Sodium in PDB 1nd4: Crystal Structure of Aminoglycoside-3'-Phosphotransferase- Iia

All present enzymatic activity of Crystal Structure of Aminoglycoside-3'-Phosphotransferase- Iia:
2.7.1.95;

The structure of Crystal Structure of Aminoglycoside-3'-Phosphotransferase- Iia, PDB code: 1nd4 was solved by D.Nurizzo, S.C.Shewry, E.N.Baker, C.A.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.048, 101.893, 71.972, 90.00, 105.58, 90.00
R / Rfree (%)	20.6 / 23.8

The structure of Crystal Structure of Aminoglycoside-3'-Phosphotransferase- Iia also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Aminoglycoside-3'-Phosphotransferase- Iia (pdb code 1nd4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Aminoglycoside-3'-Phosphotransferase- Iia, PDB code: 1nd4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Aminoglycoside-3'-Phosphotransferase- Iia


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Aminoglycoside-3'-Phosphotransferase- Iia within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1600 b:52.4 occ:1.00 O6 A:KAN1300 2.3 44.5 1.0 O A:HOH1637 2.4 44.7 1.0 SG A:CYS192 2.5 31.1 0.5 O7 A:KAN1300 2.7 46.1 1.0 C2 A:KAN1300 3.2 45.1 1.0 C3 A:KAN1300 3.4 45.3 1.0 OD1 A:ASP190 3.5 30.1 1.0 CB A:CYS192 3.5 27.5 0.5 ND2 A:ASN195 3.8 24.8 1.0 O A:HOH1688 3.9 30.7 1.0 OD2 A:ASP190 3.9 31.5 1.0 CG A:ASP190 4.0 25.2 1.0 O A:HOH1627 4.0 28.1 1.0 O A:HOH1645 4.2 41.8 1.0 CG A:PRO194 4.2 29.3 1.0 MG A:MG400 4.5 46.5 1.0 CG A:ASN195 4.5 26.0 1.0 C1 A:KAN1300 4.6 44.2 1.0 OD1 A:ASN195 4.7 25.2 1.0 C4 A:KAN1300 4.8 45.7 1.0 O A:ASP190 4.8 23.1 1.0 O9 A:KAN1300 4.9 42.8 1.0 CA A:CYS192 5.0 27.3 0.5 O A:HOH1794 5.0 46.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Aminoglycoside-3'-Phosphotransferase- Iia


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Aminoglycoside-3'-Phosphotransferase- Iia within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2600 b:46.7 occ:1.00 SG B:CYS192 2.2 34.4 0.5 O6 B:KAN2300 2.6 48.1 1.0 OD1 B:ASP190 2.7 31.0 1.0 O7 B:KAN2300 2.9 50.7 1.0 CB B:CYS192 2.9 29.1 0.5 O B:HOH2697 3.4 46.9 1.0 CG B:ASP190 3.6 30.8 1.0 C2 B:KAN2300 3.6 50.5 1.0 ND2 B:ASN195 3.6 21.2 1.0 C3 B:KAN2300 3.6 50.4 1.0 OD2 B:ASP190 3.8 32.3 1.0 O B:HOH2646 3.9 44.7 1.0 O B:HOH2612 4.0 35.1 1.0 O B:HOH2670 4.0 44.2 1.0 O B:ASP190 4.2 27.3 1.0 CA B:CYS192 4.3 28.2 0.5 CG B:PRO194 4.4 25.6 1.0 CG B:ASN195 4.4 22.9 1.0 N B:CYS192 4.4 28.9 0.5 O B:HOH2636 4.5 48.5 1.0 OD1 B:ASN195 4.8 22.7 1.0 CB B:ASP190 4.8 27.5 1.0 C B:ASP190 4.9 26.8 1.0 C1 B:KAN2300 4.9 50.4 1.0 CD B:PRO194 4.9 23.7 1.0 MG B:MG400 4.9 51.3 1.0

D.Nurizzo, S.C.Shewry, M.H.Perlin, S.A.Brown, J.N.Dholakia, R.L.Fuchs, T.Deva, E.N.Baker, C.A.Smith. The Crystal Structure of Aminoglycoside-3'-Phosphotransferase-Iia, An Enzyme Responsible For Antibiotic Resistance J.Mol.Biol. V. 327 491 2003.
ISSN: ISSN 0022-2836
PubMed: 12628253
DOI: 10.1016/S0022-2836(03)00121-9