Atomistry » Fluorine » PDB 5nk2-5o6h » 5nx6
Atomistry »
  Fluorine »
    PDB 5nk2-5o6h »
      5nx6 »

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: Thu Aug 1 12:07:55 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy