Atomistry » Chlorine » PDB 2ii3-2iwk » 2iso
Atomistry »
  Chlorine »
    PDB 2ii3-2iwk »
      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 Dec 12 09:09:08 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy