Sodium in PDB 4zip: Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand)

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand):
3.4.23.16;

The structure of Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand), PDB code: 4zip was solved by Y.-F.Wang, J.Agniswamy, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.11
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.000, 86.280, 46.130, 90.00, 90.00, 90.00
R / Rfree (%)	13 / 15.5

The structure of Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand) also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand) (pdb code 4zip). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand), PDB code: 4zip:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:16.5 occ:1.00 O A:HOH640 2.3 15.7 1.0 O A:ASP60 2.4 12.0 1.0 O A:HOH642 2.4 25.5 1.0 O A:HOH656 2.4 19.9 1.0 O A:HOH628 2.4 16.1 1.0 O A:HOH691 2.7 21.8 1.0 C A:ASP60 3.4 11.1 1.0 N A:ASP60 3.8 10.0 1.0 CA A:ASP60 4.0 11.9 1.0 O A:HOH650 4.1 19.9 0.5 O A:ARG41 4.2 12.7 1.0 CB A:ASP60 4.4 13.4 1.0 CB A:GLN61 4.4 14.1 1.0 N A:GLN61 4.4 11.4 1.0 N A:ARG41 4.5 15.7 1.0 O A:GLN61 4.6 13.8 1.0 O A:HOH661 4.6 23.1 0.5 CD1 A:ILE62 4.6 12.0 1.0 O A:PRO39 4.7 16.7 1.0 C A:TYR59 4.7 8.2 1.0 CA A:GLN61 4.7 11.4 1.0 C A:GLN61 4.7 11.4 1.0 OE1 A:GLN61 4.8 44.8 1.0 CA A:GLY40 4.9 17.9 1.0

Sodium binding site 2 out of 3 in the Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:15.9 occ:0.50 O B:HOH327 2.4 20.1 1.0 O B:HOH414 2.4 25.0 0.2 O B:ASP60 2.4 11.6 1.0 O B:HOH381 2.7 22.4 0.5 O B:HOH337 2.7 14.9 0.5 C B:ASP60 3.5 10.2 1.0 N B:ASP60 3.7 10.2 1.0 O B:HOH380 4.0 30.2 1.0 CA B:ASP60 4.0 10.1 1.0 O B:ARG41 4.3 11.9 1.0 CB B:ASP60 4.3 11.4 1.0 O B:HOH400 4.4 27.5 0.5 O B:PRO39 4.6 12.7 1.0 N B:GLN61 4.6 10.0 1.0 C B:TYR59 4.6 8.4 1.0 CD1 B:ILE62 4.6 11.2 1.0 CB B:GLN61 4.7 11.7 1.0 O B:GLN61 4.9 14.0 1.0 C B:GLN61 4.9 10.1 1.0 CA B:TYR59 4.9 8.2 1.0 CA B:GLN61 5.0 10.4 1.0 CA B:GLY40 5.0 10.6 1.0 N B:ARG41 5.0 9.7 1.0

Sodium binding site 3 out of 3 in the Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:25.3 occ:0.50 O B:HOH307 2.3 24.4 0.5 O B:HOH314 2.3 22.3 0.5 O B:HOH408 2.4 33.1 0.5 O B:HOH331 2.4 28.6 1.0 O B:HOH436 2.6 28.1 0.5 O B:HOH320 2.8 15.1 1.0 OH B:TYR59 3.8 12.1 1.0 CA B:SER37 4.1 16.6 0.5 CA B:SER37 4.1 16.6 0.5 OG B:SER37 4.1 30.3 0.5 OG B:SER37 4.2 33.7 0.5 O B:HOH311 4.3 15.2 1.0 NH2 B:ARG57 4.3 17.9 1.0 O B:LEU38 4.3 12.7 1.0 N B:LEU38 4.3 12.5 1.0 CB B:SER37 4.4 21.6 0.5 CB B:SER37 4.5 21.7 0.5 O B:MET36 4.6 14.4 1.0 O B:HOH328 4.8 22.0 0.5 C B:SER37 4.8 14.7 1.0 CZ B:TYR59 4.9 10.2 1.0

A.K.Ghosh, J.Takayama, L.A.Kassekert, J.R.Ella-Menye, S.Yashchuk, J.Agniswamy, Y.F.Wang, M.Aoki, M.Amano, I.T.Weber, H.Mitsuya. Structure-Based Design, Synthesis, X-Ray Studies, and Biological Evaluation of Novel Hiv-1 Protease Inhibitors Containing Isophthalamide-Derived P2-Ligands. Bioorg.Med.Chem.Lett. V. 25 4903 2015.
ISSN: ESSN 1464-3405
PubMed: 26096678
DOI: 10.1016/J.BMCL.2015.05.052