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Fluorine in PDB 5nx6: Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl Diphosphate

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

All present enzymatic activity of Crystal Structure of 1,8-Cineole Synthase From Streptomyces Clavuligerus in Complex with 2-Fluoroneryl 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, PDB code: 5nx6 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) 32.26 / 1.63
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.810, 60.830, 64.100, 90.04, 92.89, 101.98
R / Rfree (%) 16.6 / 19.4

Other elements in 5nx6:

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

Magnesium (Mg) 4 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 (pdb code 5nx6). 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, PDB code: 5nx6:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5nx6

Go back to Fluorine Binding Sites List in 5nx6
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:18.5
occ:0.55
 F2 A:LA6401 0.0 18.5 0.6
F2 A:LA6401 0.3 17.9 0.5
C2 A:LA6401 1.4 17.2 0.6
C2 A:LA6401 1.6 16.8 0.5
C3 A:LA6401 2.4 15.7 0.6
C1 A:LA6401 2.4 15.7 0.6
C3 A:LA6401 2.5 15.6 0.5
O1 A:LA6401 2.6 14.8 0.6
C1 A:LA6401 2.6 15.4 0.5
C4 A:LA6401 2.8 14.7 0.6
C4 A:LA6401 2.8 14.7 0.5
O A:HOH693 3.0 20.1 1.0
O A:HOH569 3.1 31.9 1.0
O1 A:LA6401 3.2 14.8 0.5
CB A:PHE179 3.3 12.5 1.0
NH2 A:ARG174 3.3 25.1 1.0
O2A A:LA6401 3.6 15.5 0.5
C5 A:LA6401 3.8 16.8 0.6
C5 A:LA6401 3.9 16.7 0.5
CZ A:PHE77 4.0 18.2 1.0
PA A:LA6401 4.0 14.5 0.5
CD2 A:PHE179 4.1 15.0 1.0
CE1 A:PHE77 4.1 17.9 1.0
PA A:LA6401 4.2 15.5 0.6
CG A:PHE179 4.2 14.4 1.0
N A:PHE179 4.3 15.5 1.0
CA A:PHE179 4.3 13.7 1.0
O A:HOH609 4.5 18.0 1.0
C7 A:LA6401 4.6 18.1 0.6
CZ A:ARG174 4.6 29.5 1.0
O2A A:LA6401 4.7 18.9 0.6
C6 A:LA6401 4.7 17.0 0.6
C6 A:LA6401 4.8 17.0 0.5
CE2 A:PHE77 4.8 20.1 1.0
C7 A:LA6401 4.9 17.9 0.5
O3A A:LA6401 4.9 14.4 0.6
O A:HOH556 5.0 18.7 1.0
O A:HOH755 5.0 51.5 1.0
C A:PHE179 5.0 13.1 1.0

Fluorine binding site 2 out of 4 in 5nx6

Go back to Fluorine Binding Sites List in 5nx6
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:17.9
occ:0.45
 F2 A:LA6401 0.0 17.9 0.5
F2 A:LA6401 0.3 18.5 0.6
C2 A:LA6401 1.1 17.2 0.6
C2 A:LA6401 1.3 16.8 0.5
C1 A:LA6401 2.2 15.7 0.6
C3 A:LA6401 2.2 15.7 0.6
C3 A:LA6401 2.3 15.6 0.5
C1 A:LA6401 2.4 15.4 0.5
O1 A:LA6401 2.5 14.8 0.6
C4 A:LA6401 2.8 14.7 0.6
C4 A:LA6401 2.8 14.7 0.5
O1 A:LA6401 3.0 14.8 0.5
O A:HOH569 3.2 31.9 1.0
O A:HOH693 3.3 20.1 1.0
CB A:PHE179 3.4 12.5 1.0
NH2 A:ARG174 3.5 25.1 1.0
O2A A:LA6401 3.6 15.5 0.5
C5 A:LA6401 3.6 16.8 0.6
C5 A:LA6401 3.7 16.7 0.5
CZ A:PHE77 3.8 18.2 1.0
PA A:LA6401 3.9 14.5 0.5
CE1 A:PHE77 4.0 17.9 1.0
CD2 A:PHE179 4.0 15.0 1.0
PA A:LA6401 4.1 15.5 0.6
CG A:PHE179 4.2 14.4 1.0
C7 A:LA6401 4.4 18.1 0.6
O A:HOH609 4.4 18.0 1.0
C6 A:LA6401 4.5 17.0 0.6
N A:PHE179 4.5 15.5 1.0
CA A:PHE179 4.5 13.7 1.0
O2A A:LA6401 4.6 18.9 0.6
C7 A:LA6401 4.6 17.9 0.5
C6 A:LA6401 4.6 17.0 0.5
CE2 A:PHE77 4.7 20.1 1.0
O3A A:LA6401 4.7 14.4 0.6
CZ A:ARG174 4.8 29.5 1.0
O3A A:LA6401 4.9 14.5 0.5
O1A A:LA6401 4.9 15.1 0.6
O1A A:LA6401 5.0 15.1 0.5

Fluorine binding site 3 out of 4 in 5nx6

Go back to Fluorine Binding Sites List in 5nx6
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:19.5
occ:0.48
 F2 B:LA6401 0.0 19.5 0.5
F2 B:LA6401 0.4 19.0 0.5
C2 B:LA6401 1.3 17.9 0.5
C2 B:LA6401 1.6 17.8 0.5
C3 B:LA6401 2.3 17.0 0.5
C3 B:LA6401 2.4 17.0 0.5
C1 B:LA6401 2.4 17.5 0.5
O1 B:LA6401 2.6 15.9 0.5
C4 B:LA6401 2.6 15.3 0.5
C4 B:LA6401 2.7 15.3 0.5
C1 B:LA6401 2.8 17.1 0.5
O B:HOH520 3.0 31.9 1.0
O B:HOH695 3.0 20.5 1.0
O1 B:LA6401 3.2 16.5 0.5
NH2 B:ARG174 3.2 28.1 1.0
CB B:PHE179 3.3 13.9 1.0
O1A B:LA6401 3.5 16.9 0.5
C5 B:LA6401 3.7 16.8 0.5
C5 B:LA6401 3.8 16.5 0.5
CZ B:PHE77 4.0 21.9 1.0
PA B:LA6401 4.0 15.8 0.5
PA B:LA6401 4.1 17.3 0.5
CD2 B:PHE179 4.2 16.6 1.0
CE1 B:PHE77 4.2 21.8 1.0
CG B:PHE179 4.2 16.1 1.0
N B:PHE179 4.3 16.1 1.0
CA B:PHE179 4.4 14.9 1.0
O B:HOH647 4.4 19.9 1.0
CZ B:ARG174 4.5 31.9 1.0
C6 B:LA6401 4.6 17.0 0.5
C7 B:LA6401 4.6 17.4 0.5
C6 B:LA6401 4.7 17.0 0.5
C7 B:LA6401 4.7 17.5 0.5
O1A B:LA6401 4.8 23.2 0.5
O B:HOH625 4.8 18.6 1.0
O3A B:LA6401 4.8 16.1 0.5
O B:HOH779 4.9 52.1 1.0
OD1 B:ASN217 4.9 18.9 1.0
CE2 B:PHE77 4.9 21.8 1.0
O2A B:LA6401 5.0 16.2 0.5

Fluorine binding site 4 out of 4 in 5nx6

Go back to Fluorine Binding Sites List in 5nx6
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:19.0
occ:0.52
 F2 B:LA6401 0.0 19.0 0.5
F2 B:LA6401 0.4 19.5 0.5
C2 B:LA6401 1.1 17.9 0.5
C2 B:LA6401 1.3 17.8 0.5
C1 B:LA6401 2.1 17.5 0.5
C3 B:LA6401 2.2 17.0 0.5
C3 B:LA6401 2.3 17.0 0.5
O1 B:LA6401 2.4 15.9 0.5
C1 B:LA6401 2.4 17.1 0.5
C4 B:LA6401 2.7 15.3 0.5
C4 B:LA6401 2.8 15.3 0.5
O1 B:LA6401 3.0 16.5 0.5
O B:HOH520 3.1 31.9 1.0
O B:HOH695 3.3 20.5 1.0
O1A B:LA6401 3.4 16.9 0.5
CB B:PHE179 3.4 13.9 1.0
NH2 B:ARG174 3.5 28.1 1.0
C5 B:LA6401 3.6 16.8 0.5
C5 B:LA6401 3.7 16.5 0.5
CZ B:PHE77 3.7 21.9 1.0
PA B:LA6401 3.8 15.8 0.5
PA B:LA6401 4.0 17.3 0.5
CE1 B:PHE77 4.0 21.8 1.0
CD2 B:PHE179 4.0 16.6 1.0
CG B:PHE179 4.2 16.1 1.0
C7 B:LA6401 4.4 17.4 0.5
C6 B:LA6401 4.4 17.0 0.5
C7 B:LA6401 4.5 17.5 0.5
O B:HOH647 4.5 19.9 1.0
C6 B:LA6401 4.5 17.0 0.5
CE2 B:PHE77 4.6 21.8 1.0
N B:PHE179 4.6 16.1 1.0
O3A B:LA6401 4.6 16.1 0.5
CA B:PHE179 4.6 14.9 1.0
O1A B:LA6401 4.6 23.2 0.5
CZ B:ARG174 4.8 31.9 1.0
O3A B:LA6401 4.8 15.9 0.5
O2A B:LA6401 4.9 16.2 0.5
O2A B:LA6401 4.9 16.1 0.5

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: Tue Jul 15 05:35:01 2025

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