Atomistry » Chlorine » PDB 4dhn-4dph » 4doc
Atomistry »
  Chlorine »
    PDB 4dhn-4dph »
      4doc »

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

Go back to Chlorine Binding Sites List in 4doc
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

Go back to Chlorine Binding Sites List in 4doc
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

Go back to Chlorine Binding Sites List in 4doc
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy