Sodium in PDB 3zso: Small Molecule Inhibitors of the Ledgf Site of Hiv Type 1 Integrase Identified By Fragment Screening and Structure Based Design

The structure of Small Molecule Inhibitors of the Ledgf Site of Hiv Type 1 Integrase Identified By Fragment Screening and Structure Based Design, PDB code: 3zso was solved by T.S.Peat, J.Newman, D.I.Rhodes, J.J.Deadman, N.Vandergraaff, G.Le, E.D.Jones, J.A.Smith, J.A.V.Coates, N.Thienthong, O.Dolezal, J.H.Ryan, G.P.Savage, C.L.Francis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.54 / 1.75
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	71.063, 71.063, 67.027, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 20.9

The binding sites of Sodium atom in the Small Molecule Inhibitors of the Ledgf Site of Hiv Type 1 Integrase Identified By Fragment Screening and Structure Based Design (pdb code 3zso). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Small Molecule Inhibitors of the Ledgf Site of Hiv Type 1 Integrase Identified By Fragment Screening and Structure Based Design, PDB code: 3zso:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Small Molecule Inhibitors of the Ledgf Site of Hiv Type 1 Integrase Identified By Fragment Screening and Structure Based Design


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Small Molecule Inhibitors of the Ledgf Site of Hiv Type 1 Integrase Identified By Fragment Screening and Structure Based Design within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1218 b:48.2 occ:1.00 O1 A:SO41214 1.5 46.3 0.7 O A:HOH2026 1.6 30.0 1.0 S A:SO41214 2.8 47.9 0.7 O4 A:SO41214 3.3 50.4 0.7 O A:HOH2025 3.3 37.7 1.0 O3 A:SO41214 3.5 34.0 0.7 N A:GLN95 3.8 16.3 1.0 O2 A:SO41214 3.9 44.7 0.7 CG A:GLN95 4.1 27.5 1.0 OG1 A:THR125 4.1 25.1 1.0 N A:GLY94 4.1 20.0 1.0 CA A:GLY94 4.3 18.5 1.0 OE1 A:GLN95 4.4 33.0 0.7 C A:GLY94 4.4 18.2 1.0 CB A:GLN95 4.6 20.6 1.0 CB A:THR125 4.7 21.3 1.0 CA A:GLN95 4.7 17.8 1.0 CD A:GLN95 4.8 27.5 0.7

Sodium binding site 2 out of 2 in the Small Molecule Inhibitors of the Ledgf Site of Hiv Type 1 Integrase Identified By Fragment Screening and Structure Based Design


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Small Molecule Inhibitors of the Ledgf Site of Hiv Type 1 Integrase Identified By Fragment Screening and Structure Based Design within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1216 b:45.5 occ:1.00 O2 B:SO41214 1.6 42.9 0.7 O B:HOH2025 1.6 30.4 1.0 S B:SO41214 2.9 46.9 0.7 O B:HOH2026 3.1 39.2 1.0 O4 B:SO41214 3.5 45.6 0.7 O1 B:SO41214 3.5 27.8 0.7 N B:GLN95 3.7 16.4 1.0 O B:HOH2027 3.8 48.4 1.0 OG1 B:THR125 3.9 22.3 0.5 O3 B:SO41214 4.0 39.7 0.7 CG B:GLN95 4.0 24.6 0.7 OG1 B:THR125 4.1 19.0 0.5 CG2 B:THR125 4.2 21.6 0.5 N B:GLY94 4.2 20.4 1.0 NE2 B:GLN95 4.2 29.8 0.7 CA B:GLY94 4.3 18.2 1.0 C B:GLY94 4.4 18.6 1.0 CB B:GLN95 4.4 20.5 1.0 CA B:GLN95 4.6 17.1 1.0 CB B:THR125 4.7 17.9 0.5 CD B:GLN95 4.7 27.1 0.7 CB B:THR125 4.7 19.1 0.5 CB B:THR93 5.0 18.2 1.0

T.S.Peat, D.I.Rhodes, N.Vandegraaff, G.Le, J.A.Smith, L.J.Clark, E.D.Jones, J.A.V.Coates, N.Thienthong, J.Newman, O.Dolezal, R.Mulder, J.H.Ryan, G.P.Savage, C.L.Francis, J.J.Deadman. Small Molecule Inhibitors of the Ledgf Site of Human Immunodeficiency Virus Integrase Identified By Fragment Screening and Structure Based Design. Plos One V. 7 40147 2012.
ISSN: ESSN 1932-6203
PubMed: 22808106
DOI: 10.1371/JOURNAL.PONE.0040147