Atomistry » Sodium » PDB 3wxt-3zu5 » 3zso
Atomistry »
  Sodium »
    PDB 3wxt-3zu5 »
      3zso »

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

Protein crystallography data

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

Sodium Binding Sites:

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 3zso

Go back to Sodium Binding Sites List in 3zso
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 3zso

Go back to Sodium Binding Sites List in 3zso
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

Reference:

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
Page generated: Mon Oct 7 14:10:09 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy