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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5vj3:

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

Fluorine Binding Sites:

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 5vj3

Go back to Fluorine Binding Sites List in 5vj3
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 5vj3

Go back to Fluorine Binding Sites List in 5vj3
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 5vj3

Go back to Fluorine Binding Sites List in 5vj3
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

Reference:

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.
Page generated: Tue Jul 15 08:36:38 2025

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