Manganese in PDB 3nv8: The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with Phosphoenol Pyruvate and Manganese (Thesit-Free)

Enzymatic activity of The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with Phosphoenol Pyruvate and Manganese (Thesit-Free)

All present enzymatic activity of The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with Phosphoenol Pyruvate and Manganese (Thesit-Free):
2.5.1.54;

Protein crystallography data

The structure of The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with Phosphoenol Pyruvate and Manganese (Thesit-Free), PDB code: 3nv8 was solved by E.J.Parker, G.B.Jameson, W.Jiao, R.H.Hutton, C.J.Webby, E.N.Baker, H.M.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	39.37 / 2.25
*Space group*	P 3₂ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	203.538, 203.538, 66.422, 90.00, 90.00, 120.00
*R / R_free (%)*	18 / 20.8

Other elements in 3nv8:

The structure of The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with Phosphoenol Pyruvate and Manganese (Thesit-Free) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with Phosphoenol Pyruvate and Manganese (Thesit-Free) (pdb code 3nv8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with Phosphoenol Pyruvate and Manganese (Thesit-Free), PDB code: 3nv8:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 3nv8

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Manganese Binding Sites List in 3nv8

Manganese binding site 1 out of 2 in the The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with Phosphoenol Pyruvate and Manganese (Thesit-Free)

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with Phosphoenol Pyruvate and Manganese (Thesit-Free) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn464 b:49.0 occ:0.75	OE2	A:GLU411	1.9	48.5	1.0
	OD2	A:ASP441	2.2	43.4	1.0
	NE2	A:HIS369	2.4	45.5	1.0
	SG	A:CYS87	2.6	33.5	1.0
	CD	A:GLU411	2.7	44.6	1.0
	OE1	A:GLU411	2.9	48.0	1.0
	CG	A:ASP441	3.2	47.9	1.0
	CE1	A:HIS369	3.3	46.2	1.0
	CD2	A:HIS369	3.4	45.8	1.0
	CB	A:ASP441	3.4	47.0	1.0
	CB	A:CYS87	3.7	26.8	1.0
	O1	A:PEP467	3.7	64.9	1.0
	O	A:HOH601	4.0	42.8	1.0
	CG	A:GLU411	4.1	38.3	1.0
	NH1	A:ARG382	4.2	49.2	1.0
	CA	A:CYS87	4.2	26.8	1.0
	OD1	A:ASP441	4.3	43.9	1.0
	NH2	A:ARG126	4.4	31.1	1.0
	ND1	A:HIS369	4.4	47.6	1.0
	CG	A:HIS369	4.5	46.1	1.0
	C1	A:PEP467	4.6	62.4	1.0
	O	A:CYS87	4.7	26.3	1.0
	CA	A:ASP441	4.7	47.7	1.0
	C	A:CYS87	4.8	25.7	1.0
	N	A:ASP441	4.8	47.5	1.0
	NH2	A:ARG382	4.9	50.5	1.0

Manganese binding site 2 out of 2 in 3nv8

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Manganese Binding Sites List in 3nv8

Manganese binding site 2 out of 2 in the The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with Phosphoenol Pyruvate and Manganese (Thesit-Free)

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase in Complex with Phosphoenol Pyruvate and Manganese (Thesit-Free) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn465 b:42.9 occ:0.50	OD2	B:ASP441	2.0	53.6	1.0
	OE2	B:GLU411	2.2	49.6	1.0
	NE2	B:HIS369	2.5	42.3	1.0
	OE1	B:GLU411	2.5	45.1	1.0
	SG	B:CYS87	2.6	37.4	1.0
	CD	B:GLU411	2.7	44.2	1.0
	CG	B:ASP441	3.0	54.3	1.0
	CE1	B:HIS369	3.0	45.8	1.0
	CB	B:ASP441	3.4	54.3	1.0
	CD2	B:HIS369	3.6	45.8	1.0
	CB	B:CYS87	3.7	31.3	1.0
	OD1	B:ASP441	4.1	52.0	1.0
	CG	B:GLU411	4.2	40.0	1.0
	NH2	B:ARG126	4.2	33.0	1.0
	ND1	B:HIS369	4.2	46.9	1.0
	CA	B:CYS87	4.3	29.8	1.0
	NH2	B:ARG382	4.3	54.9	1.0
	CG	B:HIS369	4.6	45.5	1.0
	NH1	B:ARG382	4.6	51.6	1.0
	CA	B:ASP441	4.7	55.2	1.0
	N	B:ASP441	4.8	55.4	1.0
	C	B:CYS87	5.0	29.5	1.0
	O	B:CYS87	5.0	29.6	1.0
	CZ	B:ARG382	5.0	54.2	1.0
	CZ	B:ARG126	5.0	29.8	1.0

Reference:

C.J.Webby, W.Jiao, R.D.Hutton, N.J.Blackmore, H.M.Baker, E.N.Baker, G.B.Jameson, E.J.Parker. Synergistic Allostery, A Sophisticated Regulatory Network For the Control of Aromatic Amino Acid Biosynthesis in Mycobacterium Tuberculosis J.Biol.Chem. V. 285 30567 2010.
ISSN: ISSN 0021-9258
PubMed: 20667835
DOI: 10.1074/JBC.M110.111856

Page generated: Sat Oct 5 17:21:27 2024

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