Sodium in PDB 4fm6: Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate

All present enzymatic activity of Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate:
3.4.23.16;

The structure of Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate, PDB code: 4fm6 was solved by C.H.Shen, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.060, 86.140, 46.300, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 23

The structure of Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate (pdb code 4fm6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate, PDB code: 4fm6:

Sodium binding site 1 out of 1 in the Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:24.0 occ:1.00 O B:HOH207 2.2 22.8 1.0 O B:ASP60 2.3 14.8 1.0 O B:HOH223 2.3 21.8 1.0 O B:HOH213 2.5 20.8 1.0 O B:HOH225 2.6 25.9 1.0 O B:HOH238 3.0 31.7 1.0 C B:ASP60 3.3 12.6 1.0 N B:ASP60 3.7 12.2 1.0 CA B:ASP60 3.9 13.4 1.0 O B:ARG41 4.3 17.7 1.0 N B:GLN61 4.3 12.3 1.0 CB B:ASP60 4.4 17.9 1.0 CB B:GLN61 4.4 18.0 1.0 O B:GLN61 4.6 17.2 1.0 N B:ARG41 4.6 19.3 1.0 O B:PRO39 4.6 20.6 1.0 CD1 B:ILE62 4.6 14.3 1.0 C B:TYR59 4.7 9.8 1.0 CA B:GLN61 4.7 11.7 1.0 C B:GLN61 4.7 12.7 1.0 CA B:GLY40 4.8 19.5 1.0 OE1 B:GLN61 4.8 49.0 1.0

C.H.Shen, Y.Tie, X.Yu, Y.F.Wang, A.Y.Kovalevsky, R.W.Harrison, I.T.Weber. Capturing the Reaction Pathway in Near-Atomic-Resolution Crystal Structures of Hiv-1 Protease. Biochemistry V. 51 7726 2012.
ISSN: ISSN 0006-2960
PubMed: 22963370
DOI: 10.1021/BI3008092