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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: Thu Aug 15 09:08:47 2024

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