Magnesium in PDB 1qs4: Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone

Enzymatic activity of Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone

All present enzymatic activity of Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone:
2.7.7.49;

Protein crystallography data

The structure of Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone, PDB code: 1qs4 was solved by Y.Goldgur, R.Craigie, T.Fujiwara, T.Yoshinaga, D.R.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	38.07 / 2.10
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	76.233, 46.735, 141.361, 90.00, 105.55, 90.00
*R / R_free (%)*	20.9 / 25.5

Other elements in 1qs4:

The structure of Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone (pdb code 1qs4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone, PDB code: 1qs4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1qs4

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Magnesium Binding Sites List in 1qs4

Magnesium binding site 1 out of 3 in the Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1001 b:37.1 occ:1.00	OD1	A:ASP116	2.3	30.4	1.0
	O	A:HOH1120	2.3	34.4	1.0
	OD1	A:ASP64	2.3	31.9	1.0
	O	A:HOH1076	2.3	32.4	1.0
	O	A:HOH1073	2.4	29.0	1.0
	O	A:HOH1013	2.4	37.1	1.0
	CG	A:ASP64	3.3	29.5	1.0
	CG	A:ASP116	3.3	31.2	1.0
	OD2	A:ASP64	3.5	29.6	1.0
	OD2	A:ASP116	3.8	30.7	1.0
	O	A:HOH1047	4.0	23.5	1.0
	O	A:HOH1042	4.1	34.3	1.0
	O	A:CYS65	4.3	30.7	1.0
	N	A:CYS65	4.4	29.0	1.0
	O	A:HOH1077	4.5	31.6	1.0
	CB	A:ASP116	4.6	30.9	1.0
	CB	A:ASP64	4.6	29.7	1.0
	CA	A:ASP64	5.0	29.5	1.0
	N9	A:1001004	5.0	57.3	1.0

Magnesium binding site 2 out of 3 in 1qs4

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Magnesium Binding Sites List in 1qs4

Magnesium binding site 2 out of 3 in the Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg1002 b:44.8 occ:1.00	OD1	B:ASP116	2.3	30.4	1.0
	OD1	B:ASP64	2.4	32.4	1.0
	O	B:HOH1100	2.5	39.8	1.0
	O	B:HOH1185	2.5	54.2	1.0
	O	B:HOH1118	2.5	57.3	1.0
	O	B:HOH1092	2.5	30.7	1.0
	CG	B:ASP64	3.3	30.7	1.0
	CG	B:ASP116	3.5	29.5	1.0
	OD2	B:ASP64	3.5	31.8	1.0
	OD2	B:ASP116	3.9	29.2	1.0
	O	B:CYS65	4.2	33.4	1.0
	O	B:HOH1016	4.2	22.9	1.0
	O	B:HOH1097	4.3	48.0	1.0
	N	B:CYS65	4.5	30.7	1.0
	O	B:HOH1108	4.5	48.3	1.0
	O	B:HOH1179	4.5	54.3	1.0
	CB	B:ASP64	4.7	29.2	1.0
	CB	B:ASP116	4.7	28.6	1.0
	O	B:HOH1173	4.9	50.4	1.0

Magnesium binding site 3 out of 3 in 1qs4

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Magnesium Binding Sites List in 1qs4

Magnesium binding site 3 out of 3 in the Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Core Domain of Hiv-1 Integrase Complexed with Mg++ and 1-(5- Chloroindol-3-Yl)-3-Hydroxy-3-(2H-Tetrazol-5-Yl)-Propenone within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mg1003 b:44.8 occ:1.00	O	C:HOH1050	2.3	27.8	1.0
	O	C:HOH1105	2.4	38.0	1.0
	OD1	C:ASP116	2.4	24.0	1.0
	O	C:HOH1023	2.5	22.1	1.0
	O	C:HOH1103	2.6	47.2	1.0
	OD1	C:ASP64	2.6	26.4	1.0
	CG	C:ASP116	3.5	23.7	1.0
	CG	C:ASP64	3.5	25.0	1.0
	OD2	C:ASP64	3.7	24.7	1.0
	OD2	C:ASP116	3.9	22.5	1.0
	O	C:HOH1138	3.9	44.4	1.0
	O	C:HOH1104	4.0	43.0	1.0
	O	C:HOH1024	4.4	21.0	1.0
	O	C:CYS65	4.4	24.6	1.0
	O	C:HOH1107	4.5	31.7	1.0
	N	C:CYS65	4.7	22.4	1.0
	O	C:HOH1156	4.7	52.9	1.0
	CB	C:ASP116	4.8	22.4	1.0
	O	C:HOH1131	4.9	44.5	1.0
	CB	C:ASP64	4.9	23.4	1.0

Reference:

Y.Goldgur, R.Craigie, G.H.Cohen, T.Fujiwara, T.Yoshinaga, T.Fujishita, H.Sugimoto, T.Endo, H.Murai, D.R.Davies. Structure of the Hiv-1 Integrase Catalytic Domain Complexed with An Inhibitor: A Platform For Antiviral Drug Design. Proc.Natl.Acad.Sci.Usa V. 96 13040 1999.
ISSN: ISSN 0027-8424
PubMed: 10557269
DOI: 10.1073/PNAS.96.23.13040

Page generated: Tue Aug 13 11:55:18 2024

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