Magnesium in PDB 3hav: Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex

The structure of Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex, PDB code: 3hav was solved by P.G.Young, E.N.Baker, S.B.Vakulenko, C.A.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.78 / 2.45
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	128.620, 128.620, 57.870, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 28.4

The binding sites of Magnesium atom in the Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex (pdb code 3hav). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex, PDB code: 3hav:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:79.5 occ:1.00 OD2 A:ASP210 2.7 67.2 1.0 O1G A:ATP401 2.7 65.4 0.6 O2B A:ATP401 2.7 60.5 0.6 O2A A:ATP401 2.7 49.2 1.0 O A:HOH352 2.8 69.3 1.0 CG A:ASP210 2.9 66.5 1.0 O A:HOH321 3.0 53.0 1.0 OD1 A:ASP210 3.3 71.4 1.0 CB A:ASP210 3.6 56.4 1.0 PG A:ATP401 3.9 65.3 0.6 PB A:ATP401 4.0 58.5 0.6 O3G A:ATP401 4.1 60.8 0.6 PA A:ATP401 4.1 62.4 1.0 O A:HOH370 4.3 57.9 1.0 CA A:ASP210 4.4 42.5 1.0 O3B A:ATP401 4.4 83.8 0.6 O3A A:ATP401 4.5 56.9 1.0 NZ A:LYS42 4.7 64.0 1.0 O A:HOH309 4.8 50.8 1.0

Magnesium binding site 2 out of 3 in the Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:0.2 occ:1.00 O2B B:ATP401 2.7 95.2 1.0 OD2 B:ASP210 2.9 88.2 1.0 O1G B:ATP401 2.9 84.1 1.0 CG B:ASP210 3.2 81.6 1.0 OD1 B:ASP210 3.3 87.3 1.0 O2A B:ATP401 3.4 83.0 1.0 O B:HOH320 3.5 67.1 1.0 O B:HOH348 3.6 70.9 1.0 PG B:ATP401 3.9 85.1 1.0 O3G B:ATP401 4.0 83.2 1.0 PB B:ATP401 4.0 91.2 1.0 NC1 B:SRY403 4.2 88.2 0.5 CB B:ASP210 4.2 65.8 1.0 O3B B:ATP401 4.2 0.3 1.0 NB1 B:SRY403 4.3 89.9 0.5 O B:HOH337 4.5 58.0 1.0 CA1 B:SRY403 4.5 88.4 0.5 PA B:ATP401 4.7 86.6 1.0 O3A B:ATP401 4.8 1.0 1.0 O B:HOH357 4.9 54.8 1.0 OD1 B:ASN197 5.0 54.9 1.0

Magnesium binding site 3 out of 3 in the Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Streptomycin-Atp-Aph(2")-Iia Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:38.1 occ:1.00 O2B C:ATP401 2.3 56.0 1.0 O1G C:ATP401 2.4 36.9 1.0 OD2 C:ASP210 2.5 49.4 1.0 OD1 C:ASP210 2.5 48.4 1.0 O2A C:ATP401 2.5 56.5 1.0 CG C:ASP210 2.7 49.4 1.0 PB C:ATP401 3.6 59.3 1.0 PG C:ATP401 3.7 61.8 1.0 PA C:ATP401 3.9 48.5 1.0 O3B C:ATP401 4.0 0.4 1.0 CB C:ASP210 4.1 51.3 1.0 O C:HOH339 4.2 60.2 1.0 O3A C:ATP401 4.2 45.4 1.0 O3G C:ATP401 4.3 62.7 1.0 O C:HOH303 4.3 28.4 1.0 O C:HOH322 4.5 46.0 1.0 O5' C:ATP401 4.6 41.0 1.0 NZ C:LYS42 4.8 34.3 1.0 O1B C:ATP401 4.8 72.3 1.0 O2G C:ATP401 4.9 59.9 1.0

P.G.Young, R.Walanj, V.Lakshmi, L.J.Byrnes, P.Metcalf, E.N.Baker, S.B.Vakulenko, C.A.Smith. The Crystal Structures of Substrate and Nucleotide Complexes of Enterococcus Faecium Aminoglycoside-2''-Phosphotransferase-Iia [Aph(2'')-Iia] Provide Insights Into Substrate Selectivity in the Aph(2'') Subfamily. J.Bacteriol. V. 191 4133 2009.
ISSN: ISSN 0021-9193
PubMed: 19429619
DOI: 10.1128/JB.00149-09