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Magnesium in PDB 3jpp: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl 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-Monomethyl Methylene Triphosphate, PDB code: 3jpp was solved by V.K.Batra, J.Upton, B.Kashmerov, W.A.Beard, S.H.Wilson, M.F.Goodman, C.E.Mckenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.42 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.700, 80.110, 55.550, 90.00, 107.95, 90.00
R / Rfree (%) 19.8 / 25

Other elements in 3jpp:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Sodium (Na) 4 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-Monomethyl Methylene Triphosphate (pdb code 3jpp). 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-Monomethyl Methylene Triphosphate, PDB code: 3jpp:

Magnesium binding site 1 out of 1 in 3jpp

Go back to Magnesium Binding Sites List in 3jpp
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-Monomethyl Methylene 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-Monomethyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg339

b:18.6
occ:1.00
 O1A A:G1M338 1.9 20.6 0.5
O2B A:G1M338 1.9 18.4 0.5
O1A A:G1M338 2.0 15.2 0.5
O2B A:G1M338 2.0 11.0 0.5
O1G A:G1M338 2.0 24.7 0.5
OD2 A:ASP192 2.1 17.7 1.0
OD1 A:ASP190 2.1 19.1 1.0
O1G A:G1M338 2.1 16.1 0.5
O A:HOH514 2.1 20.9 1.0
CG A:ASP190 3.1 20.1 1.0
PB A:G1M338 3.1 21.7 0.5
CG A:ASP192 3.1 17.0 1.0
PB A:G1M338 3.1 14.6 0.5
PG A:G1M338 3.1 27.3 0.5
PA A:G1M338 3.2 21.5 0.5
PG A:G1M338 3.2 19.4 0.5
PA A:G1M338 3.3 15.8 0.5
OD2 A:ASP190 3.4 19.5 1.0
O3A A:G1M338 3.5 21.0 0.5
OD1 A:ASP192 3.5 18.5 1.0
O3G A:G1M338 3.5 16.0 0.5
O3G A:G1M338 3.5 24.4 0.5
O3A A:G1M338 3.5 14.5 0.5
NA A:NA340 3.6 24.1 1.0
C3B A:G1M338 3.6 24.0 0.5
C3B A:G1M338 3.8 15.7 0.5
O A:HOH578 4.0 27.9 1.0
C5' A:G1M338 4.0 16.8 0.5
O5' A:G1M338 4.1 15.4 0.5
C5' A:G1M338 4.1 19.9 0.5
O5' A:G1M338 4.1 20.0 0.5
O A:ASP190 4.2 20.1 1.0
C A:ASP190 4.3 18.8 1.0
O A:HOH358 4.3 15.6 1.0
O2A A:G1M338 4.3 20.9 0.5
CB A:ASP190 4.4 16.8 1.0
N A:ASP190 4.4 17.1 1.0
CA A:GLY179 4.4 14.8 1.0
O2A A:G1M338 4.4 15.2 0.5
CB A:ASP192 4.4 18.1 1.0
O1B A:G1M338 4.4 21.6 0.5
O1B A:G1M338 4.5 14.8 0.5
O2G A:G1M338 4.5 28.3 0.5
N A:SER180 4.6 17.2 1.0
O2G A:G1M338 4.6 21.4 0.5
CA A:ASP190 4.6 18.9 1.0
O P:HOH273 4.7 35.2 1.0
C3B2 A:G1M338 4.7 11.0 0.5
C3B2 A:G1M338 4.8 23.7 0.5
N A:ASP192 4.8 19.2 1.0
N A:MET191 4.9 17.1 1.0
OG A:SER180 5.0 21.4 1.0

Reference:

V.K.Batra, L.C.Pedersen, W.A.Beard, S.H.Wilson, B.A.Kashemirov, T.G.Upton, M.F.Goodman, C.E.Mckenna. Halogenated Beta,Gamma-Methylene- and Ethylidene-Dgtp-Dna Ternary Complexes with Dna Polymerase Beta: Structural Evidence For Stereospecific Binding of the Fluoromethylene Analogues. J.Am.Chem.Soc. V. 132 7617 2010.
ISSN: ISSN 0002-7863
PubMed: 20465217
DOI: 10.1021/JA909370K
Page generated: Wed Aug 14 17:10:42 2024

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