Magnesium in PDB 5z83: Crystal Structure of GENB1 From Micromonospora Echinospora in Complex with Plp (Internal Aldimine)

The structure of Crystal Structure of GENB1 From Micromonospora Echinospora in Complex with Plp (Internal Aldimine), PDB code: 5z83 was solved by S.K.Hong, S.S.Cha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.80 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.140, 88.012, 116.140, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.2

The binding sites of Magnesium atom in the Crystal Structure of GENB1 From Micromonospora Echinospora in Complex with Plp (Internal Aldimine) (pdb code 5z83). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of GENB1 From Micromonospora Echinospora in Complex with Plp (Internal Aldimine), PDB code: 5z83:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of GENB1 From Micromonospora Echinospora in Complex with Plp (Internal Aldimine)


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 GENB1 From Micromonospora Echinospora in Complex with Plp (Internal Aldimine) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:15.4 occ:1.00 O A:HOH864 2.0 24.9 1.0 O A:HOH635 2.0 18.2 1.0 O A:HOH789 2.0 18.3 1.0 O A:HOH876 2.0 19.8 1.0 O A:HOH629 2.1 16.1 1.0 OD2 A:ASP345 2.3 14.7 1.0 CG A:ASP345 3.2 13.6 1.0 OD1 A:ASP345 3.4 17.6 1.0 O A:HOH947 3.8 28.1 1.0 O A:HOH642 4.0 29.7 1.0 OD2 A:ASP395 4.1 14.1 1.0 OD1 A:ASP395 4.1 15.5 1.0 O A:HOH693 4.2 24.3 1.0 O A:HOH924 4.2 27.2 1.0 O A:ALA393 4.2 13.2 1.0 O A:GLY392 4.3 17.8 1.0 O A:HOH906 4.5 24.4 1.0 CG A:ASP395 4.5 14.7 1.0 CB A:ASP345 4.6 12.4 1.0 NZ A:LYS209 4.7 18.4 1.0 CZ A:PHE342 4.8 12.2 1.0 C A:ALA393 4.8 14.0 1.0 CE2 A:PHE342 4.8 14.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of GENB1 From Micromonospora Echinospora in Complex with Plp (Internal Aldimine)


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 GENB1 From Micromonospora Echinospora in Complex with Plp (Internal Aldimine) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:20.2 occ:1.00 O B:HOH634 2.0 18.3 1.0 O B:HOH823 2.1 21.0 1.0 O B:HOH853 2.1 27.0 1.0 O B:HOH613 2.1 20.0 1.0 O B:HOH870 2.2 27.1 1.0 O B:HOH816 2.3 31.6 1.0 OD2 B:ASP345 2.3 15.2 1.0 CG B:ASP345 3.2 14.0 1.0 OD1 B:ASP345 3.3 13.6 1.0 OD2 B:ASP395 4.0 14.7 1.0 O B:HOH663 4.1 28.0 1.0 OD1 B:ASP395 4.1 17.5 1.0 O B:GLY392 4.2 18.4 1.0 O B:ALA393 4.2 16.9 1.0 O B:HOH638 4.3 21.8 1.0 CG B:ASP395 4.5 14.6 1.0 NZ B:LYS209 4.6 18.0 1.0 O B:HOH885 4.6 23.4 1.0 CB B:ASP345 4.6 10.9 1.0 CZ B:PHE342 4.8 14.8 1.0 C B:ALA393 4.8 16.6 1.0 CE2 B:PHE342 4.9 14.3 1.0 O B:HOH776 5.0 30.7 1.0

Y.H.Ban, M.C.Song, J.Y.Hwang, H.L.Shin, H.J.Kim, S.K.Hong, N.J.Lee, J.W.Park, S.S.Cha, H.W.Liu, Y.J.Yoon. Complete Reconstitution of the Diverse Pathways of Gentamicin B Biosynthesis. Nat. Chem. Biol. V. 15 295 2019.
ISSN: ESSN 1552-4469
PubMed: 30643280
DOI: 10.1038/S41589-018-0203-4