Magnesium in PDB 7adv: Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V)

Enzymatic activity of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V)

All present enzymatic activity of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V):
2.7.7.49; 2.7.7.7; 3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V), PDB code: 7adv was solved by V.E.Pye, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	50.16 / 2.65
*Space group*	P 4₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	158.61, 158.61, 122.95, 90, 90, 90
*R / R_free (%)*	19.6 / 21.9

Other elements in 7adv:

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V) also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Zinc	(Zn)	1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V) (pdb code 7adv). 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 the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V), PDB code: 7adv:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7adv

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Magnesium Binding Sites List in 7adv

Magnesium binding site 1 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V)

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 the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg401 b:52.5 occ:1.00	N24	A:R7N404	1.9	61.1	1.0
	O	A:HOH542	2.1	61.6	1.0
	OD2	A:ASP185	2.1	64.2	1.0
	OD1	A:ASP128	2.1	58.2	1.0
	O	A:HOH534	2.2	58.4	1.0
	O23	A:R7N404	2.2	58.7	1.0
	C18	A:R7N404	2.8	61.6	1.0
	N22	A:R7N404	2.9	66.4	1.0
	CG	A:ASP185	2.9	58.3	1.0
	C25	A:R7N404	3.0	55.8	1.0
	CG	A:ASP128	3.1	52.0	1.0
	OD1	A:ASP185	3.2	65.3	1.0
	OD2	A:ASP128	3.5	65.0	1.0
	O	A:HOH516	3.7	67.2	1.0
	MG	A:MG402	4.0	54.6	1.0
	C19	A:R7N404	4.1	70.0	1.0
	C16	A:R7N404	4.2	62.3	1.0
	C26	A:R7N404	4.2	76.9	1.0
	CB	A:ASP185	4.2	58.9	1.0
	OE2	A:GLU221	4.4	54.7	1.0
	N	A:TYR129	4.4	47.3	1.0
	CB	A:ASP128	4.4	49.9	1.0
	O	A:TYR129	4.5	55.8	1.0
	O	A:HOH513	4.5	65.3	1.0
	N6	D:DA17	4.5	81.8	1.0
	O	D:HOH203	4.6	54.2	1.0
	N7	D:DA17	4.6	73.6	1.0
	C27	A:R7N404	4.7	58.6	1.0
	O21	A:R7N404	4.7	61.7	1.0
	CA	A:ASP128	4.8	52.5	1.0

Magnesium binding site 2 out of 3 in 7adv

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Magnesium Binding Sites List in 7adv

Magnesium binding site 2 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V)

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 the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg402 b:54.6 occ:1.00	O23	A:R7N404	2.0	58.7	1.0
	O	D:HOH203	2.0	54.2	1.0
	O21	A:R7N404	2.0	61.7	1.0
	OD2	A:ASP128	2.0	65.0	1.0
	OE1	A:GLU221	2.1	55.5	1.0
	OE2	A:GLU221	2.1	54.7	1.0
	CD	A:GLU221	2.4	52.4	1.0
	C16	A:R7N404	2.7	62.3	1.0
	N22	A:R7N404	2.7	66.4	1.0
	CG	A:ASP128	3.2	52.0	1.0
	ND2	A:ASN224	3.6	51.6	1.0
	OD1	A:ASP128	3.7	58.2	1.0
	CG	A:GLU221	3.9	52.6	1.0
	OP1	D:DA17	3.9	78.4	1.0
	O	A:HOH516	4.0	67.2	1.0
	MG	A:MG401	4.0	52.5	1.0
	C18	A:R7N404	4.0	61.6	1.0
	C15	A:R7N404	4.1	65.0	1.0
	O	A:TYR129	4.3	55.8	1.0
	N11	A:R7N404	4.3	55.1	1.0
	F8	A:R7N404	4.3	59.9	1.0
	CB	A:ASP128	4.4	49.9	1.0
	O	A:HOH542	4.4	61.6	1.0
	N24	A:R7N404	4.6	61.1	1.0
	CB	A:GLU221	4.7	48.9	1.0
	C8	D:DA17	4.7	71.9	1.0
	N7	D:DA17	4.7	73.6	1.0
	O3'	D:DC16	4.7	65.6	1.0
	C12	A:R7N404	4.8	62.0	1.0
	OD2	A:ASP185	4.8	64.2	1.0
	P	D:DA17	4.8	57.7	1.0
	CA	A:GLU221	4.9	51.7	1.0
	CG	A:ASN224	4.9	58.2	1.0
	C2'	D:DC16	4.9	47.7	1.0

Magnesium binding site 3 out of 3 in 7adv

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Magnesium Binding Sites List in 7adv

Magnesium binding site 3 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V)

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 the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ447 (Compound 6V) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg401 b:245.3 occ:1.00	OD2	B:ASP185	2.0	98.0	1.0
	OD1	B:ASP185	2.0	98.3	1.0
	OD1	B:ASP128	2.1	102.8	1.0
	CG	B:ASP185	2.3	86.1	1.0
	CG	B:ASP128	3.3	95.0	1.0
	CB	B:ASP185	3.8	71.1	1.0
	OD2	B:ASP128	3.9	97.0	1.0
	CE2	B:PHE190	4.0	63.8	1.0
	CB	B:ASP128	4.5	69.0	1.0
	N	B:ASP185	4.6	64.1	1.0
	N	B:TYR129	4.6	60.7	1.0
	CA	B:ASP185	4.7	68.2	1.0
	CA	B:ASP128	4.7	70.1	1.0
	CD2	B:PHE190	4.7	72.0	1.0
	N	B:GLY187	4.8	65.2	1.0
	CA	B:GLY187	4.9	62.4	1.0
	C	B:ASP185	5.0	70.5	1.0

Reference:

S.J.Smith, X.Z.Zhao, D.O.Passos, V.E.Pye, P.Cherepanov, D.Lyumkis, T.R.Burke Jr., S.H.Hughes. Hiv-1 Integrase Inhibitors with Modifications That Affect Their Potencies Against Drug Resistant Integrase Mutants. Acs Infect Dis. 2021.
ISSN: ESSN 2373-8227
PubMed: 33686850
DOI: 10.1021/ACSINFECDIS.0C00819

Page generated: Wed Oct 2 09:37:42 2024

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