Magnesium in PDB 3a8m: Crystal Structure of Nitrile Hydratase Mutant Y72F Complexed with Trimethylacetonitrile

Enzymatic activity of Crystal Structure of Nitrile Hydratase Mutant Y72F Complexed with Trimethylacetonitrile

All present enzymatic activity of Crystal Structure of Nitrile Hydratase Mutant Y72F Complexed with Trimethylacetonitrile:
4.2.1.84;

Protein crystallography data

The structure of Crystal Structure of Nitrile Hydratase Mutant Y72F Complexed with Trimethylacetonitrile, PDB code: 3a8m was solved by Y.Yamanaka, K.Hashimoto, A.Ohtaki, K.Noguchi, M.Yohda, M.Odaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	25.00 / 1.32
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	114.280, 60.110, 81.811, 90.00, 125.06, 90.00
*R / R_free (%)*	15.7 / 19

Other elements in 3a8m:

The structure of Crystal Structure of Nitrile Hydratase Mutant Y72F Complexed with Trimethylacetonitrile also contains other interesting chemical elements:

Iron

(Fe)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nitrile Hydratase Mutant Y72F Complexed with Trimethylacetonitrile (pdb code 3a8m). 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 Nitrile Hydratase Mutant Y72F Complexed with Trimethylacetonitrile, PDB code: 3a8m:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3a8m

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Magnesium Binding Sites List in 3a8m

Magnesium binding site 1 out of 3 in the Crystal Structure of Nitrile Hydratase Mutant Y72F Complexed with Trimethylacetonitrile

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 Nitrile Hydratase Mutant Y72F Complexed with Trimethylacetonitrile within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg301 b:8.1 occ:0.50	O	B:HOH393	2.0	18.3	1.0
	O	B:HOH366	2.0	18.0	1.0
	O	B:HOH400	2.0	21.2	1.0
	O	B:HOH364	2.2	21.1	1.0
	O	B:HOH255	2.3	11.6	1.0
	O	B:HOH395	2.5	18.3	0.5
	O	B:HOH380	4.1	19.1	1.0
	O	B:HOH355	4.3	16.0	1.0
	CB	B:ALA144	4.4	10.1	1.0
	O	B:ASP6	4.4	8.3	1.0
	OD2	B:ASP6	4.4	8.4	1.0
	O	B:GLY3	4.5	7.6	1.0
	O	B:ASP2	4.5	8.3	1.0
	CB	B:ASP6	4.5	7.4	1.0
	CB	B:ASP2	4.6	9.2	1.0
	C	B:ASP2	4.6	7.1	1.0
	CG	B:ASP6	4.7	7.2	1.0
	OD1	B:ASP2	4.7	13.0	1.0
	CA	B:ASP2	4.7	8.3	1.0
	CG	B:ASP2	4.7	11.0	1.0

Magnesium binding site 2 out of 3 in 3a8m

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Magnesium Binding Sites List in 3a8m

Magnesium binding site 2 out of 3 in the Crystal Structure of Nitrile Hydratase Mutant Y72F Complexed with Trimethylacetonitrile

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 Nitrile Hydratase Mutant Y72F Complexed with Trimethylacetonitrile within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg302 b:12.2 occ:0.50	O	B:HOH411	1.8	19.9	1.0
	O	B:HOH278	2.1	31.8	1.0
	O	B:HOH363	2.1	18.9	1.0
	O	B:HOH422	2.2	27.0	1.0
	O	B:HOH299	2.3	35.2	1.0
	O	B:HOH374	2.3	50.0	1.0
	O	B:HOH233	4.2	9.0	1.0
	OE1	B:GLU74	4.3	10.6	1.0
	O	A:HOH295	4.4	20.7	1.0
	CE	B:MET69	4.5	12.0	0.8
	CD	B:PRO71	4.5	8.7	1.0
	O	B:MET69	4.6	8.9	1.0
	CE	B:MET69	4.6	10.3	0.2
	CG	B:PRO71	5.0	10.8	1.0

Magnesium binding site 3 out of 3 in 3a8m

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Magnesium Binding Sites List in 3a8m

Magnesium binding site 3 out of 3 in the Crystal Structure of Nitrile Hydratase Mutant Y72F Complexed with Trimethylacetonitrile

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 Nitrile Hydratase Mutant Y72F Complexed with Trimethylacetonitrile within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg303 b:14.0 occ:0.50	O	B:HOH300	1.6	25.6	1.0
	O	B:HOH264	2.0	29.0	1.0
	O	B:HOH284	2.0	28.7	1.0
	O	B:HOH375	2.1	26.8	1.0
	O	B:HOH232	2.1	25.7	1.0
	O	B:HOH379	2.2	17.8	1.0
	OE1	B:GLU96	4.2	14.2	1.0
	O	B:HOH347	4.3	15.5	1.0
	O	B:HOH271	4.4	32.7	1.0
	O	B:HOH334	4.9	36.3	1.0

Reference:

Y.Yamanaka, K.Hashimoto, A.Ohtaki, K.Noguchi, M.Yohda, M.Odaka. Kinetic and Structural Studies on Roles of the Serine Ligand and A Strictly Conserved Tyrosine Residue in Nitrile Hydratase J.Biol.Inorg.Chem. V. 15 655 2010.
ISSN: ISSN 0949-8257
PubMed: 20221653
DOI: 10.1007/S00775-010-0632-3

Page generated: Wed Aug 14 08:30:49 2024

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