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Magnesium in PDB 2q9z: Trichodiene Synthase: Complex with Inorganic Pyrophosphate Resulting From the Reaction with 2-Fluorofarnesyl Diphosphate

Enzymatic activity of Trichodiene Synthase: Complex with Inorganic Pyrophosphate Resulting From the Reaction with 2-Fluorofarnesyl Diphosphate

All present enzymatic activity of Trichodiene Synthase: Complex with Inorganic Pyrophosphate Resulting From the Reaction with 2-Fluorofarnesyl Diphosphate:
4.2.3.6;

Protein crystallography data

The structure of Trichodiene Synthase: Complex with Inorganic Pyrophosphate Resulting From the Reaction with 2-Fluorofarnesyl Diphosphate, PDB code: 2q9z was solved by L.S.Vedula, Y.Zhao, R.M.Coates, T.Koyama, D.E.Cane, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.95
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 122.191, 122.191, 150.969, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 25.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Trichodiene Synthase: Complex with Inorganic Pyrophosphate Resulting From the Reaction with 2-Fluorofarnesyl Diphosphate (pdb code 2q9z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Trichodiene Synthase: Complex with Inorganic Pyrophosphate Resulting From the Reaction with 2-Fluorofarnesyl Diphosphate, PDB code: 2q9z:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2q9z

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Magnesium binding site 1 out of 3 in the Trichodiene Synthase: Complex with Inorganic Pyrophosphate Resulting From the Reaction with 2-Fluorofarnesyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trichodiene Synthase: Complex with Inorganic Pyrophosphate Resulting From the Reaction with 2-Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:18.6
occ:1.00
 OE2 B:GLU233 2.0 0.8 1.0
OD1 B:ASN225 2.4 48.5 1.0
CD B:GLU233 2.7 0.0 1.0
O4 B:POP700 2.8 47.7 1.0
O B:POP700 2.9 47.2 1.0
OE1 B:GLU233 3.0 0.7 1.0
O1 B:POP700 3.0 45.1 1.0
OG B:SER229 3.0 86.7 1.0
P2 B:POP700 3.3 47.2 1.0
P1 B:POP700 3.5 45.2 1.0
CG B:ASN225 3.6 48.2 1.0
O6 B:POP700 3.6 50.0 1.0
NH2 B:ARG182 3.7 60.8 1.0
OD1 B:ASP226 3.9 86.6 1.0
O3 B:POP700 4.0 43.8 1.0
O B:ASN225 4.0 62.6 1.0
CG B:GLU233 4.1 1.0 1.0
CB B:SER229 4.1 88.3 1.0
ND2 B:ASN225 4.2 48.0 1.0
C B:ASN225 4.4 61.5 1.0
CA B:ASP226 4.4 72.4 1.0
CZ B:ARG182 4.5 58.9 1.0
N B:ASP226 4.6 72.3 1.0
CG B:ASP226 4.7 87.0 1.0
NH1 B:ARG182 4.7 57.7 1.0
O5 B:POP700 4.8 49.1 1.0
CB B:ASN225 4.8 47.2 1.0
MG B:MG702 4.8 25.8 1.0
O2 B:POP700 5.0 45.0 1.0

Magnesium binding site 2 out of 3 in 2q9z

Go back to Magnesium Binding Sites List in 2q9z
Magnesium binding site 2 out of 3 in the Trichodiene Synthase: Complex with Inorganic Pyrophosphate Resulting From the Reaction with 2-Fluorofarnesyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trichodiene Synthase: Complex with Inorganic Pyrophosphate Resulting From the Reaction with 2-Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:25.8
occ:1.00
 O2 B:POP700 2.4 45.0 1.0
OD2 B:ASP100 2.6 60.0 1.0
O1 B:POP700 2.6 45.1 1.0
P1 B:POP700 2.9 45.2 1.0
O5 B:POP700 2.9 49.1 1.0
OD1 B:ASP239 2.9 0.1 1.0
O4 B:POP700 3.2 47.7 1.0
P2 B:POP700 3.3 47.2 1.0
O B:POP700 3.5 47.2 1.0
CG B:ASP100 3.5 60.7 1.0
OD1 B:ASP100 3.5 62.0 1.0
MG B:MG703 3.8 42.0 1.0
CG B:ASP239 3.8 0.5 1.0
NH2 B:ARG304 4.0 90.5 1.0
NZ B:LYS232 4.1 58.6 1.0
OD1 B:ASP101 4.2 96.9 1.0
OD2 B:ASP239 4.3 0.9 1.0
O3 B:POP700 4.3 43.8 1.0
O6 B:POP700 4.8 50.0 1.0
MG B:MG701 4.8 18.6 1.0
O B:ASP100 4.9 66.8 1.0
CB B:ASP100 4.9 61.4 1.0
CD B:GLU233 4.9 0.0 1.0
CB B:ASP239 5.0 0.5 1.0
OE1 B:GLU233 5.0 0.7 1.0

Magnesium binding site 3 out of 3 in 2q9z

Go back to Magnesium Binding Sites List in 2q9z
Magnesium binding site 3 out of 3 in the Trichodiene Synthase: Complex with Inorganic Pyrophosphate Resulting From the Reaction with 2-Fluorofarnesyl Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Trichodiene Synthase: Complex with Inorganic Pyrophosphate Resulting From the Reaction with 2-Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:42.0
occ:1.00
 O2 B:POP700 2.4 45.0 1.0
OD1 B:ASP100 2.5 62.0 1.0
P1 B:POP700 3.2 45.2 1.0
OE1 B:GLU164 3.4 78.0 1.0
O1 B:POP700 3.4 45.1 1.0
O3 B:POP700 3.5 43.8 1.0
CG B:ASN185 3.6 95.2 1.0
OD1 B:ASN185 3.6 95.6 1.0
CG B:ASP100 3.6 60.7 1.0
MG B:MG702 3.8 25.8 1.0
OE2 B:GLU164 3.8 78.8 1.0
CB B:ASN185 3.8 94.1 1.0
O B:ASN185 4.0 84.3 1.0
CD B:GLU164 4.0 78.2 1.0
ND2 B:ASN185 4.1 96.6 1.0
OD2 B:ASP100 4.1 60.0 1.0
NH1 B:ARG182 4.4 57.7 1.0
C B:ASN185 4.7 84.1 1.0
O B:POP700 4.8 47.2 1.0
CB B:ASP100 4.9 61.4 1.0
CA B:ASN185 4.9 86.2 1.0

Reference:

L.S.Vedula, Y.Zhao, R.M.Coates, T.Koyama, D.E.Cane, D.W.Christianson. Exploring Biosynthetic Diversity with Trichodiene Synthase. Arch.Biochem.Biophys. V. 466 260 2007.
ISSN: ISSN 0003-9861
PubMed: 17678871
DOI: 10.1016/J.ABB.2007.06.016
Page generated: Wed Aug 14 02:41:09 2024

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