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

Enzymatic activity of 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;

Protein crystallography data

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

Magnesium Binding Sites:

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 3w0s

Go back to Magnesium Binding Sites List in 3w0s
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 3w0s

Go back to Magnesium Binding Sites List in 3w0s
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

Reference:

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
Page generated: Thu Aug 15 13:10:12 2024

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