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Iodine in PDB 3s53: Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121

Enzymatic activity of Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121

All present enzymatic activity of Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121, PDB code: 3s53 was solved by Y.-F.Tie, Y.-F.Wang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 28.931, 66.090, 92.833, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25.9

Iodine Binding Sites:

The binding sites of Iodine atom in the Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121 (pdb code 3s53). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121, PDB code: 3s53:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 3s53

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Iodine binding site 1 out of 10 in the Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I902

b:16.4
occ:0.80
 O A:HOH1086 3.2 25.6 1.0
N A:THR12 3.7 9.0 1.0
OG1 A:THR12 3.9 17.0 1.0
CA A:VAL11 4.0 6.9 1.0
CB A:VAL11 4.0 10.2 1.0
CG2 A:THR12 4.2 9.2 1.0
CB A:ALA67 4.3 14.5 1.0
CG1 A:VAL11 4.3 11.6 1.0
C A:VAL11 4.4 7.2 1.0
CA A:ALA67 4.4 17.3 1.0
CB A:THR12 4.5 9.6 1.0
CA A:THR12 4.7 9.2 1.0
O A:LEU10 4.9 8.8 1.0

Iodine binding site 2 out of 10 in 3s53

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Iodine binding site 2 out of 10 in the Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I903

b:12.6
occ:0.50
 O A:HOH1065 3.0 11.0 1.0
O A:HOH1037 3.1 29.5 1.0
NZ A:LYS7 3.6 9.7 0.3
CE A:LYS7 4.0 11.4 0.7
CD A:LYS7 4.2 9.2 0.7
CE A:LYS7 4.4 11.7 0.3
NZ A:LYS7 4.6 30.1 0.7
CD A:LYS7 4.7 8.1 0.3

Iodine binding site 3 out of 10 in 3s53

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Iodine binding site 3 out of 10 in the Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I904

b:24.2
occ:0.50
 NE A:ARG57 3.6 17.2 1.0
O A:HOH1003 3.6 12.8 1.0
NH2 A:ARG57 3.9 26.2 1.0
O A:HOH1107 4.0 33.9 1.0
CZ A:ARG57 4.2 28.2 1.0
CH2 A:TRP42 4.4 23.8 1.0
CG A:ARG57 4.4 11.0 1.0
CD A:ARG57 4.6 15.0 1.0
O A:HOH1106 4.8 34.0 1.0
CZ3 A:TRP42 4.9 14.7 1.0
O A:LYS55 5.0 11.9 1.0

Iodine binding site 4 out of 10 in 3s53

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Iodine binding site 4 out of 10 in the Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I905

b:10.3
occ:0.50
 OG1 A:THR12 3.3 17.0 1.0
N A:GLY68 3.5 13.7 1.0
CG A:GLU65 3.7 16.0 1.0
CB A:GLU65 3.9 10.1 1.0
O A:THR12 3.9 11.5 1.0
N A:ALA67 4.0 14.8 1.0
O A:GLU65 4.0 12.5 1.0
CB A:THR12 4.1 9.6 1.0
C A:THR12 4.2 8.8 1.0
C A:GLU65 4.2 10.2 1.0
CA A:GLY68 4.2 15.3 1.0
N A:LYS14 4.4 10.6 1.0
CA A:ILE13 4.4 14.9 1.0
C A:ILE13 4.4 15.1 1.0
CA A:ALA67 4.4 17.3 1.0
C A:ALA67 4.4 18.1 1.0
N A:ILE13 4.5 9.1 1.0
CB A:LYS14 4.5 11.6 1.0
N A:ILE66 4.6 8.5 1.0
C A:ILE66 4.6 11.1 1.0
CD1 A:LEU19 4.6 25.2 1.0
CA A:GLU65 4.7 11.1 1.0
CA A:ILE66 4.8 7.7 1.0
CA A:THR12 4.8 9.2 1.0
O A:ILE13 5.0 12.1 1.0

Iodine binding site 5 out of 10 in 3s53

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Iodine binding site 5 out of 10 in the Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I906

b:23.3
occ:0.50
 ND2 A:ASN83 3.5 10.8 1.0
O A:GLU35 3.9 19.9 1.0
N A:GLU35 4.0 15.3 1.0
OD1 A:ASN83 4.1 12.7 1.0
CE A:LYS20 4.1 29.5 1.0
CG A:ASN83 4.2 11.3 1.0
CB A:GLU34 4.3 10.3 1.0
O A:HOH1007 4.3 13.2 1.0
CD A:LYS20 4.4 22.9 1.0
N A:GLU34 4.4 6.9 1.0
CB A:GLU35 4.5 27.6 1.0
CG A:LYS20 4.6 28.0 1.0
CA A:GLU35 4.6 23.9 1.0
C A:GLU35 4.7 22.1 1.0
CA A:GLU34 4.7 10.8 1.0
C A:GLU34 4.7 9.1 1.0
OE2 A:GLU34 4.7 20.3 1.0
OE1 A:GLU35 4.8 45.3 1.0

Iodine binding site 6 out of 10 in 3s53

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Iodine binding site 6 out of 10 in the Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I910

b:26.6
occ:0.20
 O A:HOH1126 2.2 31.5 1.0
N A:ASN83 3.3 12.1 1.0
CG A:ASN83 3.7 11.3 1.0
CG1 A:ILE82 3.9 16.5 1.0
ND2 A:ASN83 3.9 10.8 1.0
CA A:ILE82 3.9 11.3 1.0
OD1 A:ASN83 4.0 12.7 1.0
CB A:ASN83 4.0 7.5 1.0
C A:ILE82 4.1 16.5 1.0
CA A:ASN83 4.2 7.4 1.0
CB A:ILE82 4.4 15.5 1.0
O A:GLU21 4.5 9.4 1.0
O A:HOH1007 4.6 13.2 1.0
OE2 A:GLU34 4.6 20.3 1.0
CD A:GLU34 4.8 23.6 1.0
OE1 A:GLU34 4.8 25.6 1.0
O A:HOH1110 4.9 36.5 1.0

Iodine binding site 7 out of 10 in 3s53

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Iodine binding site 7 out of 10 in the Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I901

b:16.1
occ:0.50
 N B:LYS55 3.6 14.0 1.0
CG B:PRO79 4.0 15.1 1.0
CB B:LYS55 4.1 10.8 1.0
CA B:ILE54 4.1 15.6 1.0
CB B:ILE54 4.3 20.1 1.0
CG B:LYS55 4.4 14.9 1.0
CA B:LYS55 4.4 13.2 1.0
C B:ILE54 4.4 9.5 1.0
CD B:LYS55 4.5 28.8 1.0
CG2 B:ILE54 4.5 19.3 1.0
O B:LYS55 4.7 14.7 1.0
CD B:PRO79 4.7 11.2 1.0

Iodine binding site 8 out of 10 in 3s53

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Iodine binding site 8 out of 10 in the Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I907

b:25.5
occ:0.50
 OE2 B:GLU65 2.3 50.8 1.0
O B:HOH1049 3.2 24.4 1.0
CD B:GLU65 3.4 34.4 1.0
CB B:GLU65 3.8 11.2 1.0
CG2 B:ILE63 3.9 23.6 1.0
CG B:LYS70 4.0 19.5 1.0
CG B:GLU65 4.1 20.4 1.0
CD B:LYS70 4.2 26.0 1.0
CB B:LYS70 4.2 16.1 1.0
OE1 B:GLU65 4.3 35.5 1.0
CA B:GLU65 4.4 8.0 1.0
N B:GLU65 4.5 5.4 1.0
CA B:LYS70 4.6 10.0 1.0
C B:ILE64 4.9 13.6 1.0
CE B:LYS70 5.0 34.6 1.0

Iodine binding site 9 out of 10 in 3s53

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Iodine binding site 9 out of 10 in the Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I908

b:18.9
occ:0.70
 O B:HOH1094 3.4 21.2 0.5
N B:GLY68 3.5 14.9 1.0
OG1 B:THR12 3.7 7.0 0.4
CG2 B:THR12 3.8 10.6 0.6
CG B:GLU65 3.8 20.4 1.0
O B:THR12 3.9 11.0 1.0
N B:ALA67 4.0 10.4 1.0
O B:GLU65 4.0 9.6 1.0
N B:LYS14 4.0 6.5 1.0
CB B:GLU65 4.1 11.2 1.0
C B:ILE13 4.1 8.5 1.0
CA B:ILE13 4.2 7.8 1.0
C B:THR12 4.2 8.2 1.0
CA B:ALA67 4.2 16.1 1.0
CA B:GLY68 4.3 11.0 1.0
C B:GLU65 4.3 11.3 1.0
C B:ALA67 4.3 18.4 1.0
N B:ILE13 4.3 7.8 1.0
CB B:LYS14 4.4 8.2 1.0
CB B:THR12 4.4 8.9 0.4
CB B:THR12 4.4 10.8 0.6
CD2 B:LEU19 4.6 21.8 1.0
O B:ILE13 4.7 9.5 1.0
C B:ILE66 4.7 10.5 1.0
N B:ILE66 4.8 6.7 1.0
CA B:LYS14 4.8 9.0 1.0
CA B:GLU65 4.8 8.0 1.0
CA B:THR12 5.0 6.7 0.4
CA B:ILE66 5.0 7.4 1.0
CA B:THR12 5.0 5.9 0.6

Iodine binding site 10 out of 10 in 3s53

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Iodine binding site 10 out of 10 in the Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Hiv-1 Protease Triple Mutants V32I, I47V, V82I with Antiviral Drug Darunavir in Space Group P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I909

b:32.8
occ:0.30
 O10 B:017203 1.3 32.6 0.3
S8 B:017203 1.4 25.5 0.3
O9 B:017203 1.6 20.1 0.3
O B:HOH1125 2.1 22.8 0.7
N11 B:017203 2.3 20.6 0.3
C5 B:017203 3.2 9.4 0.3
C16 B:017203 3.4 20.7 0.3
O B:HOH1072 3.5 14.1 1.0
C12 B:017203 3.5 25.9 0.3
NH2 B:ARG57 3.9 21.9 1.0
O22 B:017203 4.0 21.0 0.3
NE B:ARG57 4.0 22.5 1.0
C6 B:017203 4.0 3.9 0.3
C17 B:017203 4.0 22.6 0.3
C14 B:017203 4.1 45.4 0.3
C4 B:017203 4.2 3.6 0.3
CH2 B:TRP42 4.2 10.6 1.0
C13 B:017203 4.5 30.7 0.3
CZ B:ARG57 4.5 31.3 1.0
CZ2 B:TRP42 4.6 13.7 1.0
C21 B:017203 4.8 26.0 0.3
C19 B:017203 4.9 29.0 0.3

Reference:

Y.Tie, Y.F.Wang, P.I.Boross, T.Y.Chiu, A.K.Ghosh, J.Tozser, J.M.Louis, R.W.Harrison, I.T.Weber. Critical Differences in Hiv-1 and Hiv-2 Protease Specificity For Clinical Inhibitors. Protein Sci. V. 21 339 2012.
ISSN: ISSN 0961-8368
PubMed: 22238126
DOI: 10.1002/PRO.2019
Page generated: Sun Aug 11 16:36:30 2024

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