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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

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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

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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

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