Magnesium in PDB 4a5a: Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp

Enzymatic activity of Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp

All present enzymatic activity of Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp:
3.6.1.5;

Protein crystallography data

The structure of Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp, PDB code: 4a5a was solved by U.Krug, M.Zebisch, N.Straeter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	40.00 / 2.85
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	71.953, 150.668, 486.988, 90.00, 90.00, 90.00
*R / R_free (%)*	23.369 / 28.411

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp (pdb code 4a5a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp, PDB code: 4a5a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4a5a

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Magnesium Binding Sites List in 4a5a

Magnesium binding site 1 out of 4 in the Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp

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 the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg701 b:30.4 occ:1.00	O2G	A:ANP700	2.0	58.6	1.0
	O2B	A:ANP700	2.4	52.6	1.0
	PG	A:ANP700	3.4	53.0	1.0
	O2A	A:ANP700	3.6	58.0	1.0
	OE2	A:GLU236	3.6	36.7	1.0
	OE2	A:GLU277	3.7	43.5	1.0
	PB	A:ANP700	3.8	47.8	1.0
	NE1	A:TRP600	3.9	35.2	1.0
	N3B	A:ANP700	4.0	51.3	1.0
	O1G	A:ANP700	4.2	52.8	1.0
	OD2	A:ASP70	4.2	47.1	1.0
	CD1	A:TRP600	4.3	34.7	1.0
	NH2	A:ARG77	4.3	50.0	1.0
	OG1	A:THR188	4.3	31.2	1.0
	O3G	A:ANP700	4.5	54.3	1.0
	OD1	A:ASP70	4.5	46.8	1.0
	O3A	A:ANP700	4.6	51.8	1.0
	PA	A:ANP700	4.7	56.1	1.0
	CG	A:ASP70	4.8	44.4	1.0
	CD	A:GLU236	4.8	34.7	1.0
	CD	A:GLU277	4.9	42.0	1.0
	O1B	A:ANP700	5.0	47.6	1.0
	CA	A:GLY279	5.0	35.3	1.0

Magnesium binding site 2 out of 4 in 4a5a

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Magnesium Binding Sites List in 4a5a

Magnesium binding site 2 out of 4 in the Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp

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 the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg701 b:39.6 occ:1.00	O2G	B:ANP700	1.9	81.2	1.0
	O2B	B:ANP700	2.4	68.8	1.0
	PG	B:ANP700	3.4	78.9	1.0
	O2A	B:ANP700	3.5	93.7	1.0
	OE2	B:GLU236	3.7	39.5	1.0
	PB	B:ANP700	3.7	68.4	1.0
	OE2	B:GLU277	3.8	33.7	1.0
	NE1	B:TRP600	3.9	30.5	1.0
	N3B	B:ANP700	4.0	71.7	1.0
	OD2	B:ASP70	4.1	31.2	1.0
	NH2	B:ARG77	4.2	62.2	1.0
	O1G	B:ANP700	4.2	79.1	1.0
	OG1	B:THR188	4.3	36.9	1.0
	CD1	B:TRP600	4.3	31.5	1.0
	O3G	B:ANP700	4.4	75.2	1.0
	OD1	B:ASP70	4.5	31.7	1.0
	O3A	B:ANP700	4.6	79.7	1.0
	PA	B:ANP700	4.7	92.0	1.0
	CG	B:ASP70	4.8	30.9	1.0
	CD	B:GLU236	4.9	38.6	1.0
	O1B	B:ANP700	4.9	60.2	1.0
	CA	B:GLY279	5.0	29.3	1.0

Magnesium binding site 3 out of 4 in 4a5a

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Magnesium Binding Sites List in 4a5a

Magnesium binding site 3 out of 4 in the Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp

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 the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mg701 b:25.0 occ:1.00	O2G	C:ANP700	2.0	36.0	1.0
	O2B	C:ANP700	2.3	34.4	1.0
	PG	C:ANP700	3.5	33.0	1.0
	O2A	C:ANP700	3.6	38.8	1.0
	PB	C:ANP700	3.7	32.6	1.0
	OE2	C:GLU236	3.8	13.4	1.0
	OE2	C:GLU277	3.8	16.8	1.0
	NE1	C:TRP600	3.9	13.5	1.0
	OD2	C:ASP70	4.0	18.0	1.0
	N3B	C:ANP700	4.1	31.9	1.0
	NH2	C:ARG77	4.1	19.9	1.0
	O1G	C:ANP700	4.3	33.4	1.0
	OD1	C:ASP70	4.3	17.8	1.0
	CD1	C:TRP600	4.3	13.6	1.0
	OG1	C:THR188	4.4	15.4	1.0
	O3G	C:ANP700	4.5	32.0	1.0
	O3A	C:ANP700	4.5	35.7	1.0
	CG	C:ASP70	4.6	17.6	1.0
	PA	C:ANP700	4.6	36.3	1.0
	O1B	C:ANP700	4.8	33.2	1.0

Magnesium binding site 4 out of 4 in 4a5a

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Magnesium Binding Sites List in 4a5a

Magnesium binding site 4 out of 4 in the Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the C258S/C268S Variant of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolase 3 (NTPDASE3) in Complex with Magnesium and Amppnp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Mg701 b:25.8 occ:1.00	O2G	D:ANP700	2.1	42.5	1.0
	O2B	D:ANP700	2.4	45.0	1.0
	O2A	D:ANP700	3.4	46.0	1.0
	PG	D:ANP700	3.6	41.6	1.0
	OE2	D:GLU277	3.6	21.2	1.0
	PB	D:ANP700	3.8	41.2	1.0
	OE2	D:GLU236	3.8	19.1	1.0
	NE1	D:TRP600	3.9	12.6	1.0
	N3B	D:ANP700	4.1	40.5	1.0
	NH2	D:ARG77	4.1	20.2	1.0
	OD2	D:ASP70	4.2	17.2	1.0
	CD1	D:TRP600	4.3	12.7	1.0
	O1G	D:ANP700	4.3	45.2	1.0
	OG1	D:THR188	4.5	19.0	1.0
	O3A	D:ANP700	4.6	42.0	1.0
	PA	D:ANP700	4.6	42.0	1.0
	O3G	D:ANP700	4.6	36.7	1.0
	OD1	D:ASP70	4.6	16.8	1.0
	CD	D:GLU277	4.8	21.2	1.0
	CG	D:ASP70	4.8	16.8	1.0
	O1B	D:ANP700	4.9	37.1	1.0
	CA	D:GLY279	5.0	22.1	1.0
	CD	D:GLU236	5.0	18.2	1.0

Reference:

U.Krug, M.Zebisch, M.Krauss, N.Straeter. Structural Insight Into the Activation Mechanism of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolases By Disulfide Reduction. J.Biol.Chem. V. 287 3051 2012.
ISSN: ISSN 0021-9258
PubMed: 22130673
DOI: 10.1074/JBC.M111.294348

Page generated: Thu Aug 15 14:21:02 2024

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