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Fluorine in PDB 5nx7: Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate

Enzymatic activity of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate

All present enzymatic activity of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate:
4.2.3.7;

Protein crystallography data

The structure of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate, PDB code: 5nx7 was solved by V.Karuppiah, D.Leys, N.S.Scrutton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.42 / 1.51
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.745, 60.826, 64.258, 92.67, 89.98, 101.77
R / Rfree (%) 14.9 / 17.4

Other elements in 5nx7:

The structure of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate (pdb code 5nx7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate, PDB code: 5nx7:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5nx7

Go back to Fluorine Binding Sites List in 5nx7
Fluorine binding site 1 out of 4 in the Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:26.5
occ:0.38
 F2 A:0FV400 0.0 26.5 0.4
C2 A:0FV400 1.3 26.9 0.4
C2 A:LA6401 1.8 25.9 0.6
C1 A:LA6401 2.0 26.6 0.6
C3 A:0FV400 2.3 35.3 0.4
C3 A:LA6401 2.3 32.8 0.6
C1 A:0FV400 2.4 28.8 0.4
F2 A:LA6401 2.5 38.0 0.6
C5 A:0FV400 2.8 35.1 0.4
C7 A:LA6401 2.8 32.0 0.6
C6 A:0FV400 2.9 37.8 0.4
CZ A:PHE77 3.0 23.3 1.0
C9 A:0FV400 3.0 34.2 0.4
C5 A:LA6401 3.0 39.5 0.6
O1 A:0FV400 3.1 32.6 0.4
O1 A:LA6401 3.2 15.5 0.6
CE2 A:PHE77 3.3 24.2 1.0
C6 A:LA6401 3.3 33.2 0.6
C4 A:LA6401 3.3 35.8 0.6
C8 A:LA6401 3.4 26.0 0.6
C7 A:0FV400 3.4 37.7 0.4
C8 A:0FV400 3.5 26.9 0.4
CE1 A:PHE77 3.6 24.9 1.0
C4 A:0FV400 3.7 34.4 0.4
CD2 A:PHE179 3.7 33.9 1.0
C9 A:LA6401 3.8 20.4 0.6
O3A A:LA6401 4.0 16.0 0.6
CD2 A:PHE77 4.0 21.4 1.0
CB A:PHE179 4.0 23.5 1.0
PA A:0FV400 4.2 21.5 0.4
CD1 A:PHE77 4.3 26.9 1.0
PA A:LA6401 4.3 17.1 0.6
C10 A:LA6401 4.3 24.7 0.6
CG A:PHE179 4.3 26.1 1.0
O3A A:0FV400 4.4 25.3 0.4
CG A:PHE77 4.5 18.5 1.0
O A:HOH502 4.5 29.4 1.0
O2A A:0FV400 4.6 16.2 0.4
CE2 A:PHE179 4.7 25.6 1.0
C10 A:0FV400 4.8 34.4 0.4

Fluorine binding site 2 out of 4 in 5nx7

Go back to Fluorine Binding Sites List in 5nx7
Fluorine binding site 2 out of 4 in the Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:38.0
occ:0.62
 F2 A:LA6401 0.0 38.0 0.6
C2 A:LA6401 1.3 25.9 0.6
C3 A:LA6401 2.3 32.8 0.6
C1 A:LA6401 2.3 26.6 0.6
O1 A:LA6401 2.5 15.5 0.6
F2 A:0FV400 2.5 26.5 0.4
C2 A:0FV400 2.5 26.9 0.4
C4 A:LA6401 2.7 35.8 0.6
O1 A:0FV400 2.9 32.6 0.4
C3 A:0FV400 2.9 35.3 0.4
O A:HOH591 3.0 35.6 1.0
O A:HOH502 3.1 29.4 1.0
C1 A:0FV400 3.2 28.8 0.4
NH1 A:ARG174 3.3 70.9 1.0
CB A:PHE179 3.4 23.5 1.0
C5 A:0FV400 3.4 35.1 0.4
C5 A:LA6401 3.7 39.5 0.6
C4 A:0FV400 3.8 34.4 0.4
O2A A:0FV400 3.8 16.2 0.4
PA A:0FV400 3.9 21.5 0.4
CZ A:PHE77 4.0 23.3 1.0
N A:PHE179 4.0 23.0 1.0
PA A:LA6401 4.0 17.1 0.6
CE1 A:PHE77 4.2 24.9 1.0
CZ A:ARG174 4.2 57.7 1.0
CA A:PHE179 4.3 21.3 1.0
NH2 A:ARG174 4.4 32.2 1.0
C6 A:0FV400 4.4 37.8 0.4
CG A:PHE179 4.5 26.1 1.0
CD2 A:PHE179 4.6 33.9 1.0
C6 A:LA6401 4.6 33.2 0.6
O3A A:LA6401 4.7 16.0 0.6
O2A A:LA6401 4.7 16.3 0.6
OD1 A:ASN217 4.8 22.2 1.0
O A:HOH522 4.8 22.2 1.0
C7 A:LA6401 4.8 32.0 0.6
O1A A:LA6401 4.8 19.0 0.6
O3A A:0FV400 4.9 25.3 0.4
CE2 A:PHE77 4.9 24.2 1.0
C A:PHE179 5.0 17.4 1.0

Fluorine binding site 3 out of 4 in 5nx7

Go back to Fluorine Binding Sites List in 5nx7
Fluorine binding site 3 out of 4 in the Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F400

b:34.2
occ:0.44
 F2 B:0FV400 0.0 34.2 0.4
C2 B:0FV400 1.3 27.7 0.4
C2 B:LA6401 1.8 21.4 0.6
C1 B:LA6401 2.1 31.9 0.6
C3 B:0FV400 2.3 31.3 0.4
C3 B:LA6401 2.4 28.5 0.6
C1 B:0FV400 2.4 26.9 0.4
F2 B:LA6401 2.4 31.5 0.6
C7 B:LA6401 2.7 28.7 0.6
C5 B:0FV400 2.8 24.0 0.4
C7 B:0FV400 2.9 25.8 0.4
CZ B:PHE77 3.0 23.0 1.0
O1 B:0FV400 3.0 31.8 0.4
C5 B:LA6401 3.0 33.4 0.6
O1 B:LA6401 3.2 16.1 0.6
C8 B:0FV400 3.2 22.9 0.4
CE2 B:PHE77 3.3 24.3 1.0
C8 B:LA6401 3.3 26.7 0.6
C4 B:LA6401 3.3 24.7 0.6
C6 B:LA6401 3.3 24.0 0.6
C6 B:0FV400 3.4 23.8 0.4
CE1 B:PHE77 3.6 26.1 1.0
CD2 B:PHE179 3.7 37.8 1.0
C9 B:LA6401 3.7 27.7 0.6
C9 B:0FV400 3.7 26.2 0.4
C4 B:0FV400 3.7 25.2 0.4
C10 B:0FV400 3.9 28.7 0.4
O3A B:LA6401 4.0 15.3 0.6
CD2 B:PHE77 4.1 22.2 1.0
CB B:PHE179 4.1 21.9 1.0
PA B:0FV400 4.2 15.7 0.4
O3A B:0FV400 4.2 21.5 0.4
PA B:LA6401 4.3 19.7 0.6
CD1 B:PHE77 4.3 20.5 1.0
CG B:PHE179 4.4 22.1 1.0
C10 B:LA6401 4.5 21.8 0.6
O B:HOH524 4.5 31.0 1.0
CG B:PHE77 4.6 17.1 1.0
CE2 B:PHE179 4.6 27.0 1.0
O1A B:0FV400 4.8 21.0 0.4

Fluorine binding site 4 out of 4 in 5nx7

Go back to Fluorine Binding Sites List in 5nx7
Fluorine binding site 4 out of 4 in the Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate and 2- Fluorogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:31.5
occ:0.56
 F2 B:LA6401 0.0 31.5 0.6
C2 B:LA6401 1.3 21.4 0.6
C1 B:LA6401 2.3 31.9 0.6
C3 B:LA6401 2.3 28.5 0.6
F2 B:0FV400 2.4 34.2 0.4
C2 B:0FV400 2.5 27.7 0.4
O1 B:LA6401 2.5 16.1 0.6
O1 B:0FV400 2.7 31.8 0.4
C4 B:LA6401 2.8 24.7 0.6
C3 B:0FV400 2.9 31.3 0.4
O B:HOH587 3.1 36.2 1.0
NH1 B:ARG174 3.2 64.5 1.0
O B:HOH524 3.2 31.0 1.0
C1 B:0FV400 3.2 26.9 0.4
CB B:PHE179 3.3 21.9 1.0
C5 B:0FV400 3.4 24.0 0.4
C5 B:LA6401 3.8 33.4 0.6
C4 B:0FV400 3.8 25.2 0.4
CZ B:PHE77 3.9 23.0 1.0
PA B:0FV400 4.0 15.7 0.4
CE1 B:PHE77 4.0 26.1 1.0
N B:PHE179 4.1 24.9 1.0
O1A B:0FV400 4.1 21.0 0.4
PA B:LA6401 4.1 19.7 0.6
CA B:PHE179 4.2 20.2 1.0
CZ B:ARG174 4.3 54.9 1.0
CG B:PHE179 4.3 22.1 1.0
CD2 B:PHE179 4.4 37.8 1.0
NH2 B:ARG174 4.5 27.7 1.0
C6 B:LA6401 4.7 24.0 0.6
C7 B:LA6401 4.7 28.7 0.6
O3A B:LA6401 4.7 15.3 0.6
C6 B:0FV400 4.8 23.8 0.4
O1A B:LA6401 4.8 17.0 0.6
CE2 B:PHE77 4.8 24.3 1.0
O3A B:0FV400 4.8 21.5 0.4
O2A B:LA6401 4.9 18.0 0.6
C7 B:0FV400 4.9 25.8 0.4
O B:HOH512 4.9 23.2 1.0
OD1 B:ASN217 4.9 21.6 1.0
C B:PHE179 4.9 18.0 1.0

Reference:

V.Karuppiah, K.E.Ranaghan, N.G.H.Leferink, L.O.Johannissen, M.Shanmugam, A.Ni Cheallaigh, N.J.Bennett, L.J.Kearsey, E.Takano, J.M.Gardiner, M.W.Van Der Kamp, S.Hay, A.J.Mulholland, D.Leys, N.S.Scrutton. Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase. Acs Catal V. 7 6268 2017.
ISSN: ESSN 2155-5435
PubMed: 28966840
DOI: 10.1021/ACSCATAL.7B01924
Page generated: Sun Dec 13 12:29:06 2020

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