Magnesium in PDB 5j1e: Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase

Enzymatic activity of Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase

All present enzymatic activity of Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase:
2.7.7.49; 2.7.7.7; 3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase, PDB code: 5j1e was solved by K.A.Kirby, S.G.Sarafianos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	63.77 / 2.90
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	69.070, 89.310, 108.220, 105.47, 92.69, 110.80
*R / R_free (%)*	25.4 / 29.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase (pdb code 5j1e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase, PDB code: 5j1e:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5j1e

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Magnesium Binding Sites List in 5j1e

Magnesium binding site 1 out of 3 in the Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg601 b:0.2 occ:1.00	OD2	A:ASP443	2.1	68.0	1.0
	OD1	A:ASP443	2.1	63.0	1.0
	OD2	A:ASP498	2.1	84.0	1.0
	CG	A:ASP443	2.3	61.8	1.0
	CG	A:ASP498	3.1	80.3	1.0
	OD1	A:ASP498	3.4	88.3	1.0
	OD1	A:ASP549	3.5	0.6	1.0
	CB	A:ASP443	3.8	59.2	1.0
	OE2	A:GLU478	3.8	79.0	1.0
	CG	A:ASP549	4.4	0.0	1.0
	CB	A:ASP549	4.4	97.2	1.0
	O	A:GLY444	4.4	58.9	1.0
	OD1	A:ASN545	4.4	64.8	1.0
	CB	A:ASP498	4.4	70.4	1.0
	CA	A:ASP443	4.7	53.8	1.0
	CD	A:GLU478	4.8	77.7	1.0
	N	A:GLY444	4.9	52.2	1.0
	OE1	A:GLU478	4.9	76.1	1.0
	CB	A:ALA538	5.0	83.5	1.0
	CA	A:ASP549	5.0	91.0	1.0

Magnesium binding site 2 out of 3 in 5j1e

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Magnesium Binding Sites List in 5j1e

Magnesium binding site 2 out of 3 in the Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mg601 b:66.1 occ:1.00	OE2	C:GLU478	2.1	63.1	1.0
	OD2	C:ASP498	2.1	67.8	1.0
	OD1	C:ASP443	2.1	63.6	1.0
	OD1	C:ASP498	2.1	77.2	1.0
	O05	C:6FT603	2.2	60.8	0.7
	O01	C:6FT603	2.2	73.6	0.7
	CG	C:ASP498	2.3	69.1	1.0
	CD	C:GLU478	3.1	65.8	1.0
	CG	C:ASP443	3.2	59.7	1.0
	C02	C:6FT603	3.2	73.4	0.7
	C04	C:6FT603	3.3	62.9	0.7
	MG	C:MG602	3.3	67.5	1.0
	OE1	C:GLU478	3.5	68.3	1.0
	OD2	C:ASP443	3.6	58.9	1.0
	C03	C:6FT603	3.7	68.9	0.7
	CB	C:ASP498	3.8	60.5	1.0
	O	C:GLY444	4.3	67.8	1.0
	O06	C:6FT603	4.3	60.6	0.7
	CG	C:GLU478	4.4	62.2	1.0
	C	C:ASP498	4.4	59.4	1.0
	CB	C:ASP443	4.4	58.1	1.0
	C27	C:6FT603	4.5	77.3	0.7
	CA	C:ASP498	4.6	58.3	1.0
	N	C:SER499	4.7	56.8	1.0
	N	C:GLY444	4.7	61.6	1.0
	O	C:ASP498	4.7	63.3	1.0
	CA	C:ASP443	4.8	59.8	1.0
	N	C:ASP498	4.8	54.9	1.0
	O28	C:6FT603	4.8	81.3	0.7
	CB	C:ALA538	4.9	61.8	1.0
	CB	C:SER499	5.0	55.2	1.0

Magnesium binding site 3 out of 3 in 5j1e

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Magnesium Binding Sites List in 5j1e

Magnesium binding site 3 out of 3 in the Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Hydroxypyridone Carboxylic Acid Active-Site Rnase H Inhibitor in Complex with Hiv Reverse Transcriptase within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mg602 b:67.5 occ:1.00	OD1	C:ASP549	2.1	68.8	1.0
	OD2	C:ASP443	2.1	58.9	1.0
	O01	C:6FT603	2.3	73.6	0.7
	O28	C:6FT603	2.4	81.3	0.7
	C02	C:6FT603	3.0	73.4	0.7
	CG	C:ASP443	3.0	59.7	1.0
	C27	C:6FT603	3.1	77.3	0.7
	CG	C:ASP549	3.2	69.8	1.0
	OD1	C:ASP443	3.2	63.6	1.0
	MG	C:MG601	3.3	66.1	1.0
	OD2	C:ASP498	3.4	67.8	1.0
	CB	C:ASP549	3.7	69.8	1.0
	O	C:GLY444	4.2	67.8	1.0
	NE2	C:HIS539	4.2	68.2	1.0
	OD2	C:ASP549	4.3	67.6	1.0
	CA	C:ASP549	4.3	64.6	1.0
	C03	C:6FT603	4.4	68.9	0.7
	CB	C:ASP443	4.5	58.1	1.0
	CG	C:ASP498	4.5	69.1	1.0
	C26	C:6FT603	4.6	76.6	0.7
	O05	C:6FT603	4.7	60.8	0.7
	OE2	C:GLU478	4.7	63.1	1.0
	CD2	C:HIS539	4.8	68.9	1.0
	OD1	C:ASP498	4.9	77.2	1.0
	CG2	C:VAL552	5.0	76.7	1.0

Reference:

J.Kankanala, K.A.Kirby, F.Liu, L.Miller, E.Nagy, D.J.Wilson, M.A.Parniak, S.G.Sarafianos, Z.Wang. Design, Synthesis, and Biological Evaluations of Hydroxypyridonecarboxylic Acids As Inhibitors of Hiv Reverse Transcriptase Associated Rnase H. J.Med.Chem. V. 59 5051 2016.
ISSN: ISSN 0022-2623
PubMed: 27094954
DOI: 10.1021/ACS.JMEDCHEM.6B00465

Page generated: Tue Aug 12 11:57:36 2025

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