Magnesium in PDB 8dxm: Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromophenol at the Knuckles Site

Enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromophenol at the Knuckles Site

All present enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromophenol at the Knuckles Site:
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- Bromophenol at the Knuckles Site, PDB code: 8dxm 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) 42.15 / 1.99
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.512, 72.969, 109.422, 90, 100.6, 90
R / Rfree (%) 19.7 / 20.8

Other elements in 8dxm:

The structure of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromophenol at the Knuckles Site also contains other interesting chemical elements:

Bromine (Br) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromophenol at the Knuckles Site (pdb code 8dxm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromophenol at the Knuckles Site, PDB code: 8dxm:

Magnesium binding site 1 out of 1 in 8dxm

Go back to Magnesium Binding Sites List in 8dxm
Magnesium binding site 1 out of 1 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromophenol at the Knuckles Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Bromophenol at the Knuckles Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:63.3
occ:1.00
 O A:HOH859 1.9 53.3 1.0
O A:HOH865 2.1 61.1 1.0
O A:HOH710 2.2 53.7 1.0
O A:HOH772 2.3 46.0 1.0
OD1 A:ASP549 2.5 57.2 1.0
OD2 A:ASP443 2.5 50.3 1.0
OD1 A:ASP443 3.2 44.3 1.0
CG A:ASP443 3.2 43.9 1.0
CG A:ASP549 3.4 61.1 1.0
OD2 A:ASP498 3.6 39.0 1.0
O A:HOH740 3.8 47.9 1.0
CB A:ASP549 3.9 54.6 1.0
O A:HOH895 4.1 55.4 1.0
O A:GLY444 4.3 42.5 1.0
CE1 A:HIS539 4.3 64.2 1.0
OD1 A:ASP498 4.4 39.1 1.0
CG A:ASP498 4.4 41.8 1.0
OD2 A:ASP549 4.5 60.9 1.0
NE2 A:HIS539 4.5 65.4 1.0
CA A:ASP549 4.6 56.1 1.0
CB A:ASP443 4.7 35.3 1.0
OG A:SER553 4.7 78.7 1.0
CB A:ALA538 4.9 45.7 1.0
O A:HOH724 5.0 43.6 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 23:33:22 2023

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