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Chlorine in PDB 4fl8: Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate

Enzymatic activity of Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate

All present enzymatic activity of Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate, PDB code: 4fl8 was solved by Y.F.Tie, 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 / 1.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.405, 86.199, 46.357, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 17.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate (pdb code 4fl8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate, PDB code: 4fl8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4fl8

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Chlorine binding site 1 out of 5 in the Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl101

b:17.3
occ:1.00
 O A:HOH1052 3.1 33.5 1.0
N A:THR74 3.2 11.8 1.0
ND2 A:ASN88 3.3 12.0 1.0
CA A:GLY73 3.8 12.2 1.0
OG1 A:THR74 3.8 16.8 1.0
CB A:ASN88 3.8 9.9 1.0
CB A:THR74 3.9 14.0 1.0
C A:GLY73 4.0 11.4 1.0
CG A:ASN88 4.1 10.5 1.0
CA A:THR74 4.1 11.3 1.0
O A:HOH1012 4.5 21.9 1.0
O A:HOH1045 4.5 40.2 1.0
O A:ASN88 4.7 11.6 1.0
O A:THR74 4.7 12.2 1.0
O A:HOH1087 4.8 38.9 0.5
CA A:ASN88 4.9 9.3 1.0
C A:THR74 5.0 11.2 1.0

Chlorine binding site 2 out of 5 in 4fl8

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Chlorine binding site 2 out of 5 in the Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl102

b:43.1
occ:1.00
 O A:HOH1091 2.7 45.5 1.0
N A:ARG8 3.1 13.4 1.0
CG A:ARG8 3.5 13.7 1.0
CB A:ARG8 3.7 12.4 1.0
CD A:ARG8 3.9 15.9 1.0
CA A:LYS7 3.9 17.6 1.0
C A:LYS7 4.0 13.5 1.0
CB A:LYS7 4.0 25.0 1.0
CA A:ARG8 4.0 12.7 1.0
O A:HOH1032 4.1 36.4 1.0
NE A:ARG8 4.3 15.9 1.0
NH2 B:ARG87 4.4 13.4 1.0
CG A:LYS7 4.7 38.1 1.0
CD A:LYS7 4.8 50.5 1.0
O A:ARG8 5.0 14.6 1.0
CZ B:ARG87 5.0 12.6 1.0
CZ A:ARG8 5.0 18.8 1.0

Chlorine binding site 3 out of 5 in 4fl8

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Chlorine binding site 3 out of 5 in the Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl103

b:34.5
occ:1.00
 O A:HOH1029 3.0 34.5 1.0
OE1 A:GLN18 3.2 33.4 1.0
N A:SER37 3.3 15.2 1.0
CA A:MET36 3.8 12.3 1.0
CB A:SER37 3.9 19.7 0.4
CB A:MET36 4.0 14.6 1.0
C A:MET36 4.0 13.2 1.0
CB A:SER37 4.0 21.8 0.6
CD A:GLN18 4.2 21.7 1.0
CA A:SER37 4.2 17.2 0.4
CA A:SER37 4.3 16.9 0.6
NE2 A:GLN18 4.4 24.4 1.0
OG A:SER37 4.5 30.7 0.6
O A:SER37 4.8 17.8 1.0

Chlorine binding site 4 out of 5 in 4fl8

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Chlorine binding site 4 out of 5 in the Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:18.7
occ:1.00
 NE1 B:TRP6 3.3 12.9 1.0
O A:HOH1004 3.3 14.4 1.0
CZ2 B:TRP6 3.8 12.2 1.0
CE2 B:TRP6 3.9 11.4 1.0
CG2 B:THR4 4.4 18.7 1.0
CD1 B:TRP6 4.4 12.2 1.0
O B:HOH674 4.9 37.2 1.0
CB B:THR4 4.9 14.6 1.0

Chlorine binding site 5 out of 5 in 4fl8

Go back to Chlorine Binding Sites List in 4fl8
Chlorine binding site 5 out of 5 in the Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Hiv-1 Protease Complexed with Gem-Diol-Amine Tetrahedral Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:15.5
occ:0.75
 O B:HOH606 3.0 18.4 1.0
O B:HOH691 3.1 21.3 0.5
N B:THR74 3.1 10.4 1.0
ND2 B:ASN88 3.2 10.8 1.0
OG1 B:THR74 3.7 13.8 1.0
CA B:GLY73 3.7 10.6 1.0
CB B:THR74 3.8 10.7 1.0
CB B:ASN88 3.9 9.7 1.0
C B:GLY73 4.0 9.6 1.0
CG B:ASN88 4.0 10.0 1.0
CA B:THR74 4.1 9.7 1.0
O B:HOH608 4.1 16.0 1.0
NE2 B:GLN92 4.4 12.1 1.0
CD2 B:LEU89 4.5 13.9 1.0
O B:ASN88 4.5 12.4 1.0
O B:THR74 4.7 10.2 1.0
C B:ASN88 4.8 9.5 1.0
CA B:ASN88 4.8 9.2 1.0
C B:THR74 4.9 9.5 1.0
O B:HOH642 5.0 62.4 1.0
O B:HOH696 5.0 33.1 1.0

Reference:

C.H.Shen, Y.Tie, X.Yu, Y.F.Wang, A.Y.Kovalevsky, R.W.Harrison, I.T.Weber. Capturing the Reaction Pathway in Near-Atomic-Resolution Crystal Structures of Hiv-1 Protease. Biochemistry V. 51 7726 2012.
ISSN: ISSN 0006-2960
PubMed: 22963370
DOI: 10.1021/BI3008092
Page generated: Sun Jul 21 13:49:10 2024

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