Magnesium in PDB 5np9: Crystal Structure of Bacillus Subtilis Ydib in Complex with Adp

The structure of Crystal Structure of Bacillus Subtilis Ydib in Complex with Adp, PDB code: 5np9 was solved by L.Ballut, N.Aghajari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.06 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	84.030, 111.770, 35.680, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 22.8

The binding sites of Magnesium atom in the Crystal Structure of Bacillus Subtilis Ydib in Complex with Adp (pdb code 5np9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Bacillus Subtilis Ydib in Complex with Adp, PDB code: 5np9:

Magnesium binding site 1 out of 1 in the Crystal Structure of Bacillus Subtilis Ydib in Complex with Adp


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 Bacillus Subtilis Ydib in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:26.8 occ:1.00 OG1 A:THR42 2.1 24.6 1.0 O2B A:ADP201 2.1 23.3 1.0 OE1 A:GLU106 2.1 25.3 1.0 O A:HOH316 2.2 23.6 1.0 O A:HOH306 2.2 20.4 1.0 O A:HOH311 2.2 20.1 1.0 CD A:GLU106 3.1 25.1 1.0 CB A:THR42 3.2 20.7 1.0 OE2 A:GLU106 3.3 28.8 1.0 PB A:ADP201 3.3 31.5 1.0 O3B A:ADP201 3.6 33.1 1.0 N A:THR42 3.7 23.6 1.0 CA A:THR42 4.0 24.1 1.0 O2A A:ADP201 4.0 28.6 1.0 O A:HOH373 4.1 43.6 1.0 OD2 A:ASP80 4.2 27.2 1.0 OG A:SER60 4.2 25.9 1.0 O A:HOH317 4.3 26.7 1.0 O1B A:ADP201 4.3 27.9 1.0 CG2 A:THR42 4.4 20.7 1.0 O3A A:ADP201 4.4 31.4 1.0 CE A:LYS41 4.4 30.3 1.0 CG A:GLU106 4.5 23.7 1.0 CB A:SER60 4.5 21.9 1.0 CB A:LYS41 4.6 24.2 1.0 PA A:ADP201 4.6 30.3 1.0 C A:LYS41 4.7 29.0 1.0 NZ A:LYS41 4.7 27.8 1.0 CB A:GLU106 4.9 26.7 1.0 CA A:SER60 4.9 24.1 1.0 O1A A:ADP201 5.0 28.5 1.0

H.A.Nguyen, T.El Khoury, S.Guiral, M.H.Laaberki, M.P.Candusso, F.Galisson, A.E.Foucher, S.Kesraoui, L.Ballut, S.Vallet, C.Orelle, L.Zucchini, J.Martin, A.Page, J.Attieh, N.Aghajari, C.Grangeasse, J.M.Jault. Expanding the Kinome World: A New Protein Kinase Family Widely Conserved in Bacteria. J. Mol. Biol. V. 429 3056 2017.
ISSN: ESSN 1089-8638
PubMed: 28890133
DOI: 10.1016/J.JMB.2017.08.016