Atomistry » Chlorine » PDB 2ii4-2iws » 2iso
Atomistry »
  Chlorine »
    PDB 2ii4-2iws »
      2iso »

Chlorine in PDB 2iso: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Difluoromethylene Triphosphate

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Difluoromethylene Triphosphate

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Difluoromethylene Triphosphate:
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- Difluoromethylene Triphosphate, PDB code: 2iso was solved by C.A.Sucato, T.G.Upton, B.A.Kashemirov, V.Martinek, Y.Xiang, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.35 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.700, 80.500, 55.400, 90.00, 108.00, 90.00
R / Rfree (%) 20.1 / 26

Other elements in 2iso:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Difluoromethylene Triphosphate also contains other interesting chemical elements:

Fluorine (F) 2 atoms
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- Difluoromethylene Triphosphate (pdb code 2iso). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 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- Difluoromethylene Triphosphate, PDB code: 2iso:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2iso

Go back to Chlorine Binding Sites List in 2iso
Chlorine binding site 1 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Difluoromethylene Triphosphate


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- Difluoromethylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl343

b:35.4
occ:1.00
 O A:HOH367 3.0 29.5 1.0
N A:CYS267 3.3 20.5 1.0
CA A:GLN264 3.5 25.1 1.0
C A:GLN264 3.6 25.0 1.0
N A:TYR266 3.7 22.0 1.0
SG A:CYS267 3.7 19.5 1.0
O A:HOH502 3.7 32.4 1.0
CG1 A:VAL313 3.7 30.2 1.0
CB A:VAL313 3.8 30.3 1.0
O A:GLN264 3.8 25.7 1.0
CB A:CYS267 3.8 19.3 1.0
CB A:TYR266 3.8 26.4 1.0
O A:ASP263 3.8 25.9 1.0
N A:TYR265 4.0 23.6 1.0
CA A:TYR266 4.1 21.7 1.0
C A:TYR266 4.1 21.3 1.0
CA A:CYS267 4.1 19.1 1.0
O A:TYR296 4.2 22.8 1.0
CB A:GLN264 4.3 26.9 1.0
C A:TYR265 4.5 21.9 1.0
CD2 A:TYR266 4.5 30.6 1.0
CG2 A:VAL313 4.5 30.0 1.0
N A:GLN264 4.6 25.7 1.0
O A:VAL313 4.6 31.2 1.0
C A:ASP263 4.6 25.8 1.0
CG A:TYR266 4.7 28.4 1.0
CA A:TYR265 4.8 22.5 1.0
CG A:GLN264 4.8 29.3 1.0
C A:VAL313 5.0 31.4 1.0
CA A:VAL313 5.0 31.1 1.0

Chlorine binding site 2 out of 4 in 2iso

Go back to Chlorine Binding Sites List in 2iso
Chlorine binding site 2 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Difluoromethylene Triphosphate


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- Difluoromethylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl344

b:33.7
occ:1.00
 N A:HIS34 3.4 28.4 1.0
CB A:ALA32 3.4 25.3 1.0
CB A:HIS34 3.4 29.6 1.0
CA A:ALA32 3.5 27.7 1.0
C A:ALA32 3.5 27.4 1.0
N A:LYS35 3.6 26.2 1.0
O A:HOH560 3.8 52.0 1.0
O A:ALA32 3.8 25.6 1.0
CA A:HIS34 3.8 28.3 1.0
CD2 A:HIS34 3.9 32.8 1.0
N A:ILE33 3.9 27.1 1.0
CG A:HIS34 4.0 32.6 1.0
C A:HIS34 4.2 27.5 1.0
CG A:LYS35 4.2 28.7 1.0
C A:ILE33 4.4 28.6 1.0
O A:HOH376 4.5 32.5 1.0
CB A:LYS35 4.5 26.6 1.0
CA A:LYS35 4.6 25.7 1.0
CA A:ILE33 4.7 29.2 1.0
O6 D:DG1 4.9 31.2 1.0
N A:ALA32 5.0 26.5 1.0

Chlorine binding site 3 out of 4 in 2iso

Go back to Chlorine Binding Sites List in 2iso
Chlorine binding site 3 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Difluoromethylene Triphosphate


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- Difluoromethylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl345

b:48.7
occ:1.00
 N A:LEU82 3.2 28.7 1.0
O A:HOH589 3.4 39.3 1.0
NH2 A:ARG89 3.4 45.0 1.0
NH1 A:ARG89 3.5 45.2 1.0
CD1 A:LEU85 3.7 27.5 1.0
CA A:LYS81 3.8 30.5 1.0
CB A:LYS81 3.9 33.3 1.0
O A:LEU82 3.9 25.5 1.0
CZ A:ARG89 3.9 44.9 1.0
CB A:LEU85 3.9 29.6 1.0
C A:LYS81 3.9 29.7 1.0
OE2 A:GLU86 4.0 49.0 1.0
CB A:LEU82 4.1 28.2 1.0
CA A:LEU82 4.1 27.9 1.0
C A:LEU82 4.4 28.0 1.0
CG A:LEU85 4.5 28.9 1.0
CD A:GLU86 4.9 48.6 1.0
CG A:GLU86 4.9 45.0 1.0

Chlorine binding site 4 out of 4 in 2iso

Go back to Chlorine Binding Sites List in 2iso
Chlorine binding site 4 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Difluoromethylene Triphosphate


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- Difluoromethylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl346

b:32.5
occ:1.00
 NH2 A:ARG299 2.9 37.7 1.0
OG1 A:THR297 3.0 26.4 1.0
O A:HOH429 3.1 30.9 1.0
ND2 A:ASN294 3.1 23.4 1.0
NE A:ARG299 3.2 35.7 1.0
CZ A:ARG299 3.5 38.6 1.0
O A:HOH633 3.9 40.7 1.0
OD1 A:ASN294 3.9 24.4 1.0
CG A:ASN294 4.0 21.4 1.0
CB A:TYR296 4.0 23.3 1.0
CB A:THR297 4.2 25.2 1.0
CG2 A:THR297 4.2 25.0 1.0
CD2 A:TYR296 4.3 24.3 1.0
O A:HOH389 4.4 25.3 1.0
CD A:ARG299 4.4 31.7 1.0
N A:THR297 4.6 22.8 1.0
CG A:TYR296 4.6 23.0 1.0
NH1 A:ARG299 4.8 39.9 1.0
CA A:THR297 5.0 23.3 1.0

Reference:

C.A.Sucato, T.G.Upton, B.A.Kashemirov, V.K.Batra, V.Martinek, Y.Xiang, W.A.Beard, L.C.Pedersen, S.H.Wilson, C.E.Mckenna, J.Florian, A.Warshel, M.F.Goodman. Modifying the Beta,Gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of Dna Polymerase Beta. Biochemistry V. 46 461 2007.
ISSN: ISSN 0006-2960
PubMed: 17209556
DOI: 10.1021/BI061517B
Page generated: Sat Jul 20 08:21:47 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy