Magnesium in PDB 9c7j: Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate

Enzymatic activity of Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate

All present enzymatic activity of Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate:
4.2.1.138; 4.2.3.89;

Protein crystallography data

The structure of Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate, PDB code: 9c7j was solved by R.Prem Kumar, B.Y.Black, D.D.Oprian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.648, 89.606, 114.814, 90, 90.71, 90
R / Rfree (%) 20.4 / 24.9

Other elements in 9c7j:

The structure of Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate (pdb code 9c7j). 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 Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate, PDB code: 9c7j:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 9c7j

Go back to Magnesium Binding Sites List in 9c7j
Magnesium binding site 1 out of 3 in the Crystal Structure of Caryolan-1-Ol Synthase Complexed 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 Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:53.8
occ:1.00
 OD2 A:ASP83 2.1 50.1 1.0
OD2 A:ASP87 2.4 64.3 1.0
O3A A:FPF401 2.8 69.7 1.0
CG A:ASP83 2.8 43.6 1.0
OD1 A:ASP83 2.8 51.8 1.0
O1B A:FPF401 2.9 79.3 1.0
P2 A:FPF401 3.3 83.0 1.0
O1 A:FPF401 3.5 69.8 1.0
C1 A:FPF401 3.6 56.5 1.0
CG A:ASP87 3.6 61.3 1.0
P1 A:FPF401 3.8 82.1 1.0
O2B A:FPF401 4.0 69.2 1.0
CB A:ASP83 4.3 43.2 1.0
O A:HOH502 4.4 51.5 1.0
OD1 A:ASP87 4.4 66.0 1.0
CB A:ASP87 4.4 59.0 1.0
O3B A:FPF401 4.7 73.1 1.0
O1A A:FPF401 4.7 69.6 1.0
C2 A:FPF401 4.7 52.1 1.0
F A:FPF401 4.8 57.0 1.0
O2A A:FPF401 4.9 66.4 1.0
OH A:TYR152 5.0 37.7 1.0
CE1 A:TYR152 5.0 42.2 1.0

Magnesium binding site 2 out of 3 in 9c7j

Go back to Magnesium Binding Sites List in 9c7j
Magnesium binding site 2 out of 3 in the Crystal Structure of Caryolan-1-Ol Synthase Complexed 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 Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:50.0
occ:1.00
 O2B C:FPF401 2.3 76.2 0.8
OD1 C:ASP83 2.7 49.4 1.0
OD2 C:ASP83 3.1 54.6 1.0
CG C:ASP83 3.2 46.1 1.0
P2 C:FPF401 3.7 80.1 0.8
OD2 C:ASP87 3.8 60.2 1.0
O1B C:FPF401 4.1 69.0 0.8
O1A C:FPF401 4.1 75.9 0.8
C1 C:FPF401 4.2 60.9 0.8
O1 C:FPF401 4.3 62.9 0.8
CE1 C:TYR152 4.5 36.5 1.0
O3B C:FPF401 4.6 67.0 0.8
P1 C:FPF401 4.6 65.7 0.8
O3A C:FPF401 4.6 65.0 0.8
CB C:ASP83 4.7 41.4 1.0
CG C:ASP87 4.8 72.5 1.0
OH C:TYR152 4.8 36.7 1.0
C4 C:FPF401 5.0 48.1 0.8

Magnesium binding site 3 out of 3 in 9c7j

Go back to Magnesium Binding Sites List in 9c7j
Magnesium binding site 3 out of 3 in the Crystal Structure of Caryolan-1-Ol Synthase Complexed 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 Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:59.0
occ:0.85
 OD2 D:ASP87 2.1 67.9 1.0
OD2 D:ASP83 2.2 55.5 1.0
O1B D:FPF401 2.3 88.8 1.0
OD1 D:ASP83 2.6 52.6 1.0
CG D:ASP83 2.7 47.7 1.0
O1 D:FPF401 3.3 73.3 1.0
CG D:ASP87 3.3 68.2 1.0
C1 D:FPF401 3.6 63.8 1.0
P2 D:FPF401 3.7 100.0 1.0
CB D:ASP87 4.1 68.4 1.0
O3A D:FPF401 4.1 76.3 1.0
CB D:ASP83 4.2 36.7 1.0
OD1 D:ASP87 4.3 65.3 1.0
P1 D:FPF401 4.3 80.6 1.0
O3B D:FPF401 4.3 81.7 1.0
O2B D:FPF401 4.7 90.5 1.0
O1A D:FPF401 4.7 63.8 1.0
CE1 D:TYR152 4.9 38.7 1.0
O D:ASP83 4.9 46.9 1.0

Reference:

R.P.Kumar, J.O.Matos, B.Y.Black, W.H.Ellenburg, J.Chen, M.Patterson, J.A.Gehtman, D.L.Theobald, I.J.Krauss, D.D.Oprian. Crystal Structure of Caryolan-1-Ol Synthase, A Sesquiterpene Synthase Catalyzing An Initial Anti-Markovnikov Cyclization Reaction. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 39400323
DOI: 10.1021/ACS.BIOCHEM.4C00547
Page generated: Wed Nov 13 12:46:58 2024

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