Magnesium in PDB 8dxg: Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 Site

Enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 Site

All present enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 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 5- (Trifluoromethyl)Pyridin-2-Ol at W24 Site, PDB code: 8dxg 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)*	38.09 / 2.10
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	162.623, 73.003, 109.791, 90, 100.56, 90
*R / R_free (%)*	20.1 / 22.5

Other elements in 8dxg:

The structure of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 Site also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 Site (pdb code 8dxg). 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 5- (Trifluoromethyl)Pyridin-2-Ol at W24 Site, PDB code: 8dxg:

Magnesium binding site 1 out of 1 in 8dxg

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Magnesium Binding Sites List in 8dxg

Magnesium binding site 1 out of 1 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 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 5- (Trifluoromethyl)Pyridin-2-Ol at W24 Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg608 b:58.5 occ:1.00	O	A:HOH710	2.2	59.5	1.0
	OD1	A:ASP549	2.2	53.9	1.0
	O	A:HOH772	2.3	48.0	1.0
	O	A:HOH769	2.3	43.0	1.0
	OD2	A:ASP443	2.3	51.7	1.0
	CG	A:ASP443	3.1	44.9	1.0
	OD1	A:ASP443	3.2	40.5	1.0
	CG	A:ASP549	3.3	58.2	1.0
	CB	A:ASP549	3.8	50.6	1.0
	O	A:HOH786	3.9	46.0	1.0
	OD2	A:ASP498	4.0	40.5	1.0
	O	A:GLY444	4.2	39.1	1.0
	OD2	A:ASP549	4.3	58.7	1.0
	CA	A:ASP549	4.4	51.5	1.0
	CE1	A:HIS539	4.4	60.2	1.0
	OD1	A:ASP498	4.5	35.9	1.0
	O	A:HOH790	4.5	48.8	1.0
	NE2	A:HIS539	4.5	58.6	1.0
	CB	A:ASP443	4.6	35.0	1.0
	CG	A:ASP498	4.6	35.9	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: Fri Oct 4 00:57:31 2024

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