Atomistry » Magnesium » PDB 3jay-3jwr » 3jpr
Atomistry »
  Magnesium »
    PDB 3jay-3jwr »
      3jpr »

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

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Dimethyl 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-Dimethyl Methylene Triphosphate, PDB code: 3jpr 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) 25.46 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.630, 80.100, 55.330, 90.00, 108.07, 90.00
R / Rfree (%) 20.1 / 25.3

Other elements in 3jpr:

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

Chlorine (Cl) 3 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-Dimethyl Methylene Triphosphate (pdb code 3jpr). 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-Dimethyl Methylene Triphosphate, PDB code: 3jpr:

Magnesium binding site 1 out of 1 in 3jpr

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

b:16.5
occ:1.00
O1A A:G2M338 1.9 11.8 1.0
OD1 A:ASP190 1.9 22.4 1.0
OD2 A:ASP192 2.0 18.3 1.0
O1G A:G2M338 2.1 19.9 1.0
O A:HOH506 2.1 30.3 1.0
O2B A:G2M338 2.1 16.4 1.0
CG A:ASP192 2.9 20.0 1.0
CG A:ASP190 3.0 22.3 1.0
PA A:G2M338 3.2 19.7 1.0
PB A:G2M338 3.2 18.1 1.0
OD1 A:ASP192 3.2 24.0 1.0
PG A:G2M338 3.3 23.6 1.0
NA A:NA340 3.3 21.4 1.0
OD2 A:ASP190 3.5 26.6 1.0
O3A A:G2M338 3.5 18.2 1.0
O3G A:G2M338 3.7 19.2 1.0
C3B A:G2M338 3.8 20.0 1.0
O A:ASP190 4.0 22.4 1.0
O A:HOH513 4.0 21.0 1.0
O5' A:G2M338 4.1 19.1 1.0
C5' A:G2M338 4.1 19.4 1.0
C A:ASP190 4.2 20.6 1.0
CB A:ASP190 4.3 20.9 1.0
CB A:ASP192 4.3 21.5 1.0
N A:ASP190 4.3 20.5 1.0
O2A A:G2M338 4.3 20.0 1.0
O A:HOH351 4.4 18.7 1.0
CA A:ASP190 4.5 19.6 1.0
C3B2 A:G2M338 4.5 19.6 1.0
CA A:GLY179 4.5 21.4 1.0
O P:HOH328 4.6 32.8 1.0
O1B A:G2M338 4.6 20.7 1.0
O2G A:G2M338 4.6 25.4 1.0
N A:ASP192 4.8 19.9 1.0
N A:SER180 4.8 21.5 1.0
N A:MET191 4.8 19.8 1.0
C A:MET191 5.0 20.8 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: Mon Dec 14 08:20:12 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy