42.4 1.0
CE1 A:PHE76 5.0 31.5 1.0
O A:HOH601 5.0 29.0 1.0

Chlorine binding site 4 out of 6 in 4dob

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Chlorine binding site 4 out of 6 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene 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-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:36.9
occ:1.00
 OG1 A:THR297 3.1 25.2 1.0
ND2 A:ASN294 3.2 22.5 1.0
NE A:ARG299 3.7 39.0 0.9
NH2 A:ARG299 3.7 39.2 0.9
CG2 A:THR297 3.7 20.4 1.0
CB A:TYR296 3.9 29.1 1.0
OD1 A:ASN294 3.9 22.2 1.0
CG A:ASN294 4.0 24.1 1.0
CB A:THR297 4.0 26.0 1.0
CZ A:ARG299 4.1 43.3 0.9
CD2 A:TYR296 4.1 25.4 1.0
CG A:TYR296 4.5 29.7 1.0
O T:HOH106 4.6 33.6 1.0
N A:THR297 4.7 20.3 1.0
CD A:ARG299 4.8 38.4 0.9
O A:HOH527 4.8 22.9 1.0
CA A:THR297 5.0 25.4 1.0

Chlorine binding site 5 out of 6 in 4dob

Go back to Chlorine Binding Sites List in 4dob
Chlorine binding site 5 out of 6 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene 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-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:47.6
occ:1.00
 N A:LYS331 3.1 28.4 1.0
CG A:LYS331 3.4 35.0 1.0
CD A:PRO330 3.4 24.1 1.0
CD A:LYS331 3.4 46.8 1.0
CB A:LYS331 3.5 30.5 1.0
CB A:PRO330 3.6 24.9 1.0
N A:PRO330 3.7 27.5 1.0
CG A:PRO330 3.8 24.3 1.0
CB A:GLU329 3.8 37.2 1.0
CA A:LYS331 3.9 28.9 1.0
C A:PRO330 4.0 23.4 1.0
CA A:PRO330 4.0 26.5 1.0
C A:GLU329 4.2 24.4 1.0
OE1 A:GLU329 4.3 38.6 1.0
CE A:LYS331 4.3 47.2 1.0
O A:ARG182 4.5 20.8 1.0
CA A:GLU329 4.6 29.7 1.0
CG A:GLU329 4.8 39.0 1.0
O A:GLU329 4.9 25.0 1.0
CD A:GLU329 5.0 41.2 1.0

Chlorine binding site 6 out of 6 in 4dob

Go back to Chlorine Binding Sites List in 4dob
Chlorine binding site 6 out of 6 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene 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 6 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:34.2
occ:1.00
 CL1 A:GRC410 0.0 34.2 1.0
C3B A:GRC410 1.8 21.8 1.0
PG A:GRC410 2.9 25.3 1.0
O3G A:GRC410 3.0 22.4 1.0
PB A:GRC410 3.0 16.1 1.0
O1B A:GRC410 3.1 17.9 1.0
O A:HOH688 3.3 35.0 1.0
O A:HOH620 3.3 32.1 1.0
O2G A:GRC410 3.4 27.8 1.0
NH2 A:ARG183 3.5 19.1 1.0
O A:HOH509 3.9 21.4 1.0
O2B A:GRC410 3.9 15.1 1.0
CB A:SER180 4.0 20.4 1.0
O3A A:GRC410 4.0 16.7 1.0
O1G A:GRC410 4.1 21.8 1.0
OG A:SER180 4.3 21.9 1.0
CZ A:ARG183 4.5 18.3 1.0
NH1 A:ARG183 4.7 17.6 1.0
CA A:SER180 4.9 15.6 1.0
N A:SER180 4.9 17.4 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: Sun Jul 21 12:14:13 2024

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