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Magnesium 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
Chlorine (Cl) 4 atoms
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was 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:

Magnesium binding site 1 out of 1 in 2iso

Go back to Magnesium Binding Sites List in 2iso
Magnesium binding site 1 out of 1 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 Magnesium with other atoms in the Mg 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:Mg339

b:13.5
occ:1.00
 O1A A:GFF338 1.8 15.2 1.0
OD1 A:ASP190 1.9 15.8 1.0
O1G A:GFF338 2.0 21.9 1.0
O A:HOH347 2.0 24.8 1.0
O2B A:GFF338 2.1 15.5 1.0
OD2 A:ASP192 2.1 13.4 1.0
CG A:ASP190 2.8 17.3 1.0
OD2 A:ASP190 3.1 20.3 1.0
P2 A:GFF338 3.1 17.9 1.0
CG A:ASP192 3.1 17.3 1.0
P1 A:GFF338 3.1 20.4 1.0
P3 A:GFF338 3.3 26.0 1.0
NA A:NA340 3.3 22.8 1.0
O3A A:GFF338 3.5 18.1 1.0
OD1 A:ASP192 3.5 21.4 1.0
O3G A:GFF338 3.8 22.8 1.0
C3B A:GFF338 3.8 21.7 1.0
O5' A:GFF338 4.0 18.1 1.0
C5' A:GFF338 4.1 19.9 1.0
O A:ASP190 4.1 19.7 1.0
CB A:ASP190 4.1 16.6 1.0
C A:ASP190 4.2 19.1 1.0
N A:ASP190 4.2 17.0 1.0
O2A A:GFF338 4.2 17.6 1.0
O A:HOH531 4.3 26.5 1.0
O A:HOH352 4.4 15.1 1.0
CA A:ASP190 4.4 17.0 1.0
CB A:ASP192 4.4 18.8 1.0
O1B A:GFF338 4.5 18.5 1.0
O2G A:GFF338 4.6 27.4 1.0
F2B A:GFF338 4.6 20.9 1.0
CA A:GLY179 4.7 16.1 1.0
O P:HOH427 4.8 45.4 1.0
N A:MET191 4.8 17.0 1.0
F1B A:GFF338 4.8 21.0 1.0
N A:SER180 4.9 17.4 1.0
N A:ASP192 4.9 18.0 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: Wed Aug 14 00:16:01 2024

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