Magnesium 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 / R_free (%)*	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:

Iodine

(I)

3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was determined in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4- Iodopyrazole at Multiple Sites, PDB code: 8dxl:

Magnesium binding site 1 out of 1 in 8dxl

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Magnesium Binding Sites List in 8dxl

Magnesium binding site 1 out of 1 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 Magnesium with other atoms in the Mg 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:Mg607 b:59.0 occ:1.00	O	A:HOH758	2.2	56.1	1.0
	O	A:HOH979	2.2	62.1	1.0
	O	A:HOH727	2.3	51.8	1.0
	O	A:HOH708	2.4	49.9	1.0
	OD1	A:ASP549	2.5	82.4	1.0
	OD2	A:ASP443	2.7	50.0	1.0
	CG	A:ASP549	3.2	82.6	1.0
	CG	A:ASP443	3.5	44.3	1.0
	OD1	A:ASP443	3.6	43.3	1.0
	CB	A:ASP549	3.8	72.8	1.0
	O	A:HOH914	3.8	55.5	1.0
	OD2	A:ASP549	4.0	85.0	1.0
	O	A:HOH1080	4.0	49.0	1.0
	CE1	A:HIS539	4.1	62.1	1.0
	O	A:HOH818	4.2	47.0	1.0
	NE2	A:HIS539	4.3	60.7	1.0
	O	A:GLY444	4.3	39.9	1.0
	OD1	A:ASP498	4.3	41.7	1.0
	OG	A:SER553	4.5	80.0	1.0
	OD2	A:ASP498	4.5	50.4	1.0
	CA	A:ASP549	4.6	71.1	1.0
	CG	A:ASP498	4.8	41.8	1.0
	ND1	A:HIS539	5.0	59.5	1.0
	CB	A:ASP443	5.0	37.1	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 00:58:26 2024

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