Magnesium in PDB 6np3: Aac-Via Bound to Gentamicin

All present enzymatic activity of Aac-Via Bound to Gentamicin:
2.3.1.81;

The structure of Aac-Via Bound to Gentamicin, PDB code: 6np3 was solved by P.Kumar, M.J.Cuneo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.23 / 1.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.196, 86.302, 50.140, 90.00, 119.86, 90.00
R / Rfree (%)	12.7 / 13.9

The binding sites of Magnesium atom in the Aac-Via Bound to Gentamicin (pdb code 6np3). 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 Aac-Via Bound to Gentamicin, PDB code: 6np3:

Magnesium binding site 1 out of 1 in the Aac-Via Bound to Gentamicin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Aac-Via Bound to Gentamicin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:42.3 occ:0.50 O A:HOH472 2.0 13.0 1.0 O A:HOH493 2.4 35.6 1.0 OD2 A:ASP145 3.0 15.9 1.0 CG A:ASP145 3.8 12.8 1.0 HD21 A:ASN73 3.9 16.2 1.0 O A:THR71 3.9 14.3 1.0 OD1 A:ASP145 3.9 13.2 1.0 O A:HOH433 3.9 29.1 1.0 HE1 A:HIS171 4.1 16.7 1.0 HB A:THR71 4.2 20.8 1.0 HE2 A:HIS171 4.3 17.3 1.0 HB2 A:PRO144 4.3 15.2 1.0 O A:HOH583 4.5 15.0 1.0 O A:HOH766 4.6 31.5 1.0 ND2 A:ASN73 4.6 13.5 1.0 HD22 A:ASN73 4.7 16.2 1.0 CE1 A:HIS171 4.8 13.9 1.0 NE2 A:HIS171 4.8 14.4 1.0 HG2 A:PRO144 5.0 15.0 1.0 C A:THR71 5.0 13.1 1.0

P.Kumar, P.K.Agarwal, M.B.Waddell, T.Mittag, E.H.Serpersu, M.J.Cuneo. Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of A Catalytic Triad. Angew.Chem.Int.Ed.Engl. V. 58 16260 2019.
ISSN: ESSN 1521-3773
PubMed: 31515870
DOI: 10.1002/ANIE.201908535