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Bromine in PDB 8dxk: Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites

Enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites

All present enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13;

Protein crystallography data

The structure of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites, PDB code: 8dxk was solved by A.Chopra, F.X.Ruiz, J.D.Bauman, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.471, 72.983, 109.316, 90, 100.69, 90
R / Rfree (%) 18.1 / 21.5

Other elements in 8dxk:

The structure of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites (pdb code 8dxk). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites, PDB code: 8dxk:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 8dxk

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Bromine binding site 1 out of 8 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br609

b:278.2
occ:0.45
 BR4 A:BYZ609 0.0 278.2 0.5
C4 A:BYZ609 1.9 167.9 0.5
C3 A:BYZ609 2.9 160.8 0.5
C5 A:BYZ609 3.0 163.2 0.5
CD1 A:ILE5 3.2 88.7 1.0
CG2 A:VAL118 3.3 42.1 1.0
CD1 A:ILE167 3.6 45.5 1.0
CE A:MET164 3.7 31.0 1.0
CD1 A:LEU214 3.9 72.5 1.0
N2 A:BYZ609 4.0 174.4 0.5
N1 A:BYZ609 4.1 176.4 0.5
CB A:SER163 4.1 30.9 1.0
CB A:ALA114 4.2 54.9 1.0
CD1 A:ILE5 4.2 53.4 0.0
CG1 A:ILE5 4.3 66.3 1.0
N A:MET164 4.5 29.6 1.0
C A:SER163 4.5 30.3 1.0
CG2 A:ILE5 4.7 54.1 1.0
O A:SER163 4.7 29.1 1.0
CB A:VAL118 4.7 40.1 1.0
CA A:MET164 4.7 32.8 1.0
CE1 A:PHE160 4.8 45.4 1.0
CD2 A:LEU214 4.8 70.7 1.0
O A:ALA114 4.9 62.7 1.0
CG1 A:ILE5 4.9 54.9 0.0
CG1 A:ILE167 4.9 41.7 1.0
CD1 A:PHE160 5.0 41.4 1.0
CG A:LEU214 5.0 64.3 1.0
CA A:SER163 5.0 28.0 1.0

Bromine binding site 2 out of 8 in 8dxk

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Bromine binding site 2 out of 8 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br610

b:208.5
occ:1.00
 BR4 A:BYZ610 0.0 208.5 1.0
C4 A:BYZ610 1.9 93.8 1.0
C3 A:BYZ610 2.9 86.6 1.0
C5 A:BYZ610 3.0 88.1 1.0
O A:HOH963 3.1 38.3 1.0
OG1 A:THR165 3.5 40.0 1.0
O B:HOH739 3.6 43.5 1.0
CD B:PRO140 3.8 45.5 1.0
CG B:PRO140 3.9 46.0 1.0
O A:HOH761 4.0 54.1 1.0
N2 A:BYZ610 4.0 106.6 1.0
N1 A:BYZ610 4.1 102.1 1.0
CA A:THR165 4.2 37.4 1.0
CB A:THR165 4.2 36.4 1.0
CD1 A:LEU168 4.3 35.7 1.0
CG2 A:THR165 4.4 44.7 1.0
O A:ILE180 4.8 38.3 1.0
CB A:LEU168 4.8 34.1 1.0
N A:THR165 5.0 33.7 1.0

Bromine binding site 3 out of 8 in 8dxk

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Bromine binding site 3 out of 8 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br611

b:171.1
occ:1.00
 BR4 A:BYZ611 0.0 171.1 1.0
C4 A:BYZ611 1.9 75.9 1.0
C3 A:BYZ611 2.9 82.9 1.0
C5 A:BYZ611 2.9 82.6 1.0
N B:GLY333 3.8 38.8 1.0
C B:GLN332 3.8 38.2 1.0
CA B:GLY333 3.8 38.1 1.0
O B:GLN332 3.9 37.0 1.0
O B:LYS331 3.9 30.0 1.0
O A:THR403 4.0 35.3 1.0
N2 A:BYZ611 4.0 89.8 1.0
N1 A:BYZ611 4.0 87.8 1.0
O A:TYR405 4.2 24.5 1.0
CG B:LYS331 4.4 27.3 1.0
CE B:LYS331 4.4 33.9 1.0
O A:GLU404 4.5 32.8 1.0
CA B:GLN332 4.5 29.6 1.0
C B:LYS331 4.6 28.6 1.0
C A:GLU404 4.6 29.3 1.0
CD B:LYS331 4.7 24.3 1.0
NZ B:LYS424 4.7 46.6 1.0
CA A:GLU404 4.7 32.2 1.0
C A:TYR405 4.9 25.9 1.0
N B:GLN332 4.9 29.4 1.0
C A:THR403 5.0 28.4 1.0

Bromine binding site 4 out of 8 in 8dxk

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Bromine binding site 4 out of 8 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br612

b:208.1
occ:1.00
 BR4 A:BYZ612 0.0 208.1 1.0
C4 A:BYZ612 1.9 115.8 1.0
C3 A:BYZ612 2.9 99.1 1.0
C5 A:BYZ612 3.0 119.0 1.0
O A:HOH972 3.5 73.9 1.0
O B:ASN137 3.6 29.5 1.0
N B:PRO140 3.9 38.6 1.0
N2 A:BYZ612 4.0 107.0 1.0
N1 A:BYZ612 4.1 121.3 1.0
C B:THR139 4.1 35.7 1.0
CA B:PRO140 4.2 35.3 1.0
CG1 A:VAL90 4.3 77.9 1.0
CD B:PRO140 4.3 45.5 1.0
CG B:PRO140 4.3 46.0 1.0
O B:HOH786 4.3 49.2 1.0
O B:THR139 4.4 35.0 1.0
O A:HOH963 4.4 38.3 1.0
CA B:THR139 4.5 31.8 1.0
O B:GLU138 4.6 28.9 1.0
C B:ASN137 4.7 26.4 1.0
C B:GLU138 4.7 35.0 1.0
O A:VAL90 4.7 110.8 1.0
O B:HOH739 4.7 43.5 1.0
N B:THR139 4.7 30.9 1.0
CE1 A:TYR181 4.7 42.3 1.0
CB B:PRO140 4.7 41.5 1.0

Bromine binding site 5 out of 8 in 8dxk

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Bromine binding site 5 out of 8 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br613

b:227.9
occ:1.00
 BR4 A:BYZ613 0.0 227.9 1.0
C4 A:BYZ613 1.9 117.6 1.0
C3 A:BYZ613 2.9 111.4 1.0
C5 A:BYZ613 3.0 112.4 1.0
O A:GLY359 3.9 59.2 1.0
N A:GLU514 3.9 47.7 1.0
N2 A:BYZ613 4.0 121.6 1.0
C A:SER513 4.1 48.0 1.0
N1 A:BYZ613 4.1 116.0 1.0
CG A:GLU514 4.1 77.0 1.0
CZ A:ARG356 4.2 57.6 1.0
O A:ALA360 4.2 49.4 1.0
NE A:ARG356 4.2 57.6 1.0
OE1 A:GLU514 4.3 85.5 1.0
CG2 A:THR362 4.3 32.2 1.0
NH1 A:ARG356 4.3 53.9 1.0
CA A:SER513 4.4 45.2 1.0
O A:SER513 4.5 44.7 1.0
CD A:ARG356 4.5 46.8 1.0
NH2 A:ARG356 4.6 63.9 1.0
CA A:GLU514 4.6 59.8 1.0
N A:SER513 4.6 40.4 1.0
O A:LYS512 4.6 34.6 1.0
CB A:GLU514 4.7 55.6 1.0
CD A:GLU514 4.7 90.7 1.0
C A:LYS512 4.7 41.5 1.0
C A:ALA360 4.8 54.5 1.0

Bromine binding site 6 out of 8 in 8dxk

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Bromine binding site 6 out of 8 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br508

b:114.5
occ:0.26
 BR4 B:BYZ508 0.0 114.5 0.3
O B:HOH797 1.6 45.5 0.6
C4 B:BYZ508 1.9 47.9 0.3
C3 B:BYZ508 2.9 45.8 0.3
C5 B:BYZ508 3.0 43.8 0.3
OD1 B:ASN137 3.2 44.8 1.0
O B:HOH758 3.2 40.6 1.0
O B:SER134 3.3 25.3 1.0
CG B:ASN137 3.6 46.1 1.0
ND2 B:ASN137 3.7 44.4 1.0
O A:VAL381 3.8 22.9 1.0
N B:ASN137 4.0 28.0 1.0
O B:HOH807 4.0 39.7 1.0
N2 B:BYZ508 4.0 46.9 0.3
CG1 A:VAL381 4.0 26.4 1.0
N B:ASN136 4.0 24.5 1.0
O A:HOH835 4.0 35.0 0.7
N1 B:BYZ508 4.1 45.5 0.3
CA A:VAL381 4.2 24.3 1.0
C B:SER134 4.4 25.6 1.0
C A:VAL381 4.4 24.0 1.0
O B:HOH731 4.4 38.8 1.0
CA B:ASN136 4.6 25.1 1.0
O B:HOH829 4.6 61.7 1.0
CB A:VAL381 4.6 26.0 1.0
C B:ASN136 4.6 28.3 1.0
CA B:ASN137 4.7 30.4 1.0
CB B:ASN137 4.7 34.9 1.0
C B:ILE135 4.7 29.7 1.0
CB B:PRO133 4.7 28.0 1.0
CA B:ILE135 4.8 28.1 1.0
CG2 A:VAL381 4.9 24.7 1.0

Bromine binding site 7 out of 8 in 8dxk

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Bromine binding site 7 out of 8 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br509

b:219.3
occ:1.00
 BR4 B:BYZ509 0.0 219.3 1.0
C4 B:BYZ509 1.9 108.9 1.0
C3 B:BYZ509 2.9 106.4 1.0
C5 B:BYZ509 3.0 127.7 1.0
OH B:TYR232 3.1 76.9 1.0
CG B:LYS374 3.7 40.5 1.0
CD2 B:LEU234 3.8 52.5 1.0
O B:HOH646 3.9 64.1 1.0
N2 B:BYZ509 4.0 134.2 1.0
CZ B:TYR232 4.1 69.6 1.0
N1 B:BYZ509 4.1 137.6 1.0
CB B:LYS374 4.1 31.7 1.0
CA B:LYS374 4.3 31.3 1.0
CE B:LYS374 4.3 61.3 1.0
O3 B:SO4507 4.4 80.7 1.0
CG2 B:THR377 4.4 31.0 1.0
O B:LYS374 4.6 27.2 1.0
CE2 B:TYR232 4.6 69.9 1.0
CD B:LYS374 4.6 50.0 1.0
CB B:THR377 4.7 34.6 1.0
CZ2 B:TRP239 4.8 46.9 1.0
O4 B:SO4507 4.9 70.6 1.0
CE1 B:TYR232 4.9 65.7 1.0
C B:LYS374 4.9 28.1 1.0

Bromine binding site 8 out of 8 in 8dxk

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Bromine binding site 8 out of 8 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromopyrazole at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br510

b:197.1
occ:1.00
 BR4 B:BYZ510 0.0 197.1 1.0
C4 B:BYZ510 1.9 82.8 1.0
C3 B:BYZ510 2.9 85.4 1.0
C5 B:BYZ510 3.0 66.4 1.0
N B:ILE411 3.2 24.3 1.0
O B:ILE411 3.5 24.8 1.0
O B:HOH795 3.6 40.4 1.0
CB B:TRP410 3.7 31.5 1.0
CA B:TRP410 3.7 34.1 1.0
C B:TRP410 4.0 29.4 1.0
N2 B:BYZ510 4.0 75.6 1.0
N1 B:BYZ510 4.1 72.7 1.0
C B:ILE411 4.2 24.8 1.0
CA B:ILE411 4.2 23.6 1.0
ND2 B:ASN81 4.4 30.8 1.0
O B:GLY152 4.6 31.0 1.0
CB B:ILE411 4.7 30.0 1.0
CG B:ARG78 4.8 29.1 1.0
CE B:MET184 5.0 49.6 1.0
CG B:MET184 5.0 43.5 1.0

Reference:

A.Chopra, J.D.Bauman, F.X.Ruiz, E.Arnold. Halo Library, A Tool For Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening. J.Med.Chem. V. 66 6013 2023.
ISSN: ISSN 0022-2623
PubMed: 37115705
DOI: 10.1021/ACS.JMEDCHEM.2C01681
Page generated: Thu Jul 11 05:06:02 2024

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