Magnesium in PDB 5nmx: Crystal Structure of the Pyrrolizidine Alkaloid N-Oxygenase From Zonocerus Variegatus in Complex with Fad and Nadp+

The structure of Crystal Structure of the Pyrrolizidine Alkaloid N-Oxygenase From Zonocerus Variegatus in Complex with Fad and Nadp+, PDB code: 5nmx was solved by A.Scheidig, C.Kubitza, A.Faust, D.Ober, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.13 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	74.076, 76.082, 81.669, 71.81, 81.64, 82.04
R / Rfree (%)	17.4 / 20.2

The binding sites of Magnesium atom in the Crystal Structure of the Pyrrolizidine Alkaloid N-Oxygenase From Zonocerus Variegatus in Complex with Fad and Nadp+ (pdb code 5nmx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Pyrrolizidine Alkaloid N-Oxygenase From Zonocerus Variegatus in Complex with Fad and Nadp+, PDB code: 5nmx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Pyrrolizidine Alkaloid N-Oxygenase From Zonocerus Variegatus in Complex with Fad and Nadp+


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 the Pyrrolizidine Alkaloid N-Oxygenase From Zonocerus Variegatus in Complex with Fad and Nadp+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:27.9 occ:1.00 O B:HOH987 1.9 32.3 1.0 O B:HOH795 2.0 20.9 1.0 O B:HOH718 2.0 26.9 1.0 O B:HOH980 2.3 35.0 1.0 O B:HOH988 2.5 39.9 1.0 OE2 A:GLU50 4.1 55.0 1.0 O B:ARG183 4.3 15.4 1.0 O B:PRO181 4.3 15.8 1.0 O B:GLU180 4.3 14.6 1.0 O B:HOH1029 4.3 40.7 1.0 O B:HOH943 4.4 41.3 1.0 CE B:LYS185 4.6 28.2 1.0 CB B:ARG183 4.7 15.2 1.0 C B:PRO181 4.8 14.8 1.0 CA B:PRO181 4.9 14.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Pyrrolizidine Alkaloid N-Oxygenase From Zonocerus Variegatus in Complex with Fad and Nadp+


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 the Pyrrolizidine Alkaloid N-Oxygenase From Zonocerus Variegatus in Complex with Fad and Nadp+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:23.3 occ:1.00 O C:HOH624 2.0 20.7 1.0 O C:HOH694 2.1 26.4 1.0 O C:HOH702 2.1 18.4 1.0 O C:ALA372 3.8 15.9 1.0 O C:HOH939 4.2 33.2 1.0 OE1 C:GLU368 4.2 58.9 1.0 O C:GLU367 4.2 16.2 1.0 O C:HOH628 4.2 32.4 1.0 O C:HOH649 4.2 34.0 1.0 OG1 C:THR374 4.4 21.0 1.0 C C:GLU367 4.8 16.6 1.0 CA C:GLY371 4.9 23.8 1.0 CA C:GLU368 5.0 22.8 1.0 CD C:GLU368 5.0 55.5 1.0 C C:ALA372 5.0 14.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Pyrrolizidine Alkaloid N-Oxygenase From Zonocerus Variegatus in Complex with Fad and Nadp+


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 the Pyrrolizidine Alkaloid N-Oxygenase From Zonocerus Variegatus in Complex with Fad and Nadp+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:19.1 occ:1.00 O D:HOH815 2.0 19.2 1.0 O D:HOH893 2.1 18.4 1.0 O D:HOH671 2.1 20.2 1.0 O D:HOH611 2.2 22.8 1.0 O D:ALA372 3.9 16.1 1.0 O D:HOH648 4.1 36.8 1.0 O D:HOH639 4.2 32.3 1.0 O D:HOH723 4.2 31.6 1.0 OE1 D:GLU368 4.2 45.4 1.0 O D:GLU367 4.2 17.1 1.0 O D:HOH876 4.2 37.2 1.0 OG1 D:THR374 4.3 21.5 1.0 C D:GLU367 4.7 17.4 1.0 CD D:GLU368 4.9 46.2 1.0 CA D:GLU368 4.9 21.5 1.0 N D:GLU368 5.0 18.5 1.0

C.Kubitza, A.Faust, M.Gutt, L.Gath, D.Ober, A.J.Scheidig. Crystal Structure of Pyrrolizidine Alkaloid N-Oxygenase From the Grasshopper Zonocerus Variegatus. Acta Crystallogr D Struct V. 74 422 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 29717713
DOI: 10.1107/S2059798318003510