Nickel in PDB 1iid: Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla

Enzymatic activity of Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla

All present enzymatic activity of Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla:
2.3.1.97;

Protein crystallography data

The structure of Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla, PDB code: 1iid was solved by T.A.Farazi, J.I.Gordon, G.Waksman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	29.72 / 2.50
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	75.129, 97.060, 141.809, 90.00, 90.00, 90.00
*R / R_free (%)*	24.2 / 28.8

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla (pdb code 1iid). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla, PDB code: 1iid:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1iid

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Nickel Binding Sites List in 1iid

Nickel binding site 1 out of 2 in the Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla

Mono view

Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ni1 b:67.9 occ:1.00	OD1	A:ASP37	2.2	63.7	1.0
	O	A:ALA34	2.3	66.1	1.0
	NE2	A:HIS38	2.5	51.2	1.0
	CA	A:ALA34	2.6	67.0	1.0
	OD2	A:ASP37	2.6	63.7	1.0
	C	A:ALA34	2.7	66.6	1.0
	CG	A:ASP37	2.7	63.2	1.0
	CE1	A:HIS38	2.9	51.0	1.0
	N	A:ALA34	3.3	66.8	1.0
	CD2	A:HIS38	3.5	50.7	1.0
	CB	A:ALA34	3.8	67.5	1.0
	N	A:MET35	3.9	66.0	1.0
	ND1	A:HIS38	3.9	50.3	1.0
	CB	A:ASP37	4.2	62.0	1.0
	CG	A:HIS38	4.3	52.2	1.0
	O	A:VAL209	4.5	47.3	1.0
	N	A:ASP37	4.6	61.3	1.0
	O	A:ASP37	4.7	59.0	1.0
	CA	A:MET35	4.7	66.2	1.0
	CA	A:ASP37	4.8	60.5	1.0
	C	A:ASP37	4.8	59.2	1.0
	CE1	A:PHE49	4.9	33.5	1.0

Nickel binding site 2 out of 2 in 1iid

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Nickel Binding Sites List in 1iid

Nickel binding site 2 out of 2 in the Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla

Mono view

Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Saccharomyces Cerevisiae N- Myristoyltransferase with Bound S-(2-Oxo)Pentadecylcoa and the Octapeptide Glyaskla within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ni2 b:62.4 occ:1.00	ND1	A:HIS296	2.4	47.5	1.0
	O	A:HOH534	2.4	41.3	1.0
	O	A:HOH552	2.7	50.4	1.0
	CG	A:HIS296	3.3	47.4	1.0
	CE1	A:HIS296	3.4	47.5	1.0
	CB	A:HIS296	3.5	45.4	1.0
	O	A:HOH535	4.1	40.5	1.0
	CA	A:HIS296	4.1	43.0	1.0
	O	A:LYS125	4.2	48.7	1.0
	CD2	A:HIS296	4.4	47.5	1.0
	NE2	A:HIS296	4.5	48.5	1.0
	O	A:HIS296	5.0	41.3	1.0
	C	A:HIS296	5.0	42.8	1.0

Reference:

T.A.Farazi, G.Waksman, J.I.Gordon. Structures of Saccharomyces Cerevisiae N-Myristoyltransferase with Bound Myristoylcoa and Peptide Provide Insights About Substrate Recognition and Catalysis. Biochemistry V. 40 6335 2001.
ISSN: ISSN 0006-2960
PubMed: 11371195
DOI: 10.1021/BI0101401

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