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

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene 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- Methylene Triphosphate, PDB code: 2isp 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) 22.36 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.700, 80.400, 55.500, 90.00, 107.90, 90.00
R / Rfree (%) 20.1 / 26.1

Other elements in 2isp:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate 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- Methylene Triphosphate (pdb code 2isp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 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- Methylene Triphosphate, PDB code: 2isp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 2isp

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Chlorine binding site 1 out of 5 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene 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- Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl343

b:41.8
occ:1.00
 O A:HOH357 3.0 26.6 1.0
N A:CYS267 3.3 18.5 1.0
O A:HOH570 3.4 31.2 1.0
CA A:GLN264 3.5 24.2 1.0
C A:GLN264 3.6 23.6 1.0
SG A:CYS267 3.7 19.8 1.0
CB A:CYS267 3.7 19.5 1.0
N A:TYR266 3.8 20.6 1.0
O A:GLN264 3.9 24.4 1.0
CG1 A:VAL313 3.9 22.6 1.0
CB A:VAL313 3.9 25.2 1.0
CB A:TYR266 3.9 22.6 1.0
O A:ASP263 4.0 26.3 1.0
N A:TYR265 4.0 23.3 1.0
CA A:CYS267 4.1 18.4 1.0
CA A:TYR266 4.1 21.1 1.0
C A:TYR266 4.2 20.0 1.0
O A:TYR296 4.3 21.9 1.0
CB A:GLN264 4.3 25.2 1.0
CD2 A:TYR266 4.5 28.6 1.0
C A:TYR265 4.5 22.0 1.0
N A:GLN264 4.6 24.9 1.0
O A:VAL313 4.6 26.8 1.0
CG2 A:VAL313 4.7 25.4 1.0
CG A:TYR266 4.7 26.6 1.0
C A:ASP263 4.7 25.5 1.0
CG A:GLN264 4.8 24.9 1.0
CA A:TYR265 4.9 21.6 1.0

Chlorine binding site 2 out of 5 in 2isp

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Chlorine binding site 2 out of 5 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene 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- Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl344

b:42.8
occ:1.00
 CB A:ALA32 3.3 28.3 1.0
N A:HIS34 3.3 27.3 1.0
N A:LYS35 3.4 24.9 1.0
C A:ALA32 3.4 30.6 1.0
CB A:HIS34 3.4 27.8 1.0
CA A:ALA32 3.5 30.2 1.0
O A:ALA32 3.6 31.0 1.0
CA A:HIS34 3.7 27.3 1.0
N A:ILE33 3.9 30.1 1.0
CG A:LYS35 3.9 26.7 1.0
C A:HIS34 4.0 27.2 1.0
CG A:HIS34 4.1 31.5 1.0
CD2 A:HIS34 4.1 31.4 1.0
CB A:LYS35 4.3 25.5 1.0
C A:ILE33 4.3 29.8 1.0
CA A:LYS35 4.4 24.1 1.0
O A:HOH471 4.6 34.2 1.0
CA A:ILE33 4.7 31.0 1.0
O6 D:DG1 4.8 33.8 1.0
CD A:LYS35 4.9 28.2 1.0
N A:ALA32 4.9 30.0 1.0
CG2 A:ILE33 5.0 32.5 1.0

Chlorine binding site 3 out of 5 in 2isp

Go back to Chlorine Binding Sites List in 2isp
Chlorine binding site 3 out of 5 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene 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- Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl345

b:49.9
occ:1.00
 N A:LEU82 3.3 31.4 1.0
NH2 A:ARG89 3.4 46.4 1.0
O A:HOH539 3.6 35.0 1.0
NH1 A:ARG89 3.7 43.4 1.0
CA A:LYS81 3.7 34.2 1.0
OE2 A:GLU86 3.9 50.0 1.0
CD1 A:LEU85 3.9 32.2 1.0
C A:LYS81 4.0 33.1 1.0
CB A:LYS81 4.0 36.4 1.0
CZ A:ARG89 4.1 43.6 1.0
O A:LEU82 4.1 31.8 1.0
CB A:LEU85 4.2 32.1 1.0
CB A:LEU82 4.2 30.9 1.0
CA A:LEU82 4.2 32.2 1.0
C A:LEU82 4.6 32.9 1.0
CG A:LEU85 4.7 32.0 1.0
O A:GLY80 4.8 36.8 1.0
CD A:GLU86 4.9 50.3 1.0
CE1 A:PHE76 5.0 26.4 1.0
N A:LYS81 5.0 34.4 1.0

Chlorine binding site 4 out of 5 in 2isp

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Chlorine binding site 4 out of 5 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene 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- Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl346

b:34.6
occ:1.00
 NH2 A:ARG299 2.7 24.4 0.5
ND2 A:ASN294 3.1 20.5 1.0
OG1 A:THR297 3.1 23.1 1.0
CZ A:ARG299 3.3 25.7 0.5
NH1 A:ARG299 3.5 33.5 0.5
NE A:ARG299 3.5 25.7 0.5
CZ A:ARG299 3.6 32.0 0.5
NH2 A:ARG299 4.0 31.4 0.5
CG A:ASN294 4.0 20.8 1.0
OD1 A:ASN294 4.0 20.9 1.0
CB A:TYR296 4.1 22.8 1.0
NE A:ARG299 4.1 31.1 0.5
CD2 A:TYR296 4.2 23.6 1.0
CB A:THR297 4.3 23.4 1.0
CG2 A:THR297 4.3 24.2 1.0
NH1 A:ARG299 4.4 24.6 0.5
O A:HOH449 4.4 22.2 1.0
CD A:ARG299 4.6 31.2 0.5
CG A:TYR296 4.6 23.3 1.0
N A:THR297 4.7 21.6 1.0
CD A:ARG299 4.7 27.7 0.5
O T:HOH270 4.8 43.0 1.0

Chlorine binding site 5 out of 5 in 2isp

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Chlorine binding site 5 out of 5 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Methylene Triphosphate


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- Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl347

b:45.9
occ:1.00
 N A:LYS331 3.2 24.1 1.0
CD A:PRO330 3.4 22.2 1.0
CG A:LYS331 3.5 30.7 1.0
CB A:LYS331 3.5 28.0 1.0
N A:PRO330 3.6 23.3 1.0
CD A:LYS331 3.7 34.2 1.0
CB A:PRO330 3.7 21.0 1.0
CB A:GLU329 3.7 28.7 1.0
CA A:LYS331 3.9 26.2 1.0
CG A:PRO330 4.0 21.1 1.0
CA A:PRO330 4.0 22.6 1.0
C A:PRO330 4.1 24.1 1.0
OE1 A:GLU329 4.1 36.9 1.0
C A:GLU329 4.1 24.4 1.0
CA A:GLU329 4.5 25.5 1.0
CE A:LYS331 4.6 35.6 1.0
CG A:GLU329 4.7 32.0 1.0
O A:ARG182 4.7 17.9 1.0
O A:GLU329 4.8 24.6 1.0
CD A:GLU329 4.9 35.0 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 08:22:11 2024

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