Magnesium in PDB 3w0s: Crystal Structure of Aminoglycoside Phosphotransferase Aph(4)-Ia, Ternary Complex with Amp-Pnp and Hygromycin B

All present enzymatic activity of Crystal Structure of Aminoglycoside Phosphotransferase Aph(4)-Ia, Ternary Complex with Amp-Pnp and Hygromycin B:
2.7.1.163;

The structure of Crystal Structure of Aminoglycoside Phosphotransferase Aph(4)-Ia, Ternary Complex with Amp-Pnp and Hygromycin B, PDB code: 3w0s was solved by D.Iino, Y.Takakura, K.Fukano, Y.Sasaki, T.Hoshino, K.Ohsawa, A.Nakamura, S.Yajima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.50 / 1.77
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.025, 70.025, 124.187, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 19.8

The binding sites of Magnesium atom in the Crystal Structure of Aminoglycoside Phosphotransferase Aph(4)-Ia, Ternary Complex with Amp-Pnp and Hygromycin B (pdb code 3w0s). 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 Aminoglycoside Phosphotransferase Aph(4)-Ia, Ternary Complex with Amp-Pnp and Hygromycin B, PDB code: 3w0s:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Aminoglycoside Phosphotransferase Aph(4)-Ia, Ternary Complex with Amp-Pnp and Hygromycin B


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 Aminoglycoside Phosphotransferase Aph(4)-Ia, Ternary Complex with Amp-Pnp and Hygromycin B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:40.9 occ:1.00 O2A A:ANP402 2.1 25.9 1.0 O A:HOH1198 2.1 33.9 1.0 O1G A:ANP402 2.2 25.8 1.0 O A:HOH1312 2.2 44.9 1.0 O1B A:ANP402 2.2 25.5 1.0 O A:HOH1302 2.3 41.6 1.0 PB A:ANP402 3.2 23.9 1.0 PA A:ANP402 3.3 24.6 1.0 PG A:ANP402 3.3 26.1 1.0 N3B A:ANP402 3.6 24.6 1.0 O3A A:ANP402 3.6 24.9 1.0 O2G A:ANP402 3.7 30.7 1.0 O5' A:ANP402 4.1 23.9 1.0 O1A A:ANP402 4.4 24.9 1.0 O3G A:ANP402 4.5 26.2 1.0 OG A:SER29 4.6 39.4 1.0 O2B A:ANP402 4.6 18.9 1.0 O A:HOH1226 4.7 32.2 1.0 CB A:SER29 4.7 33.5 1.0 O A:HOH1168 4.9 34.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Aminoglycoside Phosphotransferase Aph(4)-Ia, Ternary Complex with Amp-Pnp and Hygromycin B


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 Aminoglycoside Phosphotransferase Aph(4)-Ia, Ternary Complex with Amp-Pnp and Hygromycin B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:19.1 occ:1.00 O A:HOH1111 2.3 17.7 1.0 OD1 A:ASN202 2.3 19.3 1.0 O14 A:HY0401 2.5 15.7 1.0 O11 A:HY0401 2.6 16.3 1.0 O29 A:HY0401 2.7 17.4 1.0 O18 A:HY0401 2.7 15.8 1.0 O21 A:HY0401 2.8 18.2 1.0 O30 A:HY0401 2.9 17.7 1.0 C13 A:HY0401 3.0 16.1 1.0 CG A:ASN202 3.1 16.4 1.0 C12 A:HY0401 3.3 16.2 1.0 C5 A:HY0401 3.4 18.2 1.0 ND2 A:ASN202 3.4 15.6 1.0 C16 A:HY0401 3.5 16.1 1.0 C15 A:HY0401 3.5 17.3 1.0 C6 A:HY0401 3.6 17.1 1.0 C24 A:HY0401 3.6 19.8 1.0 C23 A:HY0401 3.6 19.1 1.0 C17 A:HY0401 3.8 15.8 1.0 C19 A:HY0401 4.1 16.4 1.0 O22 A:HY0401 4.1 17.2 1.0 O A:HOH1192 4.2 26.9 1.0 OG A:SER201 4.2 17.2 1.0 CB A:ASN202 4.2 16.3 1.0 C25 A:HY0401 4.3 19.6 1.0 OD1 A:ASP198 4.4 17.9 1.0 O A:HOH1226 4.4 32.2 1.0 O2G A:ANP402 4.6 30.7 1.0 OE1 A:GLN101 4.8 18.8 1.0 C4 A:HY0401 4.8 17.6 1.0 O20 A:HY0401 4.8 17.6 1.0 O28 A:HY0401 4.8 17.8 1.0 C1 A:HY0401 4.9 18.3 1.0 N A:ASN202 5.0 15.9 1.0 O31 A:HY0401 5.0 18.4 1.0

D.Iino, Y.Takakura, K.Fukano, Y.Sasaki, T.Hoshino, K.Ohsawa, A.Nakamura, S.Yajima. Crystal Structures of the Ternary Complex of Aph(4)-Ia/Hph with Hygromycin B and An Atp Analog Using A Thermostable Mutant. J.Struct.Biol. V. 183 76 2013.
ISSN: ISSN 1047-8477
PubMed: 23747390
DOI: 10.1016/J.JSB.2013.05.023