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

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate: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-Monochlororomethylene Triphosphate: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-Monochlororomethylene Triphosphate:Binding of S-Isomer, PDB code: 4doc 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) 21.22 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.688, 80.019, 55.716, 90.00, 107.68, 90.00
R / Rfree (%) 20 / 24.9

Other elements in 4doc:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate:Binding of S-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:Binding of S-Isomer (pdb code 4doc). 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:Binding of S-Isomer, PDB code: 4doc:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4doc

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

b:35.1
occ:1.00
 O A:HOH515 3.1 24.9 1.0
N A:CYS267 3.2 20.8 1.0
N A:TYR266 3.5 20.2 1.0
C A:GLN264 3.5 22.6 1.0
CA A:GLN264 3.6 21.0 1.0
CG1 A:VAL313 3.6 24.8 1.0
O A:HOH826 3.7 38.7 1.0
O A:GLN264 3.7 23.2 1.0
CB A:TYR266 3.7 23.5 1.0
SG A:CYS267 3.8 20.7 1.0
O A:ASP263 3.8 23.8 1.0
CB A:CYS267 3.9 19.4 1.0
CA A:TYR266 3.9 22.6 1.0
CB A:VAL313 3.9 29.3 1.0
N A:TYR265 4.0 20.8 1.0
C A:TYR266 4.0 22.4 1.0
CA A:CYS267 4.1 19.3 1.0
O A:TYR296 4.3 18.5 1.0
CD2 A:TYR266 4.3 28.5 1.0
C A:TYR265 4.4 23.2 1.0
CB A:GLN264 4.5 24.0 1.0
O A:VAL313 4.5 30.3 1.0
CG A:TYR266 4.5 27.9 1.0
N A:GLN264 4.5 21.2 1.0
C A:ASP263 4.6 26.2 1.0
CG2 A:VAL313 4.7 25.3 1.0
CA A:TYR265 4.8 23.8 1.0
CG A:GLN264 5.0 24.5 1.0

Chlorine binding site 2 out of 6 in 4doc

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

b:39.9
occ:1.00
 N A:HIS34 3.4 31.3 1.0
CB A:ALA32 3.5 28.1 1.0
CB A:HIS34 3.5 37.5 1.0
C A:ALA32 3.6 30.2 1.0
N A:LYS35 3.6 29.0 1.0
CA A:ALA32 3.6 30.3 1.0
CA A:HIS34 3.8 33.0 1.0
O A:ALA32 3.8 28.9 1.0
N A:ILE33 3.9 31.3 1.0
CD2 A:HIS34 4.0 41.6 1.0
CG A:LYS35 4.1 30.3 1.0
CG A:HIS34 4.1 41.5 1.0
C A:HIS34 4.1 30.9 1.0
C A:ILE33 4.4 29.0 1.0
CB A:LYS35 4.5 26.7 1.0
O A:HOH591 4.5 37.2 1.0
O6 D:DG1 4.6 42.1 1.0
CA A:LYS35 4.6 28.7 1.0
O A:HOH631 4.7 39.0 1.0
CA A:ILE33 4.8 34.8 1.0

Chlorine binding site 3 out of 6 in 4doc

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

b:46.8
occ:1.00
 O A:HOH729 2.8 33.7 1.0
NH2 A:ARG89 3.1 47.4 1.0
N A:LEU82 3.4 27.4 1.0
NH1 A:ARG89 3.6 38.2 1.0
OE2 A:GLU86 3.7 52.5 1.0
CZ A:ARG89 3.8 40.3 1.0
CA A:LYS81 3.9 30.0 1.0
CB A:LYS81 3.9 37.5 1.0
CD1 A:LEU85 3.9 28.4 1.0
CB A:LEU85 4.0 27.0 1.0
C A:LYS81 4.1 31.3 1.0
CB A:LEU82 4.2 31.9 1.0
O A:LEU82 4.2 30.1 1.0
CA A:LEU82 4.3 31.4 1.0
CG A:LEU85 4.6 25.9 1.0
C A:LEU82 4.7 29.0 1.0
CD A:GLU86 4.7 50.8 1.0
CE1 A:PHE76 4.9 32.3 1.0
OE1 A:GLU21 4.9 28.2 1.0
CD1 A:PHE76 5.0 27.4 1.0
O A:HOH574 5.0 29.2 1.0
O A:HOH765 5.0 34.5 1.0

Chlorine binding site 4 out of 6 in 4doc

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

b:34.7
occ:1.00
 O A:HOH702 2.9 35.5 1.0
NH2 A:ARG299 3.0 29.6 0.9
OG1 A:THR297 3.2 23.3 1.0
ND2 A:ASN294 3.4 22.4 1.0
NE A:ARG299 3.4 36.4 0.9
CZ A:ARG299 3.6 37.7 0.9
CG2 A:THR297 3.8 25.7 1.0
CB A:TYR296 3.9 26.6 1.0
OD1 A:ASN294 4.0 22.2 1.0
CB A:THR297 4.1 26.1 1.0
CD2 A:TYR296 4.1 21.7 1.0
CG A:ASN294 4.1 21.7 1.0
O A:HOH754 4.2 36.0 1.0
CG A:TYR296 4.4 22.1 1.0
O T:HOH123 4.5 43.4 1.0
CD A:ARG299 4.7 28.4 0.9
N A:THR297 4.7 23.0 1.0
O T:HOH126 4.8 46.3 1.0
O A:HOH529 4.8 21.4 1.0
NH1 A:ARG299 4.9 35.9 0.9
O T:HOH116 4.9 36.9 1.0

Chlorine binding site 5 out of 6 in 4doc

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

b:39.3
occ:1.00
 N A:LYS331 3.1 25.0 1.0
CB A:LYS331 3.5 28.6 1.0
CD A:PRO330 3.5 21.5 1.0
N A:PRO330 3.7 23.5 1.0
CB A:GLU329 3.8 30.2 1.0
CB A:PRO330 3.8 19.0 1.0
CA A:LYS331 3.8 26.8 1.0
CG A:PRO330 3.9 23.4 1.0
C A:PRO330 4.0 23.1 1.0
CA A:PRO330 4.1 22.7 1.0
C A:GLU329 4.2 24.6 1.0
OE1 A:GLU329 4.3 39.0 1.0
CA A:GLU329 4.5 26.5 1.0
O A:ARG182 4.5 18.3 1.0
CG A:LYS331 4.6 43.0 1.0
CG A:GLU329 4.7 35.7 1.0
O A:GLU329 4.9 22.1 1.0
CD A:GLU329 5.0 38.1 1.0

Chlorine binding site 6 out of 6 in 4doc

Go back to Chlorine Binding Sites List in 4doc
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:Binding of S-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:Binding of S-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:33.3
occ:1.00
 CL3B A:G1C410 0.0 33.3 1.0
C3B A:G1C410 1.8 22.5 1.0
PG A:G1C410 2.8 22.7 1.0
PB A:G1C410 2.8 17.1 1.0
O3A A:G1C410 2.9 16.4 1.0
O2G A:G1C410 3.0 30.9 1.0
O1G A:G1C410 3.4 19.2 1.0
O A:HOH660 3.5 37.6 1.0
O1B A:G1C410 3.5 19.2 1.0
O A:HOH523 3.5 21.6 1.0
O A:HOH796 3.6 27.9 1.0
O A:HOH503 3.7 18.1 1.0
O2A A:G1C410 3.9 19.5 1.0
PA A:G1C410 3.9 17.5 1.0
O A:HOH595 4.0 34.5 1.0
O2B A:G1C410 4.1 16.9 1.0
O3G A:G1C410 4.2 25.9 1.0
O A:HOH716 4.3 30.9 1.0
O A:HOH759 4.3 35.9 1.0
O1A A:G1C410 4.4 17.7 1.0
MG A:MG401 4.8 17.6 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 12:14:16 2024

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