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Iodine in PDB 8dxl: Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Iodopyrazole at Multiple Sites

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

All present enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Iodopyrazole 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- Iodopyrazole at Multiple Sites, PDB code: 8dxl 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) 41.20 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.318, 73.314, 109.398, 90, 100.62, 90
R / Rfree (%) 18.2 / 20.8

Other elements in 8dxl:

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

Magnesium (Mg) 1 atom

Iodine Binding Sites:

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

Iodine binding site 1 out of 3 in 8dxl

Go back to Iodine Binding Sites List in 8dxl
Iodine binding site 1 out of 3 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Iodopyrazole at Multiple Sites


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Iodopyrazole at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I611

b:91.3
occ:0.38
 I4 A:PYZ611 0.0 91.3 0.4
O A:HOH1061 0.5 68.8 0.2
C4 A:PYZ611 2.1 48.2 0.4
OG1 A:THR165 3.1 42.6 1.0
O A:HOH973 3.1 36.4 1.0
C3 A:PYZ611 3.1 51.4 0.4
C5 A:PYZ611 3.1 51.2 0.4
O A:HOH858 3.6 42.9 1.0
O A:HOH1075 3.9 53.0 0.7
CB A:THR165 4.0 39.4 1.0
CA A:THR165 4.0 40.9 1.0
CD B:PRO140 4.1 42.2 1.0
O A:HOH930 4.1 49.5 0.6
CG B:PRO140 4.1 44.2 1.0
CD1 A:LEU168 4.1 41.1 1.0
N2 A:PYZ611 4.2 53.9 0.4
N1 A:PYZ611 4.3 55.1 0.4
CG2 A:THR165 4.4 47.5 1.0
N A:THR165 4.7 36.5 1.0
CB A:GLN182 4.8 54.8 1.0
O A:ILE180 4.9 37.6 1.0
N A:GLN182 4.9 46.5 1.0
CB A:LEU168 4.9 39.4 1.0

Iodine binding site 2 out of 3 in 8dxl

Go back to Iodine Binding Sites List in 8dxl
Iodine binding site 2 out of 3 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Iodopyrazole at Multiple Sites


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Iodopyrazole at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I612

b:50.4
occ:0.24
 I4 A:PYZ612 0.0 50.4 0.2
C4 A:PYZ612 2.1 53.2 0.2
C3 A:PYZ612 3.1 55.4 0.2
C5 A:PYZ612 3.1 54.0 0.2
CG A:MET164 3.2 48.7 1.0
SD A:MET164 3.2 63.7 1.0
N A:MET164 3.4 31.1 1.0
CD1 A:ILE167 3.5 41.9 1.0
CA A:MET164 3.6 37.6 1.0
C A:SER163 3.7 33.5 1.0
CB A:SER163 3.8 36.6 1.0
CB A:MET164 4.0 37.7 1.0
CE1 A:PHE160 4.1 49.2 1.0
O A:SER163 4.1 33.0 1.0
N2 A:PYZ612 4.2 55.4 0.2
N1 A:PYZ612 4.2 55.9 0.2
CD1 A:PHE160 4.3 44.3 1.0
O A:PHE160 4.3 29.5 1.0
CA A:SER163 4.3 34.8 1.0
CD1 A:LEU214 4.5 51.9 1.0
CB A:ALA114 4.5 59.0 1.0
CG1 A:VAL118 4.7 43.8 1.0
CG1 A:ILE167 4.8 36.4 1.0
CZ A:PHE160 4.9 53.0 1.0
CD1 A:ILE5 4.9 55.8 1.0
CG2 A:VAL118 4.9 53.2 1.0
CE A:MET164 4.9 40.0 1.0

Iodine binding site 3 out of 3 in 8dxl

Go back to Iodine Binding Sites List in 8dxl
Iodine binding site 3 out of 3 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Iodopyrazole at Multiple Sites


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Iodopyrazole at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I507

b:61.4
occ:0.31
 I4 B:PYZ507 0.0 61.4 0.3
C4 B:PYZ507 2.1 47.0 0.3
C3 B:PYZ507 3.1 53.8 0.3
C5 B:PYZ507 3.1 43.5 0.3
NH2 B:ARG358 3.6 92.5 1.0
CB B:GLN373 3.9 25.9 1.0
O B:HOH616 3.9 49.1 1.0
CD B:GLN373 4.1 31.2 1.0
NE2 B:GLN373 4.2 33.7 1.0
O B:HOH883 4.2 47.5 0.8
OE1 B:GLN373 4.2 37.6 1.0
N2 B:PYZ507 4.2 50.8 0.3
O B:GLU370 4.3 27.6 1.0
N1 B:PYZ507 4.3 44.0 0.3
CA B:GLU370 4.4 26.7 1.0
CB B:GLU370 4.4 34.6 1.0
CG B:GLU370 4.4 52.3 1.0
CG B:LYS374 4.6 36.5 1.0
CG B:GLN373 4.6 30.4 1.0
C B:GLU370 4.8 25.3 1.0
OE1 B:GLN407 4.8 75.8 1.0
CZ B:ARG358 4.9 98.1 1.0
OH B:TYR232 4.9 54.0 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 27 17:46:28 2023

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