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Magnesium 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:

Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5nx6

Go back to Magnesium Binding Sites List in 5nx6
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg402

b:16.0
occ:1.00
 O3B A:LA6401 1.9 14.5 0.5
O1A A:LA6401 1.9 15.1 0.5
O3B A:LA6401 2.0 14.3 0.6
O A:HOH524 2.0 13.0 1.0
OD1 A:ASN220 2.1 14.3 1.0
OE2 A:GLU228 2.1 17.7 1.0
OG A:SER224 2.2 14.5 1.0
O1A A:LA6401 2.3 15.1 0.6
PA A:LA6401 3.1 14.5 0.5
CG A:ASN220 3.1 13.7 1.0
CD A:GLU228 3.1 17.8 1.0
PB A:LA6401 3.2 14.5 0.5
CB A:SER224 3.2 14.2 1.0
PB A:LA6401 3.3 14.6 0.6
O3A A:LA6401 3.4 14.5 0.5
PA A:LA6401 3.4 15.5 0.6
ND2 A:ASN220 3.5 14.3 1.0
O3A A:LA6401 3.5 14.4 0.6
OE1 A:GLU228 3.5 17.4 1.0
O1 A:LA6401 3.7 14.8 0.5
O1B A:LA6401 3.8 15.6 0.5
O A:ASN220 3.9 13.8 1.0
O A:HOH530 3.9 23.8 1.0
O A:HOH505 4.0 20.3 1.0
O1B A:LA6401 4.1 19.0 0.6
O A:HOH609 4.2 18.0 1.0
C A:ASN220 4.3 13.6 1.0
O2A A:LA6401 4.3 15.5 0.5
CG A:GLU228 4.3 16.7 1.0
OD1 A:ASP221 4.4 16.7 1.0
O1 A:LA6401 4.4 14.8 0.6
CB A:ASN220 4.4 12.0 1.0
O2B A:LA6401 4.4 14.2 0.5
O2A A:LA6401 4.5 18.9 0.6
O2B A:LA6401 4.6 14.8 0.6
CA A:SER224 4.6 14.1 1.0
N A:ASP221 4.6 13.1 1.0
CA A:ASP221 4.6 14.3 1.0
C1 A:LA6401 4.8 15.7 0.6
MG A:MG403 4.9 28.6 1.0
C A:SER224 5.0 14.8 1.0
O A:SER224 5.0 16.2 1.0
C1 A:LA6401 5.0 15.4 0.5
CA A:ASN220 5.0 12.5 1.0

Magnesium binding site 2 out of 4 in 5nx6

Go back to Magnesium Binding Sites List in 5nx6
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg403

b:28.6
occ:1.00
 O A:HOH502 1.9 24.9 1.0
O2A A:LA6401 2.0 18.9 0.6
O1B A:LA6401 2.1 19.0 0.6
O A:HOH505 2.1 20.3 1.0
OD2 A:ASP81 2.2 24.1 0.6
O A:HOH508 2.3 39.5 1.0
O A:HOH501 2.5 23.9 1.0
OD2 A:ASP81 2.7 22.7 0.4
O1B A:LA6401 2.9 15.6 0.5
PA A:LA6401 3.0 15.5 0.6
O3A A:LA6401 3.0 14.5 0.5
O3A A:LA6401 3.1 14.4 0.6
O2A A:LA6401 3.2 15.5 0.5
PB A:LA6401 3.2 14.6 0.6
CG A:ASP81 3.3 21.0 0.6
CG A:ASP81 3.3 21.6 0.4
OD1 A:ASP81 3.4 22.8 0.4
PA A:LA6401 3.5 14.5 0.5
O1A A:LA6401 3.6 15.1 0.6
PB A:LA6401 3.6 14.5 0.5
OD1 A:ASP81 3.6 22.6 0.6
O A:HOH642 3.9 34.8 1.0
O1A A:LA6401 3.9 15.1 0.5
NH2 A:ARG314 4.1 18.1 1.0
O3B A:LA6401 4.1 14.3 0.6
NZ A:LYS227 4.1 22.3 1.0
O2B A:LA6401 4.3 14.8 0.6
OE2 A:GLU228 4.3 17.7 1.0
O1 A:LA6401 4.4 14.8 0.6
OD2 A:ASP233 4.4 29.1 1.0
CB A:ASP81 4.5 23.1 0.4
O3B A:LA6401 4.5 14.5 0.5
CB A:ASP81 4.6 22.7 0.6
OD2 A:ASP85 4.6 76.8 1.0
OD1 A:ASP82 4.6 20.2 0.6
O2B A:LA6401 4.7 14.2 0.5
O A:HOH530 4.7 23.8 1.0
CZ A:PHE77 4.7 18.2 1.0
O A:HOH708 4.9 21.3 1.0
MG A:MG402 4.9 16.0 1.0

Magnesium binding site 3 out of 4 in 5nx6

Go back to Magnesium Binding Sites List in 5nx6
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg402

b:17.1
occ:1.00
 O2B B:LA6401 1.9 16.2 0.5
O2B B:LA6401 2.0 16.3 0.5
O2A B:LA6401 2.0 16.1 0.5
O2A B:LA6401 2.1 16.2 0.5
OD1 B:ASN220 2.1 14.5 1.0
OE2 B:GLU228 2.1 18.6 1.0
O B:HOH509 2.1 13.9 1.0
OG B:SER224 2.2 15.8 1.0
CG B:ASN220 3.1 13.8 1.0
PA B:LA6401 3.1 15.8 0.5
CD B:GLU228 3.1 19.6 1.0
PB B:LA6401 3.2 16.5 0.5
PB B:LA6401 3.2 16.6 0.5
CB B:SER224 3.2 15.4 1.0
PA B:LA6401 3.3 17.3 0.5
O3A B:LA6401 3.4 16.1 0.5
ND2 B:ASN220 3.4 14.4 1.0
O3A B:LA6401 3.4 15.9 0.5
OE1 B:GLU228 3.5 20.5 1.0
O1 B:LA6401 3.7 16.5 0.5
O3B B:LA6401 3.8 17.1 0.5
O3B B:LA6401 3.9 20.2 0.5
O B:ASN220 3.9 13.5 1.0
O B:HOH512 3.9 19.3 1.0
O B:HOH565 4.0 26.5 1.0
O B:HOH647 4.3 19.9 1.0
O1 B:LA6401 4.3 15.9 0.5
C B:ASN220 4.3 13.1 1.0
CG B:GLU228 4.4 18.5 1.0
OD1 B:ASP221 4.4 17.4 1.0
O1A B:LA6401 4.4 23.2 0.5
O1A B:LA6401 4.4 16.9 0.5
O1B B:LA6401 4.4 17.2 0.5
CB B:ASN220 4.5 13.0 1.0
O1B B:LA6401 4.5 17.8 0.5
CA B:SER224 4.6 15.2 1.0
N B:ASP221 4.7 12.5 1.0
CA B:ASP221 4.7 13.7 1.0
C1 B:LA6401 4.7 17.5 0.5
MG B:MG403 4.9 30.4 1.0
C1 B:LA6401 4.9 17.1 0.5
C B:SER224 4.9 15.5 1.0
O B:SER224 4.9 16.3 1.0

Magnesium binding site 4 out of 4 in 5nx6

Go back to Magnesium Binding Sites List in 5nx6
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg403

b:30.4
occ:1.00
 O B:HOH502 2.0 21.9 1.0
O B:HOH512 2.0 19.3 1.0
O1A B:LA6401 2.1 23.2 0.5
O3B B:LA6401 2.1 20.2 0.5
O B:HOH515 2.1 29.1 1.0
O B:HOH501 2.4 19.8 1.0
OD2 B:ASP81 2.6 36.7 1.0
O3A B:LA6401 2.9 15.9 0.5
O3B B:LA6401 2.9 17.1 0.5
PA B:LA6401 3.1 17.3 0.5
O1A B:LA6401 3.3 16.9 0.5
CG B:ASP81 3.3 33.3 1.0
O3A B:LA6401 3.3 16.1 0.5
PB B:LA6401 3.3 16.6 0.5
OD1 B:ASP81 3.4 33.5 1.0
PA B:LA6401 3.5 15.8 0.5
PB B:LA6401 3.5 16.5 0.5
O2A B:LA6401 3.7 16.2 0.5
O2A B:LA6401 3.8 16.1 0.5
NZ B:LYS227 4.0 24.6 1.0
NH2 B:ARG314 4.2 22.2 1.0
OD2 B:ASP233 4.2 27.9 1.0
O B:HOH601 4.2 42.3 1.0
O2B B:LA6401 4.2 16.3 0.5
OE2 B:GLU228 4.3 18.6 1.0
O1B B:LA6401 4.4 17.8 0.5
O2B B:LA6401 4.4 16.2 0.5
O1 B:LA6401 4.5 15.9 0.5
O1B B:LA6401 4.6 17.2 0.5
O B:HOH565 4.6 26.5 1.0
CB B:ASP81 4.6 28.1 1.0
O B:HOH639 4.7 26.9 1.0
OD1 B:ASP82 4.7 31.4 0.6
CZ B:PHE77 4.9 21.9 1.0
MG B:MG402 4.9 17.1 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: Mon Dec 14 20:57:13 2020

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