Nickel in PDB 7z1j: Escherichia Coli Periplasmic Phytase Appa, Complex with Phosphate

Enzymatic activity of Escherichia Coli Periplasmic Phytase Appa, Complex with Phosphate

All present enzymatic activity of Escherichia Coli Periplasmic Phytase Appa, Complex with Phosphate:
3.1.3.2; 3.1.3.26;

Protein crystallography data

The structure of Escherichia Coli Periplasmic Phytase Appa, Complex with Phosphate, PDB code: 7z1j was solved by I.M.Acquistapace, C.A.Brearley, A.M.Hemmings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	49.85 / 1.85
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	63.57, 47.63, 65.7, 90, 101, 90
*R / R_free (%)*	14.8 / 22.7

Other elements in 7z1j:

The structure of Escherichia Coli Periplasmic Phytase Appa, Complex with Phosphate also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Escherichia Coli Periplasmic Phytase Appa, Complex with Phosphate (pdb code 7z1j). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Escherichia Coli Periplasmic Phytase Appa, Complex with Phosphate, PDB code: 7z1j:

Nickel binding site 1 out of 1 in 7z1j

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Nickel Binding Sites List in 7z1j

Nickel binding site 1 out of 1 in the Escherichia Coli Periplasmic Phytase Appa, Complex with Phosphate

Mono view

Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Escherichia Coli Periplasmic Phytase Appa, Complex with Phosphate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ni503 b:30.0 occ:1.00	O	A:HOH605	2.1	32.6	1.0
	CE1	A:HIS250	2.3	12.4	1.0
	OD1	A:ASP325	2.3	15.3	1.0
	OD2	A:ASP325	2.4	11.9	1.0
	OG1	A:THR327	2.4	14.3	1.0
	O	A:THR327	2.5	12.7	1.0
	CG	A:ASP325	2.7	11.0	1.0
	NE2	A:HIS250	3.0	12.7	1.0
	C	A:THR327	3.2	10.7	1.0
	ND1	A:HIS250	3.3	14.0	1.0
	CB	A:THR327	3.5	12.6	1.0
	CA	A:THR327	3.7	10.2	1.0
	NH1	A:ARG16	3.7	17.8	1.0
	OE2	A:GLU219	3.8	29.6	1.0
	N	A:THR327	3.9	9.1	1.0
	O	A:HOH613	4.0	41.2	1.0
	O	A:HOH705	4.0	18.8	1.0
	OD2	A:ASP304	4.1	17.3	1.0
	CB	A:ASP304	4.1	14.2	1.0
	CB	A:ASP325	4.2	6.5	1.0
	N	A:PRO328	4.2	7.8	1.0
	CD2	A:HIS250	4.3	10.8	1.0
	CZ	A:ARG16	4.3	15.9	1.0
	CG	A:HIS250	4.4	11.8	1.0
	CA	A:PRO328	4.6	7.2	1.0
	CG	A:ASP304	4.6	15.6	1.0
	CD	A:GLU219	4.7	27.2	1.0
	CG2	A:THR327	4.8	12.1	1.0
	NH2	A:ARG16	4.8	14.9	1.0
	NE	A:ARG16	4.9	13.6	1.0
	CA	A:ASP325	5.0	8.3	1.0

Reference:

I.M.Acquistapace, E.J.Thompson, I.Kuhn, M.R.Bedford, C.A.Brearley, A.M.Hemmings. Insights to the Structural Basis For the Stereospecificity of the Escherichia Coli Phytase, Appa. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 35683026
DOI: 10.3390/IJMS23116346

Page generated: Fri Apr 7 19:27:01 2023

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