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Chlorine in PDB 4fm6: Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate

Enzymatic activity of Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate

All present enzymatic activity of Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate, PDB code: 4fm6 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 / 1.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.060, 86.140, 46.300, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 23

Other elements in 4fm6:

The structure of Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate (pdb code 4fm6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate, PDB code: 4fm6:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4fm6

Go back to Chlorine Binding Sites List in 4fm6
Chlorine binding site 1 out of 6 in the Hiv-1 Protease Mutant V32I Complexed with Reaction 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 Mutant V32I Complexed with Reaction Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl102

b:17.0
occ:1.00
 N B:THR74 3.2 10.4 1.0
ND2 B:ASN88 3.2 11.7 1.0
CA B:GLY73 3.7 10.2 1.0
OG1 B:THR74 3.8 17.0 1.0
CB B:ASN88 3.8 10.2 1.0
CB B:THR74 3.8 11.2 1.0
C B:GLY73 4.0 8.4 1.0
CG B:ASN88 4.0 9.8 1.0
CA B:THR74 4.1 9.2 1.0
O B:HOH209 4.4 22.1 1.0
O B:ASN88 4.7 11.8 1.0
O B:THR74 4.7 11.3 1.0
CA B:ASN88 4.9 9.6 1.0
C B:THR74 4.9 9.1 1.0

Chlorine binding site 2 out of 6 in 4fm6

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Chlorine binding site 2 out of 6 in the Hiv-1 Protease Mutant V32I Complexed with Reaction 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 Mutant V32I Complexed with Reaction Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl103

b:48.5
occ:1.00
 O B:HOH258 2.4 42.4 1.0
N B:ARG8 3.2 14.9 1.0
CG B:ARG8 3.5 15.7 1.0
CB B:LYS7 3.7 20.9 1.0
CB B:ARG8 3.7 13.8 1.0
O B:HOH243 3.9 33.3 1.0
CA B:LYS7 4.0 17.5 1.0
CA B:ARG8 4.0 13.3 1.0
CD B:ARG8 4.0 20.2 1.0
C B:LYS7 4.1 14.2 1.0
NE B:ARG8 4.5 22.4 1.0
NH2 A:ARG87 4.6 14.7 1.0
O B:HOH260 4.8 47.7 1.0
CG B:LYS7 4.9 34.3 1.0
O B:ARG8 4.9 15.8 1.0

Chlorine binding site 3 out of 6 in 4fm6

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Chlorine binding site 3 out of 6 in the Hiv-1 Protease Mutant V32I Complexed with Reaction 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 Mutant V32I Complexed with Reaction Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl101

b:19.4
occ:1.00
 O A:HOH238 3.0 40.3 1.0
NE1 A:TRP6 3.2 12.2 1.0
O B:HOH205 3.3 13.6 1.0
CZ2 A:TRP6 3.8 11.9 1.0
CE2 A:TRP6 3.9 11.5 1.0
CD1 A:TRP6 4.3 11.8 1.0
CG2 A:THR4 4.3 20.1 1.0
CB A:THR4 4.9 12.9 1.0

Chlorine binding site 4 out of 6 in 4fm6

Go back to Chlorine Binding Sites List in 4fm6
Chlorine binding site 4 out of 6 in the Hiv-1 Protease Mutant V32I Complexed with Reaction 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 Mutant V32I Complexed with Reaction Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl102

b:20.4
occ:1.00
 O A:HOH204 2.9 20.6 1.0
ND2 A:ASN88 3.2 12.0 1.0
N A:THR74 3.2 8.9 1.0
CA A:GLY73 3.7 10.7 1.0
OG1 A:THR74 3.8 14.3 1.0
CB A:THR74 3.8 10.7 1.0
CB A:ASN88 3.9 10.4 1.0
C A:GLY73 4.0 7.5 1.0
CG A:ASN88 4.0 10.4 1.0
CA A:THR74 4.1 9.4 1.0
O A:HOH207 4.2 15.8 1.0
NE2 A:GLN92 4.3 13.6 1.0
O A:ASN88 4.4 14.9 1.0
CD2 A:LEU89 4.5 14.4 1.0
O A:THR74 4.7 11.6 1.0
C A:ASN88 4.8 10.4 1.0
CA A:ASN88 4.8 9.6 1.0
O A:HOH248 4.9 34.1 1.0
C A:THR74 4.9 8.7 1.0

Chlorine binding site 5 out of 6 in 4fm6

Go back to Chlorine Binding Sites List in 4fm6
Chlorine binding site 5 out of 6 in the Hiv-1 Protease Mutant V32I Complexed with Reaction 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 Mutant V32I Complexed with Reaction Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl103

b:30.4
occ:1.00
 OG1 A:THR4 2.9 17.1 1.0
N A:TRP6 3.2 10.4 1.0
N A:LYS7 3.3 13.4 1.0
O A:THR4 3.4 15.1 1.0
CG A:LYS7 3.5 34.6 1.0
C A:THR4 3.6 12.1 1.0
CD A:LYS7 3.6 45.8 1.0
CB A:TRP6 3.6 10.8 1.0
O A:HOH205 3.8 18.4 1.0
CA A:TRP6 3.8 10.5 1.0
CB A:THR4 3.9 12.9 1.0
N A:LEU5 3.9 10.8 1.0
CD1 A:TRP6 3.9 11.8 1.0
C A:TRP6 4.0 10.8 1.0
C A:LEU5 4.1 8.7 1.0
CG A:TRP6 4.2 11.0 1.0
CA A:THR4 4.2 12.0 1.0
CB A:LYS7 4.3 22.3 1.0
O A:HOH220 4.3 30.1 1.0
CA A:LYS7 4.3 16.3 1.0
CA A:LEU5 4.3 9.5 1.0
O A:LYS7 4.4 12.2 1.0
N A:THR4 4.6 14.3 1.0
O A:HOH240 4.6 27.2 1.0
C A:LYS7 4.8 13.5 1.0

Chlorine binding site 6 out of 6 in 4fm6

Go back to Chlorine Binding Sites List in 4fm6
Chlorine binding site 6 out of 6 in the Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Hiv-1 Protease Mutant V32I Complexed with Reaction Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl104

b:30.5
occ:1.00
 O A:HOH264 2.7 34.7 1.0
O A:HOH265 3.0 20.6 1.0
NH2 A:ARG41 3.0 12.8 1.0
CZ A:ARG41 4.3 11.7 1.0
O A:HOH221 4.9 21.9 1.0
NH1 A:ARG41 5.0 11.2 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 13:51:39 2024

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