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Magnesium 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:

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 and 2- Fluorogeranyl Diphosphate (pdb code 5nx7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5nx7

Go back to Magnesium Binding Sites List in 5nx7
Magnesium binding site 1 out of 6 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 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 and 2- Fluorogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:18.3
occ:1.00
 O3B A:0FV400 2.0 16.7 0.4
O1A A:0FV400 2.0 20.3 0.4
O3B A:LA6401 2.0 17.4 0.6
O A:HOH533 2.0 21.7 1.0
OE2 A:GLU228 2.1 22.4 1.0
OD1 A:ASN220 2.2 18.0 1.0
O1A A:LA6401 2.2 19.0 0.6
OG A:SER224 2.3 19.7 1.0
CD A:GLU228 3.1 27.2 1.0
PB A:0FV400 3.2 11.6 0.4
CG A:ASN220 3.2 17.8 1.0
PA A:0FV400 3.2 21.5 0.4
PB A:LA6401 3.3 27.7 0.6
CB A:SER224 3.3 18.4 1.0
PA A:LA6401 3.4 17.1 0.6
O3A A:LA6401 3.4 16.0 0.6
O3A A:0FV400 3.4 25.3 0.4
OE1 A:GLU228 3.5 22.9 1.0
ND2 A:ASN220 3.6 18.8 1.0
O2B A:0FV400 3.6 25.0 0.4
O1 A:0FV400 3.8 32.6 0.4
O A:HOH544 3.9 27.5 1.0
O2B A:LA6401 3.9 18.1 0.6
O A:ASN220 4.0 15.3 1.0
O A:HOH572 4.1 22.8 1.0
NH2 A:ARG174 4.2 32.2 1.0
CG A:GLU228 4.3 25.4 1.0
O2A A:LA6401 4.3 16.3 0.6
C1 A:0FV400 4.4 28.8 0.4
C A:ASN220 4.4 14.6 1.0
O2A A:0FV400 4.4 16.2 0.4
OD1 A:ASP221 4.4 19.8 1.0
O1 A:LA6401 4.4 15.5 0.6
O1B A:0FV400 4.5 22.8 0.4
O1B A:LA6401 4.5 19.9 0.6
CB A:ASN220 4.5 16.0 1.0
CA A:SER224 4.7 16.6 1.0
N A:ASP221 4.7 14.8 1.0
CA A:ASP221 4.8 16.1 1.0
C1 A:LA6401 4.8 26.6 0.6
MG A:MG403 4.8 24.9 1.0
O A:SER224 5.0 19.9 1.0
OH A:TYR315 5.0 19.9 1.0

Magnesium binding site 2 out of 6 in 5nx7

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Magnesium binding site 2 out of 6 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 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 and 2- Fluorogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:24.9
occ:1.00
 O2A A:LA6401 2.0 16.3 0.6
O A:HOH572 2.0 22.8 1.0
O2B A:LA6401 2.1 18.1 0.6
OD2 A:ASP81 2.1 29.9 1.0
O A:HOH535 2.1 27.5 1.0
O A:HOH568 2.2 27.4 1.0
O2B A:0FV400 2.5 25.0 0.4
O3A A:0FV400 2.9 25.3 0.4
PA A:LA6401 3.1 17.1 0.6
O2A A:0FV400 3.1 16.2 0.4
CG A:ASP81 3.1 45.7 1.0
MG A:MG404 3.2 39.0 1.0
PB A:LA6401 3.3 27.7 0.6
PB A:0FV400 3.3 11.6 0.4
O3A A:LA6401 3.3 16.0 0.6
PA A:0FV400 3.4 21.5 0.4
OD1 A:ASP81 3.5 32.8 1.0
O1A A:0FV400 3.8 20.3 0.4
O1A A:LA6401 3.8 19.0 0.6
O A:HOH687 4.0 59.7 1.0
NZ A:LYS227 4.0 28.7 1.0
O3B A:LA6401 4.1 17.4 0.6
NH2 A:ARG314 4.1 24.3 1.0
OE2 A:GLU228 4.2 22.4 1.0
O1B A:0FV400 4.3 22.8 0.4
O A:HOH560 4.4 34.8 1.0
O3B A:0FV400 4.4 16.7 0.4
O1B A:LA6401 4.4 19.9 0.6
O A:HOH627 4.4 35.9 1.0
O1 A:LA6401 4.5 15.5 0.6
CB A:ASP81 4.5 29.4 1.0
O A:HOH501 4.5 32.3 1.0
O A:HOH544 4.5 27.5 1.0
OD2 A:ASP85 4.6 44.5 1.0
OD1 A:ASP82 4.7 33.3 1.0
O A:HOH502 4.8 29.4 1.0
MG A:MG402 4.8 18.3 1.0
OD1 A:ASP85 4.9 54.7 1.0
O1 A:0FV400 4.9 32.6 0.4
O A:HOH704 4.9 25.8 1.0

Magnesium binding site 3 out of 6 in 5nx7

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Magnesium binding site 3 out of 6 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 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 and 2- Fluorogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:39.0
occ:1.00
 O A:HOH560 2.1 34.8 1.0
O A:HOH568 2.1 27.4 1.0
O A:HOH502 2.1 29.4 1.0
OD1 A:ASP81 2.2 32.8 1.0
O2A A:LA6401 2.2 16.3 0.6
O A:HOH504 2.2 50.5 1.0
O2A A:0FV400 2.2 16.2 0.4
CG A:ASP81 3.1 45.7 1.0
MG A:MG403 3.2 24.9 1.0
OD2 A:ASP81 3.3 29.9 1.0
PA A:LA6401 3.4 17.1 0.6
PA A:0FV400 3.7 21.5 0.4
O1 A:LA6401 3.7 15.5 0.6
O A:HOH546 3.8 38.2 1.0
O A:HOH627 3.8 35.9 1.0
OE2 A:GLU155 4.1 32.6 0.6
O A:HOH544 4.2 27.5 1.0
O A:HOH501 4.2 32.3 1.0
O3A A:0FV400 4.3 25.3 0.4
O1A A:LA6401 4.3 19.0 0.6
OE1 A:GLU155 4.4 38.0 0.6
O A:HOH572 4.4 22.8 1.0
CB A:ASP81 4.5 29.4 1.0
O1A A:0FV400 4.5 20.3 0.4
CZ A:PHE77 4.5 23.3 1.0
O3A A:LA6401 4.6 16.0 0.6
CD A:GLU155 4.7 48.2 0.6
O1 A:0FV400 4.7 32.6 0.4
NH1 A:ARG174 4.7 70.9 1.0
CE1 A:PHE77 4.8 24.9 1.0
O A:HOH535 4.9 27.5 1.0
O2B A:LA6401 4.9 18.1 0.6
C1 A:LA6401 4.9 26.6 0.6

Magnesium binding site 4 out of 6 in 5nx7

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Magnesium binding site 4 out of 6 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 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 and 2- Fluorogeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:17.4
occ:1.00
 O2A B:0FV400 1.9 13.3 0.4
O1B B:LA6401 1.9 15.6 0.6
OE2 B:GLU228 2.1 21.4 1.0
O1B B:0FV400 2.1 17.8 0.4
O B:HOH520 2.1 19.8 1.0
OD1 B:ASN220 2.1 17.0 1.0
O2A B:LA6401 2.3 18.0 0.6
OG B:SER224 2.3 18.9 1.0
CD B:GLU228 3.1 22.9 1.0
CG B:ASN220 3.1 15.1 1.0
PB B:LA6401 3.2 12.0 0.6
PA B:0FV400 3.2 15.7 0.4
CB B:SER224 3.3 18.3 1.0
O3A B:LA6401 3.4 15.3 0.6
PB B:0FV400 3.4 36.5 0.4
PA B:LA6401 3.4 19.7 0.6
OE1 B:GLU228 3.5 21.1 1.0
ND2 B:ASN220 3.5 18.8 1.0
O3A B:0FV400 3.6 21.5 0.4
O3B B:LA6401 3.9 19.4 0.6
O3B B:0FV400 3.9 22.9 0.4
O B:HOH543 3.9 26.4 1.0
O1 B:0FV400 4.0 31.8 0.4
O B:ASN220 4.0 15.5 1.0
NH2 B:ARG174 4.1 27.7 1.0
O B:HOH619 4.2 23.6 1.0
C1 B:0FV400 4.3 26.9 0.4
O1A B:LA6401 4.3 17.0 0.6
CG B:GLU228 4.3 23.1 1.0
O1A B:0FV400 4.3 21.0 0.4
OD1 B:ASP221 4.4 18.6 1.0
C B:ASN220 4.4 16.2 1.0
O1 B:LA6401 4.4 16.1 0.6
O2B B:LA6401 4.4 23.7 0.6
CB B:ASN220 4.5 15.1 1.0
O2B B:0FV400 4.6 16.0 0.4
CA B:SER224 4.7 17.5 1.0
C1 B:LA6401 4.7 31.9 0.6
N B:ASP221 4.7 14.8 1.0
CA B:ASP221 4.7 14.7 1.0
MG B:MG403 4.9 22.0 1.0
O B:SER224 5.0 20.3 1.0
OH B:TYR315 5.0 18.7 1.0

Magnesium binding site 5 out of 6 in 5nx7

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Magnesium binding site 5 out of 6 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 Magnesium with other atoms in the Mg binding site number 5 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:Mg403

b:22.0
occ:1.00
 O B:HOH531 2.0 27.9 1.0
O1A B:LA6401 2.0 17.0 0.6
O B:HOH619 2.0 23.6 1.0
O3B B:LA6401 2.1 19.4 0.6
OD2 B:ASP81 2.1 26.1 1.0
O B:HOH536 2.1 26.7 1.0
O3B B:0FV400 2.5 22.9 0.4
O3A B:0FV400 2.9 21.5 0.4
O1A B:0FV400 3.0 21.0 0.4
CG B:ASP81 3.1 37.5 1.0
PA B:LA6401 3.2 19.7 0.6
MG B:MG404 3.2 30.9 1.0
PB B:0FV400 3.3 36.5 0.4
PA B:0FV400 3.4 15.7 0.4
PB B:LA6401 3.4 12.0 0.6
OD1 B:ASP81 3.4 30.2 1.0
O3A B:LA6401 3.4 15.3 0.6
O2A B:LA6401 3.8 18.0 0.6
NZ B:LYS227 3.9 26.1 1.0
O2A B:0FV400 3.9 13.3 0.4
O B:HOH505 4.1 59.4 1.0
NH2 B:ARG314 4.2 22.9 1.0
O1B B:LA6401 4.2 15.6 0.6
O1B B:0FV400 4.2 17.8 0.4
OE2 B:GLU228 4.3 21.4 1.0
O B:HOH511 4.3 36.2 1.0
O2B B:0FV400 4.4 16.0 0.4
OD2 B:ASP85 4.4 57.0 1.0
O B:HOH543 4.4 26.4 1.0
O B:HOH503 4.4 40.1 1.0
CB B:ASP81 4.5 25.2 1.0
O2B B:LA6401 4.5 23.7 0.6
O1 B:LA6401 4.5 16.1 0.6
O B:HOH636 4.5 36.5 1.0
OD1 B:ASP82 4.7 29.7 1.0
OD1 B:ASP85 4.8 59.4 1.0
O B:HOH524 4.8 31.0 1.0
O1 B:0FV400 4.9 31.8 0.4
O B:HOH702 4.9 24.4 1.0
MG B:MG402 4.9 17.4 1.0

Magnesium binding site 6 out of 6 in 5nx7

Go back to Magnesium Binding Sites List in 5nx7
Magnesium binding site 6 out of 6 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 Magnesium with other atoms in the Mg binding site number 6 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:Mg404

b:30.9
occ:1.00
 O B:HOH511 2.1 36.2 1.0
O B:HOH536 2.1 26.7 1.0
OD1 B:ASP81 2.1 30.2 1.0
O1A B:0FV400 2.2 21.0 0.4
O B:HOH524 2.2 31.0 1.0
O1A B:LA6401 2.2 17.0 0.6
O B:HOH504 2.3 37.2 1.0
CG B:ASP81 3.0 37.5 1.0
MG B:MG403 3.2 22.0 1.0
OD2 B:ASP81 3.3 26.1 1.0
PA B:LA6401 3.4 19.7 0.6
PA B:0FV400 3.6 15.7 0.4
O1 B:LA6401 3.7 16.1 0.6
O B:HOH529 3.7 36.3 1.0
O B:HOH636 3.8 36.5 1.0
O B:HOH503 4.1 40.1 1.0
O B:HOH543 4.2 26.4 1.0
O3A B:0FV400 4.2 21.5 0.4
OE2 B:GLU155 4.2 28.7 0.5
O2A B:LA6401 4.3 18.0 0.6
OE1 B:GLU155 4.3 30.1 0.5
O B:HOH619 4.4 23.6 1.0
CB B:ASP81 4.4 25.2 1.0
O1 B:0FV400 4.5 31.8 0.4
CZ B:PHE77 4.5 23.0 1.0
O2A B:0FV400 4.6 13.3 0.4
O3A B:LA6401 4.6 15.3 0.6
CD B:GLU155 4.7 38.1 0.5
O B:HOH531 4.8 27.9 1.0
CE1 B:PHE77 4.8 26.1 1.0
O3B B:LA6401 4.8 19.4 0.6
O B:HOH590 4.9 64.8 1.0
C1 B:LA6401 4.9 31.9 0.6

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 Sep 29 23:41:38 2024

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