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Chlorine in PDB 4hdp: Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519

Enzymatic activity of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519

All present enzymatic activity of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519, PDB code: 4hdp was solved by C.H.Shen, H.Zhang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.22
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.592, 85.945, 46.070, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.3

Other elements in 4hdp:

The structure of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519 (pdb code 4hdp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519, PDB code: 4hdp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4hdp

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Chlorine binding site 1 out of 6 in the Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:10.8
occ:0.80
 O B:HOH1069 3.1 29.9 1.0
N B:THR74 3.2 10.3 1.0
ND2 B:ASN88 3.2 11.1 1.0
CA B:GLY73 3.7 10.9 1.0
CB B:ASN88 3.8 8.7 1.0
OG1 B:THR74 3.8 13.0 1.0
CB B:THR74 3.9 11.0 1.0
C B:GLY73 4.0 9.9 1.0
CG B:ASN88 4.0 10.4 1.0
CA B:THR74 4.1 9.7 1.0
O B:HOH1032 4.3 17.8 1.0
O B:HOH1092 4.5 42.3 1.0
O B:ASN88 4.6 10.0 1.0
O B:THR74 4.8 10.0 1.0
CA B:ASN88 4.8 9.2 1.0
O B:HOH1080 4.9 34.0 1.0
C B:ASN88 5.0 8.6 1.0
C B:THR74 5.0 10.4 1.0

Chlorine binding site 2 out of 6 in 4hdp

Go back to Chlorine Binding Sites List in 4hdp
Chlorine binding site 2 out of 6 in the Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:31.5
occ:1.00
 O B:HOH1097 3.1 41.9 1.0
N B:ARG8 3.1 10.2 1.0
CG B:ARG8 3.6 11.3 1.0
CB B:LYS7 3.8 20.1 1.0
CA B:LYS7 3.8 11.8 1.0
CB B:ARG8 3.8 9.5 1.0
C B:LYS7 3.9 10.2 1.0
CD B:ARG8 3.9 13.7 1.0
CD B:LYS7 4.1 49.0 1.0
CA B:ARG8 4.1 9.8 1.0
O B:HOH1026 4.1 24.3 1.0
NH2 A:ARG87 4.4 10.8 1.0
NE B:ARG8 4.4 13.5 1.0
CG B:LYS7 4.5 33.2 1.0

Chlorine binding site 3 out of 6 in 4hdp

Go back to Chlorine Binding Sites List in 4hdp
Chlorine binding site 3 out of 6 in the Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:32.8
occ:1.00
 O B:HOH1082 2.6 39.2 1.0
N B:THR12 3.2 12.7 1.0
O B:HOH1104 3.7 32.1 0.5
CB B:VAL11 3.8 14.5 1.0
CB B:ALA67 3.8 25.9 1.0
CA B:VAL11 3.8 12.2 1.0
CA B:ALA67 3.8 19.8 1.0
CB B:THR12 3.9 17.9 1.0
C B:VAL11 4.0 12.6 1.0
CA B:THR12 4.1 13.2 1.0
OG1 B:THR12 4.1 21.6 1.0
O B:THR12 4.1 14.4 1.0
CG1 B:VAL11 4.2 16.2 1.0
C B:THR12 4.6 13.1 1.0
N B:ALA67 4.7 17.4 1.0
O B:HOH1116 4.8 59.3 1.0
C B:ALA67 4.9 20.3 1.0

Chlorine binding site 4 out of 6 in 4hdp

Go back to Chlorine Binding Sites List in 4hdp
Chlorine binding site 4 out of 6 in the Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl102

b:15.5
occ:1.00
 O A:HOH212 3.1 23.0 1.0
O B:HOH1038 3.3 11.6 1.0
NE1 A:TRP6 3.3 10.6 1.0
CZ2 A:TRP6 3.9 10.8 1.0
CE2 A:TRP6 3.9 10.1 1.0
CG2 A:THR4 4.3 15.8 1.0
CD1 A:TRP6 4.5 10.6 1.0
O A:HOH274 4.8 31.1 1.0
CB A:THR4 4.9 10.9 1.0

Chlorine binding site 5 out of 6 in 4hdp

Go back to Chlorine Binding Sites List in 4hdp
Chlorine binding site 5 out of 6 in the Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl103

b:15.1
occ:0.80
 O A:HOH238 2.9 14.2 1.0
N A:THR74 3.1 9.9 1.0
ND2 A:ASN88 3.1 10.6 1.0
OG1 A:THR74 3.7 13.5 1.0
CA A:GLY73 3.7 9.8 1.0
CB A:THR74 3.8 10.5 1.0
C A:GLY73 3.9 8.7 1.0
CB A:ASN88 3.9 9.2 1.0
CA A:THR74 4.0 9.9 1.0
CG A:ASN88 4.0 9.3 1.0
O A:HOH252 4.0 14.5 1.0
NE2 A:GLN92 4.4 10.8 1.0
O A:ASN88 4.5 11.1 1.0
CD2 A:LEU89 4.5 12.1 1.0
O A:THR74 4.7 10.4 1.0
C A:ASN88 4.8 8.8 1.0
CA A:ASN88 4.9 9.1 1.0
C A:THR74 4.9 9.4 1.0
O A:HOH315 5.0 33.6 0.5

Chlorine binding site 6 out of 6 in 4hdp

Go back to Chlorine Binding Sites List in 4hdp
Chlorine binding site 6 out of 6 in the Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Hiv-1 Protease Mutants I50V Complexed with Inhibitor Grl-0519 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl104

b:31.6
occ:1.00
 N A:ARG8 3.2 9.2 1.0
CB A:LYS7 3.6 13.1 0.3
CG A:ARG8 3.7 10.8 1.0
CA A:LYS7 3.8 11.0 0.3
CA A:LYS7 3.8 10.4 0.7
CB A:ARG8 3.9 8.5 1.0
C A:LYS7 4.0 8.6 1.0
CB A:LYS7 4.0 15.3 0.7
O B:HOH1015 4.0 43.3 1.0
CD A:ARG8 4.1 11.8 1.0
CA A:ARG8 4.1 8.3 1.0
O A:HOH223 4.1 21.1 1.0
O B:HOH1075 4.5 50.6 1.0
NH2 B:ARG87 4.5 9.5 1.0
CG A:LYS7 4.6 20.0 0.7
NE A:ARG8 4.6 12.1 1.0
CG A:LYS7 4.8 14.3 0.3

Reference:

H.Zhang, Y.F.Wang, C.H.Shen, J.Agniswamy, K.V.Rao, C.X.Xu, A.K.Ghosh, R.W.Harrison, I.T.Weber. Novel P2 Tris-Tetrahydrofuran Group in Antiviral Compound 1 (Grl-0519) Fills the S2 Binding Pocket of Selected Mutants of Hiv-1 Protease. J.Med.Chem. V. 56 1074 2013.
ISSN: ISSN 0022-2623
PubMed: 23298236
DOI: 10.1021/JM301519Z
Page generated: Sun Jul 21 15:44:25 2024

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