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Magnesium in PDB 3p5r: Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate

Enzymatic activity of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate

All present enzymatic activity of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl 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 2-Fluorogeranylgeranyl Diphosphate, PDB code: 3p5r 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) 43.41 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.050, 201.980, 81.431, 90.00, 91.60, 90.00
R / Rfree (%) 18.7 / 25

Other elements in 3p5r:

The structure of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate also contains other interesting chemical elements:

Fluorine (F) 2 atoms

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 2-Fluorogeranylgeranyl Diphosphate (pdb code 3p5r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate, PDB code: 3p5r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3p5r

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Magnesium binding site 1 out of 6 in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl 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 2-Fluorogeranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:13.9
occ:1.00
 OD1 A:ASN757 2.2 12.3 1.0
O08 A:FGG911 2.2 13.5 1.0
OE2 A:GLU765 2.3 10.5 1.0
O A:HOH1339 2.3 12.6 1.0
O06 A:FGG911 2.3 15.5 1.0
OG1 A:THR761 2.4 11.0 1.0
CD A:GLU765 3.1 11.1 1.0
OE1 A:GLU765 3.2 10.3 1.0
CG A:ASN757 3.3 12.5 1.0
P04 A:FGG911 3.4 13.7 1.0
P02 A:FGG911 3.4 16.8 1.0
O A:HOH1205 3.5 10.8 1.0
O03 A:FGG911 3.6 17.7 1.0
CB A:THR761 3.6 13.3 1.0
NH1 A:ARG754 3.8 10.5 1.0
ND2 A:ASN757 3.8 14.3 1.0
O09 A:FGG911 4.1 14.6 1.0
O A:ASN757 4.2 9.6 1.0
O A:HOH992 4.2 19.5 1.0
O07 A:FGG911 4.2 16.8 1.0
OD1 A:ASP758 4.4 11.1 1.0
C A:ASN757 4.4 9.3 1.0
CG2 A:THR761 4.4 14.5 1.0
CG A:GLU765 4.4 9.6 1.0
O05 A:FGG911 4.5 14.1 1.0
CB A:ASN757 4.6 10.6 1.0
O A:HOH1208 4.7 9.9 1.0
N A:ASP758 4.7 11.4 1.0
O01 A:FGG911 4.7 21.0 1.0
CA A:THR761 4.7 12.6 1.0
C A:THR761 4.7 11.7 1.0
CA A:ASP758 4.8 10.7 1.0
O A:THR761 4.8 12.0 1.0

Magnesium binding site 2 out of 6 in 3p5r

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Magnesium binding site 2 out of 6 in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl 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 2-Fluorogeranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:16.7
occ:1.00
 O A:HOH1204 2.3 18.9 1.0
OD1 A:ASP613 2.3 12.2 1.0
O A:HOH1196 2.4 11.8 1.0
OD2 A:ASP617 2.4 12.3 1.0
O09 A:FGG911 2.4 14.6 1.0
O A:HOH1203 2.6 13.4 1.0
CG A:ASP613 3.3 13.8 1.0
CG A:ASP617 3.3 12.2 1.0
OE1 A:GLU691 3.4 12.7 1.0
CB A:ASP617 3.5 11.9 1.0
P04 A:FGG911 3.5 13.7 1.0
O05 A:FGG911 3.5 14.1 1.0
OD2 A:ASP613 3.6 12.0 1.0
CE2 A:TYR688 4.0 9.0 1.0
OE2 A:GLU691 4.0 11.1 1.0
MG A:MG903 4.1 13.8 1.0
O A:HOH992 4.2 19.5 1.0
CD A:GLU691 4.2 11.8 1.0
O A:HOH1205 4.2 10.8 1.0
O A:ASP613 4.2 13.7 1.0
O08 A:FGG911 4.3 13.5 1.0
O A:HOH1209 4.4 14.1 1.0
OD1 A:ASP617 4.5 15.6 1.0
CB A:ASP613 4.5 12.6 1.0
O A:HOH1198 4.5 10.3 1.0
N A:ASP617 4.7 12.1 1.0
CD2 A:TYR688 4.7 8.3 1.0
CA A:ASP617 4.7 12.6 1.0
O03 A:FGG911 4.7 17.7 1.0
CZ A:TYR688 4.8 9.3 1.0
OH A:TYR688 4.8 8.9 1.0
CA A:ASP613 4.8 13.6 1.0
C A:ASP613 4.8 13.2 1.0
OE1 A:GLN770 5.0 12.8 1.0

Magnesium binding site 3 out of 6 in 3p5r

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Magnesium binding site 3 out of 6 in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl 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 2-Fluorogeranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:13.8
occ:1.00
 O A:HOH971 2.3 21.5 1.0
O07 A:FGG911 2.4 16.8 1.0
OD2 A:ASP617 2.4 12.3 1.0
OD2 A:ASP613 2.4 12.0 1.0
O A:HOH992 2.4 19.5 1.0
OD1 A:ASP617 2.9 15.6 1.0
CG A:ASP617 3.0 12.2 1.0
O09 A:FGG911 3.0 14.6 1.0
CG A:ASP613 3.5 13.8 1.0
O A:HOH1378 3.6 27.7 1.0
P02 A:FGG911 3.7 16.8 1.0
NH2 A:ARG768 3.7 10.8 1.0
O A:HOH1237 3.8 19.6 1.0
O A:HOH1263 4.0 18.6 1.0
OD1 A:ASP613 4.0 12.2 1.0
OD1 A:ASP614 4.1 12.4 1.0
MG A:MG902 4.1 16.7 1.0
O03 A:FGG911 4.1 17.7 1.0
P04 A:FGG911 4.2 13.7 1.0
NE2 A:GLN770 4.3 11.8 1.0
OE2 A:GLU765 4.3 10.5 1.0
CB A:ASP617 4.4 11.9 1.0
O A:ASP613 4.5 13.7 1.0
O06 A:FGG911 4.5 15.5 1.0
C A:ASP613 4.7 13.2 1.0
CB A:ASP613 4.7 12.6 1.0
O01 A:FGG911 4.7 21.0 1.0
N A:ASP614 4.8 10.9 1.0
CZ A:ARG768 4.9 10.5 1.0
CA A:ASP614 4.9 11.6 1.0
O08 A:FGG911 5.0 13.5 1.0
O A:HOH1196 5.0 11.8 1.0

Magnesium binding site 4 out of 6 in 3p5r

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Magnesium binding site 4 out of 6 in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:12.9
occ:1.00
 OE2 B:GLU765 2.2 9.3 1.0
OD1 B:ASN757 2.3 10.6 1.0
O08 B:FGG911 2.3 14.1 1.0
O B:HOH1415 2.3 12.4 1.0
O06 B:FGG911 2.3 14.9 1.0
OG1 B:THR761 2.5 10.3 1.0
CD B:GLU765 2.9 9.9 1.0
OE1 B:GLU765 2.9 10.1 1.0
CG B:ASN757 3.3 11.8 1.0
P04 B:FGG911 3.3 14.6 1.0
P02 B:FGG911 3.4 15.5 1.0
O B:HOH1261 3.5 10.6 1.0
O03 B:FGG911 3.6 16.1 1.0
ND2 B:ASN757 3.7 14.1 1.0
NH1 B:ARG754 3.7 9.9 1.0
CB B:THR761 3.7 11.8 1.0
O09 B:FGG911 3.8 15.7 1.0
O B:HOH993 4.0 11.6 1.0
O07 B:FGG911 4.1 15.4 1.0
O B:ASN757 4.3 9.8 1.0
CG B:GLU765 4.4 12.4 1.0
OD1 B:ASP758 4.4 10.4 1.0
CG2 B:THR761 4.5 12.1 1.0
C B:ASN757 4.5 10.5 1.0
O05 B:FGG911 4.6 14.6 1.0
CB B:ASN757 4.6 11.5 1.0
O B:THR761 4.7 12.8 1.0
O B:HOH1313 4.7 12.7 1.0
C B:THR761 4.7 12.8 1.0
N B:ASP758 4.7 10.2 1.0
O01 B:FGG911 4.7 20.3 1.0
CA B:THR761 4.8 11.9 1.0
CA B:ASP758 4.8 10.0 1.0
CZ B:ARG754 4.9 10.6 1.0

Magnesium binding site 5 out of 6 in 3p5r

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Magnesium binding site 5 out of 6 in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:12.3
occ:1.00
 OD1 B:ASP613 2.3 10.6 1.0
O B:HOH1255 2.4 10.8 1.0
O09 B:FGG911 2.4 15.7 1.0
O B:HOH1257 2.4 10.1 1.0
O B:HOH994 2.4 19.8 1.0
OD2 B:ASP617 2.5 10.5 1.0
O05 B:FGG911 3.2 14.6 1.0
P04 B:FGG911 3.3 14.6 1.0
CG B:ASP613 3.4 12.6 1.0
MG B:MG903 3.4 18.5 1.0
OE1 B:GLU691 3.5 13.4 1.0
CG B:ASP617 3.5 12.9 1.0
CB B:ASP617 3.8 14.5 1.0
OD2 B:ASP613 3.9 15.2 1.0
O B:HOH1261 4.0 10.6 1.0
CE2 B:TYR688 4.1 11.8 1.0
OE2 B:GLU691 4.2 10.9 1.0
O B:HOH993 4.2 11.6 1.0
O08 B:FGG911 4.3 14.1 1.0
CD B:GLU691 4.3 11.8 1.0
O B:HOH1258 4.3 10.2 1.0
O B:ASP613 4.4 11.9 1.0
O03 B:FGG911 4.5 16.1 1.0
CB B:ASP613 4.6 12.1 1.0
OD1 B:ASP617 4.7 13.8 1.0
OH B:TYR688 4.7 11.3 1.0
CZ B:TYR688 4.7 11.3 1.0
CA B:ASP613 4.8 11.3 1.0
CD2 B:TYR688 4.8 10.9 1.0
C B:ASP613 4.8 11.5 1.0
O B:HOH1037 4.9 14.5 1.0
NE2 B:GLN770 5.0 17.8 1.0

Magnesium binding site 6 out of 6 in 3p5r

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Magnesium binding site 6 out of 6 in the Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Taxadiene Synthase From Pacific Yew (Taxus Brevifolia) in Complex with MG2+ and 2-Fluorogeranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg903

b:18.5
occ:1.00
 O07 B:FGG911 2.2 15.4 1.0
O B:HOH972 2.3 13.2 1.0
OD2 B:ASP613 2.3 15.2 1.0
OD2 B:ASP617 2.3 10.5 1.0
O B:HOH993 2.4 11.6 1.0
O09 B:FGG911 2.4 15.7 1.0
CG B:ASP613 3.0 12.6 1.0
OD1 B:ASP613 3.2 10.6 1.0
CG B:ASP617 3.3 12.9 1.0
P02 B:FGG911 3.4 15.5 1.0
MG B:MG902 3.4 12.3 1.0
OD1 B:ASP617 3.5 13.8 1.0
P04 B:FGG911 3.5 14.6 1.0
O03 B:FGG911 3.6 16.1 1.0
O B:HOH1324 4.1 18.2 1.0
O B:HOH1289 4.1 15.5 1.0
OD1 B:ASP614 4.2 13.0 1.0
OE2 B:GLU765 4.3 9.3 1.0
O06 B:FGG911 4.3 14.9 1.0
NE2 B:GLN770 4.3 17.8 1.0
NH2 B:ARG768 4.4 23.0 1.0
CB B:ASP613 4.4 12.1 1.0
O05 B:FGG911 4.5 14.6 1.0
O01 B:FGG911 4.5 20.3 1.0
O08 B:FGG911 4.5 14.1 1.0
CB B:ASP617 4.6 14.5 1.0
O B:ASP613 4.6 11.9 1.0
C B:ASP613 4.7 11.5 1.0
O B:HOH1255 4.8 10.8 1.0
O B:HOH1278 4.9 12.2 1.0
N B:ASP614 4.9 11.8 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 08:38:47 2020

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