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Magnesium in PDB 3g4f: Crystal Structure of (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl Diphosphate

Enzymatic activity of Crystal Structure of (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl Diphosphate

All present enzymatic activity of Crystal Structure of (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl Diphosphate:
4.2.3.13;

Protein crystallography data

The structure of Crystal Structure of (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl Diphosphate, PDB code: 3g4f was solved by H.A.Gennadios, L.Di Costanzo, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.70 / 2.65
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 158.195, 158.195, 158.195, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 25.6

Other elements in 3g4f:

The structure of Crystal Structure of (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl 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 (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl Diphosphate (pdb code 3g4f). 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 (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl Diphosphate, PDB code: 3g4f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3g4f

Go back to Magnesium Binding Sites List in 3g4f
Magnesium binding site 1 out of 6 in the Crystal Structure of (+)- -Cadinene Synthase From Gossypium Arboreum in Complex 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 Crystal Structure of (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:46.5
occ:1.00
O1A A:FPF801 2.3 73.0 1.0
OD2 A:ASP311 2.4 55.8 1.0
MG A:MG605 2.5 49.8 1.0
OD1 A:ASP307 2.5 65.5 1.0
O A:HOH635 2.5 45.5 1.0
OD2 A:ASP307 2.6 54.3 1.0
O1B A:FPF801 2.7 72.9 1.0
O3B A:FPF801 2.8 78.0 1.0
CG A:ASP307 2.9 51.4 1.0
P2 A:FPF801 2.9 87.3 1.0
O3A A:FPF801 3.2 77.0 1.0
P1 A:FPF801 3.2 87.2 1.0
CG A:ASP311 3.6 66.0 1.0
O A:HOH642 3.9 70.7 1.0
O2A A:FPF801 4.3 73.4 1.0
O1 A:FPF801 4.3 79.5 1.0
OD1 A:ASP311 4.4 66.4 1.0
CB A:ASP307 4.4 45.5 1.0
O2B A:FPF801 4.6 82.6 1.0
CB A:ASP311 4.6 63.2 1.0
O A:ASP307 4.9 52.0 1.0

Magnesium binding site 2 out of 6 in 3g4f

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Magnesium binding site 2 out of 6 in the Crystal Structure of (+)- -Cadinene Synthase From Gossypium Arboreum in Complex 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 Crystal Structure of (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:49.8
occ:1.00
O1B A:FPF801 2.2 72.9 1.0
MG A:MG604 2.5 46.5 1.0
OD2 A:ASP307 2.5 54.3 1.0
OD2 A:ASP311 2.7 55.8 1.0
OE1 A:GLU385 3.4 63.5 1.0
O A:HOH600 3.4 53.1 1.0
CG A:ASP311 3.5 66.0 1.0
OE2 A:GLU385 3.5 80.6 1.0
P2 A:FPF801 3.6 87.3 1.0
OD1 A:ASP311 3.6 66.4 1.0
CG A:ASP307 3.6 51.4 1.0
CD A:GLU385 3.7 69.6 1.0
O3B A:FPF801 3.8 78.0 1.0
OD1 A:ASP307 4.0 65.5 1.0
CE1 A:TYR382 4.4 42.5 1.0
CD1 A:TYR382 4.4 43.4 1.0
O3A A:FPF801 4.5 77.0 1.0
O A:HOH635 4.6 45.5 1.0
O1A A:FPF801 4.6 73.0 1.0
O2B A:FPF801 4.7 82.6 1.0
O A:ASP307 4.8 52.0 1.0
CB A:ASP307 4.9 45.5 1.0
CG A:GLU385 4.9 53.1 1.0
CB A:ASP311 5.0 63.2 1.0
CZ A:TYR382 5.0 39.8 1.0

Magnesium binding site 3 out of 6 in 3g4f

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Magnesium binding site 3 out of 6 in the Crystal Structure of (+)- -Cadinene Synthase From Gossypium Arboreum in Complex 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 Crystal Structure of (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg606

b:69.0
occ:1.00
O1 A:FPF801 2.5 79.5 1.0
O3B A:FPF801 2.5 78.0 1.0
F A:FPF801 2.7 80.4 1.0
OD1 A:ASP451 2.8 80.9 1.0
OE1 A:GLU455 2.9 90.2 1.0
OE2 A:GLU455 2.9 80.3 1.0
O2B A:FPF801 3.0 82.6 1.0
CD A:GLU455 3.0 85.2 1.0
P2 A:FPF801 3.2 87.3 1.0
C1 A:FPF801 3.2 79.3 0.2
C2 A:FPF801 3.4 77.2 1.0
CG A:ASP451 3.6 76.3 1.0
P1 A:FPF801 3.6 87.2 1.0
O3A A:FPF801 3.7 77.0 1.0
OD2 A:ASP451 3.7 74.2 1.0
O1A A:FPF801 4.1 73.0 1.0
CG A:GLU455 4.2 80.0 1.0
NH1 A:ARG448 4.3 70.6 1.0
C3 A:FPF801 4.7 82.9 1.0
O1B A:FPF801 4.7 72.9 1.0
O2A A:FPF801 4.8 73.4 1.0
O A:ASP451 4.9 75.5 1.0
NH2 A:ARG448 5.0 74.8 1.0

Magnesium binding site 4 out of 6 in 3g4f

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Magnesium binding site 4 out of 6 in the Crystal Structure of (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl 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 (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:56.6
occ:1.00
O1A B:FPF802 2.5 97.0 1.0
OD1 B:ASP307 2.5 78.2 1.0
MG B:MG602 2.6 58.1 1.0
OD2 B:ASP311 2.7 81.8 1.0
O B:HOH588 2.8 84.3 1.0
O3B B:FPF802 2.9 96.5 1.0
O3A B:FPF802 2.9 93.2 1.0
OD2 B:ASP307 2.9 69.2 1.0
CG B:ASP307 3.1 72.7 1.0
P1 B:FPF802 3.1 99.3 1.0
P2 B:FPF802 3.2 94.4 1.0
O1B B:FPF802 3.4 79.8 1.0
CG B:ASP311 3.8 83.4 1.0
O2A B:FPF802 3.8 99.4 1.0
OD1 B:ASP311 4.2 80.5 1.0
O B:ASP307 4.4 74.8 1.0
O1 B:FPF802 4.5 87.4 1.0
CB B:ASP307 4.6 70.1 1.0
O2B B:FPF802 4.8 79.2 1.0

Magnesium binding site 5 out of 6 in 3g4f

Go back to Magnesium Binding Sites List in 3g4f
Magnesium binding site 5 out of 6 in the Crystal Structure of (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl 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 (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:58.1
occ:1.00
OD2 B:ASP307 2.4 69.2 1.0
O1B B:FPF802 2.5 79.8 1.0
MG B:MG601 2.6 56.6 1.0
OE1 B:GLU385 2.9 82.8 1.0
CG B:ASP307 3.4 72.7 1.0
O3B B:FPF802 3.5 96.5 1.0
P2 B:FPF802 3.5 94.4 1.0
OD2 B:ASP311 3.6 81.8 1.0
OD1 B:ASP311 3.7 80.5 1.0
OD1 B:ASP307 3.8 78.2 1.0
CD B:GLU385 3.9 82.1 1.0
CG B:ASP311 4.1 83.4 1.0
O3A B:FPF802 4.2 93.2 1.0
CE1 B:TYR382 4.2 56.3 1.0
CD1 B:TYR382 4.3 58.1 1.0
OE2 B:GLU385 4.4 85.6 1.0
O B:ASP307 4.5 74.8 1.0
O1A B:FPF802 4.7 97.0 1.0
CB B:ASP307 4.8 70.1 1.0
O2B B:FPF802 4.9 79.2 1.0

Magnesium binding site 6 out of 6 in 3g4f

Go back to Magnesium Binding Sites List in 3g4f
Magnesium binding site 6 out of 6 in the Crystal Structure of (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl 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 (+)- -Cadinene Synthase From Gossypium Arboreum in Complex with 2-Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:66.8
occ:1.00
OE1 B:GLU455 2.5 92.1 1.0
OD1 B:ASP451 2.6 64.9 1.0
O3B B:FPF802 2.6 96.5 1.0
F B:FPF802 2.9 71.2 1.0
O2B B:FPF802 2.9 79.2 1.0
O1 B:FPF802 2.9 87.4 1.0
CD B:GLU455 3.0 83.9 1.0
OE2 B:GLU455 3.2 88.7 1.0
P2 B:FPF802 3.3 94.4 1.0
NH1 B:ARG448 3.5 85.4 1.0
O1A B:FPF802 3.6 97.0 1.0
P1 B:FPF802 3.7 99.3 1.0
CG B:ASP451 3.8 65.3 1.0
C2 B:FPF802 3.9 78.0 1.0
O3A B:FPF802 3.9 93.2 1.0
C1 B:FPF802 4.0 85.8 1.0
CG B:GLU455 4.1 68.9 1.0
OD1 B:ASP452 4.1 78.0 1.0
OD2 B:ASP451 4.3 75.8 1.0
CZ B:ARG448 4.7 83.4 1.0
O1B B:FPF802 4.7 79.8 1.0
O B:HOH610 4.8 61.3 1.0
CB B:ASP451 4.9 61.8 1.0

Reference:

H.A.Gennadios, V.Gonzalez, L.Di Costanzo, A.Li, F.Yu, D.J.Miller, R.K.Allemann, D.W.Christianson. Crystal Structure of (+)-Delta-Cadinene Synthase From Gossypium Arboreum and Evolutionary Divergence of Metal Binding Motifs For Catalysis. Biochemistry V. 48 6175 2009.
ISSN: ISSN 0006-2960
PubMed: 19489610
DOI: 10.1021/BI900483B
Page generated: Mon Dec 14 08:09:55 2020

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