Magnesium in PDB 6np5: Aac-Via Bound to Kanamycin B

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

The structure of Aac-Via Bound to Kanamycin B, PDB code: 6np5 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)	43.21 / 1.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.746, 86.429, 50.119, 90.00, 119.75, 90.00
R / Rfree (%)	12.2 / 14

The binding sites of Magnesium atom in the Aac-Via Bound to Kanamycin B (pdb code 6np5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Aac-Via Bound to Kanamycin B, PDB code: 6np5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Aac-Via Bound to Kanamycin B


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 Kanamycin B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:36.3 occ:0.50 O A:HOH406 1.2 43.4 1.0 O A:HOH521 1.9 17.7 1.0 O A:HOH796 2.2 29.3 1.0 O A:HOH680 2.6 30.7 1.0 OD2 A:ASP145 2.9 18.4 1.0 CG A:ASP145 3.7 16.9 1.0 OD1 A:ASP145 3.7 17.6 1.0 HD21 A:ASN73 3.8 19.5 1.0 O A:THR71 3.8 18.5 1.0 O A:HOH455 4.1 39.5 1.0 HB2 A:PRO144 4.1 20.0 1.0 HB A:THR71 4.2 25.4 1.0 HE1 A:HIS171 4.2 21.9 1.0 HE2 A:HIS171 4.3 21.9 1.0 ND2 A:ASN73 4.6 16.2 1.0 O A:HOH584 4.6 17.8 1.0 HD22 A:ASN73 4.7 19.5 1.0 O A:HOH748 4.8 31.4 1.0 HG2 A:PRO144 4.8 19.7 1.0 CE1 A:HIS171 4.9 18.2 1.0 NE2 A:HIS171 4.9 18.2 1.0 C A:THR71 4.9 17.2 1.0 CB A:PRO144 5.0 16.6 1.0

Magnesium binding site 2 out of 2 in the Aac-Via Bound to Kanamycin B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Aac-Via Bound to Kanamycin B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:61.4 occ:1.00 O A:HOH692 2.0 42.0 1.0 O A:HOH787 2.0 60.2 1.0 O A:HOH730 2.0 57.8 1.0 O A:HOH539 2.1 30.0 1.0 O A:HOH659 2.1 56.7 1.0 O A:HOH705 2.2 47.9 1.0 HA A:THR125 3.8 28.4 1.0 O A:HOH463 3.9 42.9 1.0 O A:HOH722 4.1 50.5 1.0 O A:ARG124 4.3 21.6 1.0 O A:HOH461 4.3 34.4 1.0 O A:THR125 4.5 25.6 1.0 O A:TYR126 4.5 22.4 1.0 O A:HOH498 4.5 30.0 1.0 HA A:PRO127 4.5 30.9 1.0 HB3 A:CYS129 4.7 22.8 1.0 H A:GLY128 4.7 28.9 1.0 CA A:THR125 4.7 23.6 1.0 C A:THR125 4.7 24.1 1.0 O A:CYS129 4.9 24.5 1.0 O A:HOH573 5.0 26.7 1.0 O A:ASP108 5.0 27.5 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