Fluorine in PDB 5vj3: Hiv Protease (Pr) in Open Form with MG2+ in Active Site and Hive-9 in Eye Site

All present enzymatic activity of Hiv Protease (Pr) in Open Form with MG2+ in Active Site and Hive-9 in Eye Site:
3.4.23.16;

The structure of Hiv Protease (Pr) in Open Form with MG2+ in Active Site and Hive-9 in Eye Site, PDB code: 5vj3 was solved by T.Tiefenbrunn, C.D.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.47 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	48.925, 48.925, 103.012, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 27.9

The structure of Hiv Protease (Pr) in Open Form with MG2+ in Active Site and Hive-9 in Eye Site also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the Hiv Protease (Pr) in Open Form with MG2+ in Active Site and Hive-9 in Eye Site (pdb code 5vj3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Hiv Protease (Pr) in Open Form with MG2+ in Active Site and Hive-9 in Eye Site, PDB code: 5vj3:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Hiv Protease (Pr) in Open Form with MG2+ in Active Site and Hive-9 in Eye Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hiv Protease (Pr) in Open Form with MG2+ in Active Site and Hive-9 in Eye Site within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:55.8 occ:0.80 F19 A:HV91101 0.0 55.8 0.8 C18 A:HV91101 1.4 53.7 0.8 F20 A:HV91101 2.2 57.0 0.8 F21 A:HV91101 2.3 38.7 0.8 C17 A:HV91101 2.4 52.0 0.8 C22 A:HV91101 2.8 54.9 0.8 O A:PRO1079 3.1 42.5 1.0 C A:PRO1079 3.3 42.6 1.0 N A:THR1080 3.4 41.1 1.0 CA A:THR1080 3.5 41.5 1.0 CG2 A:ILE1054 3.6 54.7 1.0 N16 A:HV91101 3.6 62.0 0.8 CB A:THR1080 3.7 40.7 1.0 CD A:PRO1079 3.7 39.4 1.0 N A:PRO1079 3.8 36.8 1.0 CG1 A:VAL1056 4.0 45.4 1.0 CA A:PRO1079 4.1 38.9 1.0 C23 A:HV91101 4.1 59.0 0.8 CG A:PRO1079 4.2 40.5 1.0 C A:GLY1078 4.2 35.7 1.0 CG2 A:VAL1032 4.5 41.5 1.0 CB A:ILE1054 4.5 54.7 1.0 O A:GLY1078 4.6 41.7 1.0 OG1 A:THR1080 4.6 41.6 1.0 C15 A:HV91101 4.7 62.1 0.8 CG2 A:THR1080 4.7 37.1 1.0 CB A:PRO1079 4.8 37.7 1.0 CD1 A:ILE1054 4.8 56.5 1.0 CA A:GLY1078 4.8 36.8 1.0 O A:HOH1228 4.9 48.4 1.0 N24 A:HV91101 5.0 55.7 0.8 C A:THR1080 5.0 40.2 1.0

Fluorine binding site 2 out of 3 in the Hiv Protease (Pr) in Open Form with MG2+ in Active Site and Hive-9 in Eye Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hiv Protease (Pr) in Open Form with MG2+ in Active Site and Hive-9 in Eye Site within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:57.0 occ:0.80 F20 A:HV91101 0.0 57.0 0.8 C18 A:HV91101 1.4 53.7 0.8 F19 A:HV91101 2.2 55.8 0.8 F21 A:HV91101 2.2 38.7 0.8 C17 A:HV91101 2.3 52.0 0.8 N16 A:HV91101 2.7 62.0 0.8 CG2 A:VAL1032 3.2 41.5 1.0 C22 A:HV91101 3.4 54.9 0.8 CB A:THR1080 3.7 40.7 1.0 C15 A:HV91101 4.0 62.1 0.8 CG1 A:VAL1056 4.1 45.4 1.0 OG1 A:THR1080 4.2 41.6 1.0 CG1 A:VAL1032 4.2 46.5 1.0 CB A:VAL1032 4.2 48.2 1.0 CA A:THR1080 4.3 41.5 1.0 C23 A:HV91101 4.5 59.0 0.8 CG1 A:ILE1047 4.6 58.6 1.0 CG2 A:THR1080 4.7 37.1 1.0 N A:THR1080 4.7 41.1 1.0 N24 A:HV91101 4.8 55.7 0.8 C25 A:HV91101 4.8 71.2 0.8 N14 A:HV91101 4.9 71.4 0.8 CG2 A:ILE1054 5.0 54.7 1.0 CB A:ILE1047 5.0 60.5 1.0

Fluorine binding site 3 out of 3 in the Hiv Protease (Pr) in Open Form with MG2+ in Active Site and Hive-9 in Eye Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hiv Protease (Pr) in Open Form with MG2+ in Active Site and Hive-9 in Eye Site within 5.0Å range: probe atom residue distance (Å) B Occ A:F1101 b:38.7 occ:0.80 F21 A:HV91101 0.0 38.7 0.8 C18 A:HV91101 1.4 53.7 0.8 F20 A:HV91101 2.2 57.0 0.8 F19 A:HV91101 2.3 55.8 0.8 C17 A:HV91101 2.5 52.0 0.8 N16 A:HV91101 3.0 62.0 0.8 CG2 A:ILE1054 3.1 54.7 1.0 CB A:ILE1054 3.4 54.7 1.0 CG1 A:VAL1056 3.5 45.4 1.0 C22 A:HV91101 3.5 54.9 0.8 CG1 A:ILE1047 3.8 58.6 1.0 CB A:ILE1047 3.8 60.5 1.0 O A:ILE1054 4.2 45.1 1.0 C15 A:HV91101 4.3 62.1 0.8 CG2 A:ILE1047 4.4 61.6 1.0 C A:ILE1054 4.4 47.3 1.0 CD1 A:ILE1054 4.4 56.5 1.0 CA A:ILE1054 4.4 52.9 1.0 CG1 A:ILE1054 4.5 56.2 1.0 C23 A:HV91101 4.6 59.0 0.8 C25 A:HV91101 4.8 71.2 0.8 CB A:VAL1056 5.0 44.0 1.0 N24 A:HV91101 5.0 55.7 0.8

S.Forli, T.Tiefenbrunn, M.M.Baksh, M.W.Chang, A.Perryman, D.Garg, M.Happer, Y.-C.Lin, D.Goodsell, E.L.Angelina, I.De Vera, D.Kojetin, B.E.Torbett, M.G.Finn, J.Elder, C.D.Stout, A.Olson. Fragment-Based Campaign For the Identification of Potential Exosite Binders of Hiv-1 Protease To Be Published.