Atomistry » Magnesium » PDB 3p1g-3pio » 3p5p
Atomistry »
  Magnesium »
    PDB 3p1g-3pio »
      3p5p »

Magnesium in PDB 3p5p: Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 13-Aza-13,14-Dihydrocopalyl Diphosphate

Enzymatic activity of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 13-Aza-13,14-Dihydrocopalyl Diphosphate

All present enzymatic activity of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 13-Aza-13,14-Dihydrocopalyl Diphosphate:
4.2.3.17;

Protein crystallography data

The structure of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 13-Aza-13,14-Dihydrocopalyl Diphosphate, PDB code: 3p5p was solved by M.Koksal, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.09 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.464, 72.414, 206.931, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 13-Aza-13,14-Dihydrocopalyl Diphosphate (pdb code 3p5p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 13-Aza-13,14-Dihydrocopalyl Diphosphate, PDB code: 3p5p:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3p5p

Go back to Magnesium Binding Sites List in 3p5p
Magnesium binding site 1 out of 3 in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 13-Aza-13,14-Dihydrocopalyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 13-Aza-13,14-Dihydrocopalyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:22.4
occ:1.00
 O09 A:A3C911 2.1 18.1 1.0
OE2 A:GLU765 2.2 20.4 1.0
O06 A:A3C911 2.2 23.0 1.0
OD1 A:ASN757 2.2 14.6 1.0
O A:HOH1 2.3 19.0 1.0
OG1 A:THR761 2.3 17.2 1.0
CD A:GLU765 3.1 31.4 1.0
CG A:ASN757 3.2 21.7 1.0
P04 A:A3C911 3.2 23.3 1.0
P02 A:A3C911 3.3 23.0 1.0
CB A:THR761 3.3 18.9 1.0
OE1 A:GLU765 3.5 23.8 1.0
O03 A:A3C911 3.5 22.9 1.0
ND2 A:ASN757 3.6 20.7 1.0
O A:HOH8 4.0 28.2 1.0
CG2 A:THR761 4.0 23.7 1.0
O A:HOH3 4.0 27.1 1.0
O01 A:A3C911 4.0 25.4 1.0
O A:ASN757 4.1 16.7 1.0
O08 A:A3C911 4.1 26.8 1.0
O A:HOH6 4.2 40.2 1.0
O05 A:A3C911 4.2 26.7 1.0
NH1 A:ARG754 4.2 20.0 1.0
C A:ASN757 4.4 17.1 1.0
CG A:GLU765 4.4 22.4 1.0
O07 A:A3C911 4.4 22.4 1.0
CB A:ASN757 4.5 15.1 1.0
CA A:THR761 4.6 16.5 1.0
OD1 A:ASP758 4.6 16.8 1.0
C A:THR761 4.7 16.8 1.0
O A:THR761 4.8 21.8 1.0
N A:ASP758 4.8 13.4 1.0
CA A:ASP758 4.9 15.4 1.0

Magnesium binding site 2 out of 3 in 3p5p

Go back to Magnesium Binding Sites List in 3p5p
Magnesium binding site 2 out of 3 in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 13-Aza-13,14-Dihydrocopalyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 13-Aza-13,14-Dihydrocopalyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:34.8
occ:1.00
 O A:HOH2 2.4 29.6 1.0
O A:HOH10 2.4 34.3 1.0
O A:HOH4 2.4 35.1 1.0
O A:HOH6 2.6 40.2 1.0
O07 A:A3C911 2.6 22.4 1.0
O A:HOH936 2.6 56.5 1.0
P02 A:A3C911 3.6 23.0 1.0
O03 A:A3C911 3.6 22.9 1.0
OD1 A:ASP617 3.7 67.6 1.0
O A:HOH5 3.8 34.4 1.0
O A:HOH3 3.9 27.1 1.0
OD1 A:ASP613 3.9 31.1 1.0
OD2 A:ASP617 3.9 54.5 1.0
O06 A:A3C911 4.2 23.0 1.0
CG A:ASP617 4.2 60.2 1.0
NE2 A:GLN770 4.3 56.8 1.0
O A:HOH9 4.3 36.5 1.0
OD2 A:ASP613 4.3 32.4 1.0
OE1 A:GLN770 4.3 41.3 1.0
OE1 A:GLU691 4.5 38.6 1.0
CG A:ASP613 4.5 29.7 1.0
O A:HOH937 4.6 57.5 1.0
CD A:GLN770 4.7 50.1 1.0
O01 A:A3C911 4.9 25.4 1.0

Magnesium binding site 3 out of 3 in 3p5p

Go back to Magnesium Binding Sites List in 3p5p
Magnesium binding site 3 out of 3 in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 13-Aza-13,14-Dihydrocopalyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 13-Aza-13,14-Dihydrocopalyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:48.0
occ:1.00
 O A:HOH1366 2.6 34.1 1.0
O A:HOH887 2.6 49.3 1.0
O A:HOH1611 2.6 48.0 1.0
O A:HOH1254 2.7 29.1 1.0
O A:HOH1302 2.7 27.2 1.0
O A:HOH956 3.2 58.5 1.0
O A:HOH1174 4.4 37.0 1.0
O A:GLN172 4.5 21.9 1.0
O A:HOH995 4.6 21.4 1.0
OE1 A:GLN172 4.6 22.5 1.0
O A:HOH1157 4.7 36.3 1.0
OE1 A:GLN212 4.8 33.2 1.0
O A:LEU173 4.9 20.0 1.0
O A:HOH1337 4.9 32.9 1.0

Reference:

M.Koksal, Y.Jin, R.M.Coates, R.Croteau, D.W.Christianson. Taxadiene Synthase Structure and Evolution of Modular Architecture in Terpene Biosynthesis. Nature V. 469 116 2011.
ISSN: ISSN 0028-0836
PubMed: 21160477
DOI: 10.1038/NATURE09628
Page generated: Mon Dec 14 08:38:44 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