Magnesium in PDB 6fd6: Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 30 Days Post Crystallization (with Amp and Ppi Products Fully Generated)

Enzymatic activity of Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 30 Days Post Crystallization (with Amp and Ppi Products Fully Generated)

All present enzymatic activity of Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 30 Days Post Crystallization (with Amp and Ppi Products Fully Generated):
2.4.2.7;

Protein crystallography data

The structure of Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 30 Days Post Crystallization (with Amp and Ppi Products Fully Generated), PDB code: 6fd6 was solved by P.Nioche, J.Huyet, M.Ozeir, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	44.62 / 1.80
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	47.170, 47.790, 47.920, 76.93, 61.50, 69.41
*R / R_free (%)*	15.1 / 18.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 30 Days Post Crystallization (with Amp and Ppi Products Fully Generated) (pdb code 6fd6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 30 Days Post Crystallization (with Amp and Ppi Products Fully Generated), PDB code: 6fd6:

Magnesium binding site 1 out of 1 in 6fd6

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Magnesium Binding Sites List in 6fd6

Magnesium binding site 1 out of 1 in the Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 30 Days Post Crystallization (with Amp and Ppi Products Fully Generated)

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 Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 30 Days Post Crystallization (with Amp and Ppi Products Fully Generated) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg202 b:19.1 occ:0.60	O21	B:PPV203	1.8	29.8	0.6
	O22	B:PPV203	2.2	15.5	0.6
	O	B:HOH304	2.2	26.4	1.0
	O3'	B:AMP201	2.2	16.5	1.0
	O	B:HOH333	2.5	39.1	1.0
	O2'	B:AMP201	2.8	17.4	1.0
	P1	B:PPV203	3.1	25.5	0.6
	P2	B:PPV203	3.3	21.1	0.6
	C3'	B:AMP201	3.4	15.7	1.0
	OPP	B:PPV203	3.5	24.7	0.6
	C2'	B:AMP201	3.6	15.6	1.0
	O32	B:PPV203	3.9	14.7	0.6
	NE	B:ARG67	4.0	11.4	0.5
	O31	B:PPV203	4.0	25.2	0.6
	NH2	B:ARG67	4.0	11.2	0.5
	OD1	B:ASP127	4.0	10.9	1.0
	C1'	B:AMP201	4.1	14.2	1.0
	OD1	B:ASP128	4.1	12.1	1.0
	N	B:SER66	4.1	12.4	1.0
	OD2	B:ASP127	4.2	12.6	1.0
	N	B:ARG67	4.2	11.2	1.0
	CZ	B:ARG67	4.2	12.2	0.5
	O	B:ASP65	4.2	12.4	1.0
	C4'	B:AMP201	4.2	14.0	1.0
	O11	B:PPV203	4.3	32.7	0.6
	CB	B:ARG67	4.3	11.3	0.5
	CZ	B:ARG67	4.3	27.2	0.5
	CB	B:ARG67	4.3	14.8	0.5
	O4'	B:AMP201	4.3	14.5	1.0
	NH2	B:ARG67	4.4	28.6	0.5
	CG	B:ARG67	4.5	17.4	0.5
	CG	B:ASP127	4.5	12.5	1.0
	NH1	B:ARG67	4.5	25.2	0.5
	O12	B:PPV203	4.6	20.0	0.6
	NE	B:ARG67	4.6	24.5	0.5
	C	B:ASP65	4.6	10.9	1.0
	O	B:HOH344	4.6	29.7	1.0
	CG	B:ARG67	4.8	11.3	0.5
	CA	B:ARG67	4.8	10.6	0.5
	CA	B:ARG67	4.8	12.0	0.5
	CD	B:ARG67	4.8	12.4	0.5

Reference:

J.Huyet, M.Ozeir, M.C.Burgevin, B.Pinson, F.Chesney, J.M.Remy, A.R.Siddiqi, R.Lupoli, G.Pinon, C.Saint-Marc, J.F.Gibert, R.Morales, I.Ceballos-Picot, R.Barouki, B.Daignan-Fornier, A.Olivier-Bandini, F.Auge, P.Nioche. Structural Insights Into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase. Cell Chem Biol V. 25 666 2018.
ISSN: ESSN 2451-9448
PubMed: 29576532
DOI: 10.1016/J.CHEMBIOL.2018.02.011

Page generated: Tue Oct 1 00:24:26 2024

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