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Sodium 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
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2iso

Go back to Sodium Binding Sites List in 2iso
Sodium binding site 1 out of 3 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 Sodium with other atoms in the Na 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:Na340

b:22.8
occ:1.00
OD2 A:ASP190 2.2 20.3 1.0
OD1 A:ASP192 2.2 21.4 1.0
OD2 A:ASP256 2.6 25.4 1.0
O1A A:GFF338 2.6 15.2 1.0
O P:HOH427 2.7 45.4 1.0
CG A:ASP190 2.9 17.3 1.0
OD1 A:ASP190 3.1 15.8 1.0
CG A:ASP192 3.2 17.3 1.0
MG A:MG339 3.3 13.5 1.0
OD2 A:ASP192 3.4 13.4 1.0
C3' P:DOC10 3.5 33.6 1.0
P1 A:GFF338 3.5 20.4 1.0
O5' A:GFF338 3.7 18.1 1.0
CG A:ASP256 3.7 20.9 1.0
O2A A:GFF338 4.0 17.6 1.0
C5' A:GFF338 4.0 19.9 1.0
O P:HOH377 4.2 37.8 1.0
CB A:ASP256 4.2 21.0 1.0
CB A:ASP190 4.3 16.6 1.0
C4' P:DOC10 4.5 31.0 1.0
C5' P:DOC10 4.5 30.6 1.0
CB A:ASP192 4.5 18.8 1.0
C2' P:DOC10 4.5 32.1 1.0
O A:MET191 4.6 16.5 1.0
O1G A:GFF338 4.6 21.9 1.0
O5' P:DOC10 4.6 29.5 1.0
OD1 A:ASP256 4.7 22.8 1.0
OP1 P:DOC10 4.7 23.2 1.0
NH2 A:ARG254 4.8 16.1 1.0
O A:HOH531 4.8 26.5 1.0
O3A A:GFF338 4.9 18.1 1.0
O2B A:GFF338 4.9 15.5 1.0

Sodium binding site 2 out of 3 in 2iso

Go back to Sodium Binding Sites List in 2iso
Sodium binding site 2 out of 3 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 Sodium with other atoms in the Na 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:Na341

b:26.5
occ:1.00
O A:THR101 2.2 22.8 1.0
O P:HOH27 2.5 30.8 1.0
O A:ILE106 2.5 20.5 1.0
OP1 P:DG9 2.5 20.0 1.0
O A:VAL103 2.6 19.9 1.0
O A:HOH436 2.7 32.4 1.0
C A:THR101 3.3 22.4 1.0
P P:DG9 3.5 22.6 1.0
C A:VAL103 3.5 19.7 1.0
C A:ILE106 3.5 19.1 1.0
OP2 P:DG9 3.6 21.5 1.0
N A:ILE106 3.8 18.9 1.0
O A:HOH534 3.8 32.3 1.0
CA A:THR101 3.9 23.6 1.0
N A:GLY105 4.0 17.5 1.0
CA A:SER104 4.1 20.1 1.0
N A:VAL103 4.1 22.0 1.0
N A:SER104 4.1 19.8 1.0
CA A:ILE106 4.1 18.9 1.0
C A:ARG102 4.2 21.7 1.0
N A:ARG102 4.3 21.2 1.0
C A:SER104 4.4 19.2 1.0
CA A:VAL103 4.5 19.5 1.0
O3' P:DC8 4.5 21.2 1.0
CB A:THR101 4.5 22.3 1.0
N A:GLY107 4.5 19.6 1.0
CB A:ILE106 4.5 18.8 1.0
CA A:ARG102 4.5 22.7 1.0
O A:ARG102 4.7 22.4 1.0
O5' P:DG9 4.7 24.1 1.0
C A:GLY105 4.7 21.2 1.0
O A:HOH533 4.7 31.8 1.0
CA A:GLY107 4.8 20.8 1.0
O A:LEU100 4.9 23.4 1.0
CA A:GLY105 4.9 21.2 1.0

Sodium binding site 3 out of 3 in 2iso

Go back to Sodium Binding Sites List in 2iso
Sodium binding site 3 out of 3 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 Sodium with other atoms in the Na 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:Na342

b:35.8
occ:1.00
O A:LYS60 2.2 33.7 1.0
O A:LEU62 2.5 34.3 1.0
O D:HOH364 2.5 39.1 1.0
O A:VAL65 2.6 29.5 1.0
O A:HOH467 2.6 35.6 1.0
OP1 D:DC3 2.8 33.6 1.0
C A:LYS60 3.3 33.5 1.0
C A:LEU62 3.4 33.6 1.0
C A:VAL65 3.7 29.3 1.0
P D:DC3 3.9 34.2 1.0
C A:LYS61 4.0 35.1 1.0
OP2 D:DC3 4.1 32.7 1.0
N A:VAL65 4.1 29.1 1.0
O A:LYS61 4.1 36.5 1.0
CA A:LYS60 4.1 31.7 1.0
CG A:LYS60 4.1 34.2 1.0
CA A:PRO63 4.1 34.0 1.0
N A:PRO63 4.1 34.5 1.0
N A:LEU62 4.2 34.2 1.0
CA A:VAL65 4.3 28.7 1.0
N A:LYS61 4.3 33.8 1.0
N A:GLY64 4.4 31.7 1.0
CA A:LEU62 4.4 33.3 1.0
CB A:VAL65 4.5 27.4 1.0
CA A:LYS61 4.5 35.7 1.0
C A:PRO63 4.7 33.3 1.0
CB A:LYS60 4.7 32.4 1.0
N A:GLY66 4.7 29.6 1.0
NZ A:LYS60 4.8 39.6 1.0
O A:ALA59 4.9 25.1 1.0
O3' D:DT2 5.0 34.8 1.0
CA A:GLY66 5.0 29.5 1.0
O5' D:DC3 5.0 37.6 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: Tue Dec 15 05:51:14 2020

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