Manganese in PDB 4e7l: Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution.

Enzymatic activity of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution.

All present enzymatic activity of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution.:
2.7.7.49; 2.7.7.7; 3.1.26.4;

Protein crystallography data

The structure of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution., PDB code: 4e7l was solved by G.N.Maertens, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	37.95 / 3.00
*Space group*	P 4₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	159.078, 159.078, 126.814, 90.00, 90.00, 90.00
*R / R_free (%)*	22.8 / 26.4

Other elements in 4e7l:

The structure of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution. also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution. (pdb code 4e7l). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution., PDB code: 4e7l:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4e7l

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Manganese Binding Sites List in 4e7l

Manganese binding site 1 out of 3 in the Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution.

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn402 b:67.4 occ:1.00	OD2	A:ASP128	2.5	67.6	1.0
	OE1	A:GLU221	2.6	50.9	1.0
	OE2	A:GLU221	2.6	58.0	1.0
	O3'	D:DA17	2.8	54.4	1.0
	CD	A:GLU221	2.9	49.1	1.0
	OD1	A:ASP128	3.0	53.9	1.0
	MN	A:MN403	3.0	66.4	1.0
	OP1	T:DC0	3.1	45.2	1.0
	CG	A:ASP128	3.1	54.2	1.0
	P	T:DC0	3.6	88.9	1.0
	C3'	D:DA17	3.9	35.8	1.0
	C4'	D:DA17	3.9	27.1	1.0
	O	A:TYR129	4.0	43.0	1.0
	O3'	t:DG-1	4.0	47.7	1.0
	C5'	T:DC0	4.2	45.6	1.0
	OD1	A:ASP185	4.2	58.2	1.0
	ND2	A:ASN224	4.3	37.9	1.0
	CG	A:GLU221	4.4	34.3	1.0
	O5'	T:DC0	4.4	54.0	1.0
	C2'	D:DA17	4.5	38.3	1.0
	CB	A:ASP128	4.6	52.6	1.0
	OP2	T:DC0	4.7	95.8	1.0
	C1'	D:DA17	4.8	47.3	1.0
	OP1	D:DA17	4.8	40.8	1.0
	C5'	D:DA17	4.9	35.2	1.0
	O4'	D:DA17	4.9	42.9	1.0

Manganese binding site 2 out of 3 in 4e7l

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Manganese Binding Sites List in 4e7l

Manganese binding site 2 out of 3 in the Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution.

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn403 b:66.4 occ:1.00	OD1	A:ASP185	2.4	58.2	1.0
	O3'	t:DG-1	2.5	47.7	1.0
	OD1	A:ASP128	2.7	53.9	1.0
	OP1	T:DC0	3.0	45.2	1.0
	MN	A:MN402	3.0	67.4	1.0
	CG	A:ASP128	3.5	54.2	1.0
	CG	A:ASP185	3.5	60.9	1.0
	C3'	t:DG-1	3.7	58.2	1.0
	OD2	A:ASP128	3.7	67.6	1.0
	OD2	A:ASP185	3.9	62.9	1.0
	O	A:TYR129	3.9	43.0	1.0
	C4'	t:DG-1	4.0	41.7	1.0
	N	A:TYR129	4.1	52.4	1.0
	C2'	t:DG-1	4.2	41.1	1.0
	P	T:DC0	4.4	88.9	1.0
	O3'	D:DA17	4.7	54.4	1.0
	CB	A:ASP185	4.8	57.0	1.0
	CB	A:ASP128	4.8	52.6	1.0
	CA	A:TYR129	4.8	47.7	1.0
	C	A:TYR129	4.8	42.2	1.0
	CB	A:TYR129	4.8	53.9	1.0
	C5'	T:DC0	4.9	45.6	1.0
	CA	A:ASP128	4.9	44.9	1.0
	OE2	A:GLU221	4.9	58.0	1.0
	C1'	t:DG-1	5.0	54.4	1.0

Manganese binding site 3 out of 3 in 4e7l

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Manganese Binding Sites List in 4e7l

Manganese binding site 3 out of 3 in the Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution.

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Pfv Integrase Strand Transfer Complex (Stc-Mn*) Following Reaction in Crystallo, at 3.0 A Resolution. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn402 b:53.6 occ:1.00	OD2	B:ASP128	2.4	56.0	1.0
	OD1	B:ASP128	2.4	56.7	1.0
	CG	B:ASP128	2.7	56.9	1.0
	OD1	B:ASP185	2.7	42.0	1.0
	OD2	B:ASP185	3.4	55.4	1.0
	CG	B:ASP185	3.5	52.0	1.0
	CB	B:ASP128	4.1	46.4	1.0
	N	B:TYR129	4.2	55.7	1.0
	O	B:TYR129	4.3	59.4	1.0
	CA	B:ASP128	4.6	52.8	1.0
	CE2	B:PHE190	4.9	55.4	1.0
	CB	B:ASP185	5.0	52.2	1.0
	C	B:ASP128	5.0	50.0	1.0

Reference:

S.Hare, G.N.Maertens, P.Cherepanov. 3'-Processing and Strand Transfer Catalysed By Retroviral Integrase in Crystallo. Embo J. V. 31 3020 2012.
ISSN: ISSN 0261-4189
PubMed: 22580823
DOI: 10.1038/EMBOJ.2012.118

Page generated: Sat Oct 5 19:15:10 2024

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