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Iodine in PDB 3nuo: Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir

Enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir

All present enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir, PDB code: 3nuo 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 / 1.35
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.940, 86.590, 46.130, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 19.9

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir (pdb code 3nuo). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 19 binding sites of Iodine where determined in the Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir, PDB code: 3nuo:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 19 in 3nuo

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Iodine binding site 1 out of 19 in the Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I500

b:16.2
occ:0.50
 O A:HOH1171 2.8 39.9 1.0
N A:THR74 3.6 13.8 1.0
ND2 A:ASN88 3.7 14.2 1.0
OG1 A:THR74 3.8 19.4 1.0
CB A:THR74 4.0 16.4 1.0
CB A:ASN88 4.1 11.6 1.0
CA A:GLY73 4.1 13.2 1.0
C A:GLY73 4.4 13.4 1.0
O A:HOH1044 4.4 27.7 1.0
CG A:ASN88 4.4 11.4 1.0
CA A:THR74 4.4 13.4 1.0
O A:ASN88 5.0 12.8 1.0

Iodine binding site 2 out of 19 in 3nuo

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Iodine binding site 2 out of 19 in the Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I506

b:52.1
occ:0.50
 I A:IOD507 2.0 74.7 0.5
O A:HOH1044 3.5 27.7 1.0
CG A:GLN61 3.7 34.1 1.0
O A:HOH1116 3.8 39.0 1.0
CA A:GLN61 4.0 16.9 1.0
CG1 A:ILE72 4.2 19.3 1.0
CB A:GLN61 4.3 26.9 1.0
N A:GLN61 4.3 15.2 1.0
CG2 A:ILE72 4.3 22.3 1.0
CA A:GLY73 4.4 13.2 1.0
CD1 A:ILE72 4.5 23.4 1.0
N A:GLY73 4.6 12.2 1.0
CD A:GLN61 4.7 42.8 1.0
C A:ILE72 4.7 12.7 1.0
O A:ILE72 4.8 13.4 1.0
CB A:ILE72 4.8 16.5 1.0
NE2 A:GLN61 4.9 65.8 1.0
O A:HOH1165 4.9 41.2 0.5

Iodine binding site 3 out of 19 in 3nuo

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Iodine binding site 3 out of 19 in the Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I507

b:74.7
occ:0.50
 I A:IOD506 2.0 52.1 0.5
O A:HOH1116 2.2 39.0 1.0
O A:HOH1165 4.1 41.2 0.5
CG2 A:ILE72 4.1 22.3 1.0
CD1 A:ILE72 4.4 23.4 1.0
CG A:GLN61 4.4 34.1 1.0
CG1 A:ILE72 4.6 19.3 1.0
CD A:GLN61 5.0 42.8 1.0

Iodine binding site 4 out of 19 in 3nuo

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Iodine binding site 4 out of 19 in the Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I512

b:43.1
occ:0.50
 O A:THR12 3.6 20.9 1.0
N A:GLY68 3.6 28.1 1.0
O A:GLU65 3.7 22.7 1.0
N A:ALA67 4.0 25.7 1.0
CD A:GLU65 4.1 58.1 1.0
CG A:GLU65 4.1 43.4 1.0
OE1 A:GLU65 4.1 72.8 1.0
C A:GLU65 4.1 19.8 1.0
C A:THR12 4.1 17.1 1.0
N A:LYS14 4.2 16.4 1.0
CA A:ILE13 4.2 17.1 1.0
CB A:GLU65 4.2 26.2 1.0
CA A:ALA67 4.2 26.9 1.0
C A:ILE13 4.3 17.6 1.0
C A:ALA67 4.4 26.6 1.0
CA A:GLY68 4.4 33.1 1.0
N A:ILE13 4.5 17.0 1.0
OE2 A:GLU65 4.6 78.3 1.0
N A:ILE66 4.6 19.5 1.0
C A:ILE66 4.6 23.1 1.0
CB A:LYS14 4.6 21.2 1.0
O A:HOH1203 4.7 47.8 1.0
CG2 A:THR12 4.7 24.6 1.0
CB A:THR12 4.8 22.2 1.0
CA A:GLU65 4.8 19.4 1.0
O A:ILE13 4.9 18.9 1.0
CA A:ILE66 4.9 19.5 1.0
CD2 A:LEU19 5.0 34.6 1.0

Iodine binding site 5 out of 19 in 3nuo

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Iodine binding site 5 out of 19 in the Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I513

b:27.1
occ:0.30
 N A:GLY48 3.5 13.5 1.0
O A:HOH1131 3.8 43.3 0.5
O A:GLY48 3.9 15.2 1.0
CA A:ILE47 3.9 12.2 1.0
C A:ILE47 4.2 11.8 1.0
CB A:ILE47 4.3 11.7 1.0
CE1 A:PHE53 4.4 18.7 1.0
CA A:GLY48 4.4 15.4 1.0
C21 B:478478 4.4 16.6 1.0
CG2 A:ILE47 4.5 15.4 1.0
O A:MET46 4.6 15.7 1.0
C A:GLY48 4.6 12.9 1.0
O A:HOH1125 4.6 32.3 1.0
C22 B:478478 4.9 15.3 1.0
CZ A:PHE53 5.0 21.4 1.0
O A:HOH1073 5.0 26.7 1.0

Iodine binding site 6 out of 19 in 3nuo

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Iodine binding site 6 out of 19 in the Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I514

b:48.7
occ:0.50
 N A:GLU21 3.4 15.6 1.0
OE2 A:GLU34 3.8 22.0 1.0
CA A:LYS20 3.9 17.3 1.0
ND2 A:ASN83 3.9 16.3 1.0
CB A:LYS20 4.1 19.6 1.0
C A:LYS20 4.1 16.8 1.0
CG A:LYS20 4.2 18.9 1.0
O A:GLU21 4.2 16.5 1.0
CB A:GLU21 4.3 20.4 1.0
CA A:GLU21 4.3 15.3 1.0
C A:GLU21 4.8 13.7 1.0
CD A:GLU34 4.8 23.7 1.0
O A:LEU19 4.9 25.0 1.0
OE1 A:GLU34 5.0 39.1 1.0
O A:HOH1043 5.0 24.8 1.0

Iodine binding site 7 out of 19 in 3nuo

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Iodine binding site 7 out of 19 in the Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I516

b:38.5
occ:0.30
 O A:HOH1203 2.6 47.8 1.0
O A:HOH1130 3.1 29.6 0.5
N A:THR12 3.4 18.0 1.0
CB A:ALA67 3.8 34.1 1.0
CA A:VAL11 4.1 17.0 1.0
CA A:ALA67 4.1 26.9 1.0
CB A:VAL11 4.1 21.9 1.0
OG1 A:THR12 4.2 30.0 1.0
CB A:THR12 4.2 22.2 1.0
C A:VAL11 4.3 16.3 1.0
CA A:THR12 4.3 18.5 1.0
O A:THR12 4.5 20.9 1.0
CG1 A:VAL11 4.5 24.6 1.0
C A:THR12 4.9 17.1 1.0

Iodine binding site 8 out of 19 in 3nuo

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Iodine binding site 8 out of 19 in the Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I517

b:41.7
occ:0.30
 O A:HOH1132 2.5 38.5 1.0
O A:HOH1046 3.4 22.8 1.0
N A:ILE63 3.5 18.5 1.0
CA A:ILE62 4.0 13.0 1.0
CB A:ILE63 4.3 22.9 1.0
C A:ILE62 4.3 13.7 1.0
CG2 A:ILE62 4.3 15.7 1.0
CD1 A:ILE62 4.3 17.5 1.0
O A:GLN61 4.4 19.7 1.0
CA A:ILE63 4.4 18.5 1.0
O A:ILE63 4.5 21.6 1.0
CG1 A:ILE63 4.5 26.8 1.0
CG A:PRO39 4.6 32.6 1.0
CB A:ILE62 4.7 13.5 1.0
CD1 A:ILE63 4.8 41.1 1.0
C A:ILE63 4.9 18.9 1.0

Iodine binding site 9 out of 19 in 3nuo

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Iodine binding site 9 out of 19 in the Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I501

b:17.8
occ:0.50
 O B:HOH1000 2.7 29.5 1.0
N B:THR74 3.5 12.5 1.0
ND2 B:ASN88 3.6 13.6 1.0
OG1 B:THR74 3.9 15.5 1.0
CA B:GLY73 4.1 13.2 1.0
CB B:ASN88 4.1 12.1 1.0
CB B:THR74 4.1 13.7 1.0
O B:HOH1017 4.2 18.8 1.0
C B:GLY73 4.3 12.5 1.0
O B:HOH1156 4.4 42.9 1.0
NE2 B:GLN92 4.4 15.5 1.0
CG B:ASN88 4.4 11.6 1.0
CA B:THR74 4.5 12.1 1.0
O B:ASN88 4.6 16.0 1.0
CD2 B:LEU89 4.9 16.3 1.0
C B:ASN88 5.0 12.7 1.0

Iodine binding site 10 out of 19 in 3nuo

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Iodine binding site 10 out of 19 in the Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Hiv-1 Protease Mutant L90M with Antiviral Drug Amprenavir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I502

b:31.6
occ:0.50
 I B:IOD503 2.7 54.7 0.5
OE2 B:GLU65 2.9 42.0 1.0
N B:GLY68 3.7 16.6 1.0
CD B:GLU65 3.8 37.0 1.0
O B:THR12 3.9 13.8 1.0
CG B:GLU65 3.9 30.0 1.0
CB B:GLU65 4.0 15.7 1.0
N B:LYS14 4.1 11.2 1.0
O B:GLU65 4.2 13.2 1.0
CB B:LYS14 4.2 12.4 1.0
C B:ILE13 4.2 10.9 1.0
CA B:GLY68 4.3 18.4 1.0
N B:ALA67 4.3 15.2 1.0
CA B:ILE13 4.3 10.9 1.0
C B:THR12 4.4 11.7 1.0
C B:GLU65 4.4 11.7 1.0
CG2 B:THR12 4.4 19.4 1.0
O B:HOH1049 4.5 25.7 1.0
N B:ILE13 4.6 10.7 1.0
CA B:ALA67 4.7 16.7 1.0
CD2 B:LEU19 4.7 16.4 1.0
C B:ALA67 4.7 18.1 1.0
O B:ILE13 4.7 11.9 1.0
N B:ILE66 4.8 12.2 1.0
CA B:LYS14 4.8 11.4 1.0
CA B:GLU65 4.8 12.1 1.0
CB B:THR12 4.8 16.8 1.0
C B:ILE66 4.9 13.0 1.0
O B:HOH1185 5.0 46.1 1.0

Reference:

C.H.Shen, Y.F.Wang, A.Y.Kovalevsky, R.W.Harrison, I.T.Weber. Amprenavir Complexes with Hiv-1 Protease and Its Drug-Resistant Mutants Altering Hydrophobic Clusters. Febs J. V. 277 3699 2010.
ISSN: ISSN 1742-464X
PubMed: 20695887
DOI: 10.1111/J.1742-4658.2010.07771.X
Page generated: Sun Aug 11 15:52:13 2024

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