Sodium in PDB 6c02: Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), Inactive (T205A), N594S, with Alpha,Beta-Methylene-Atp (Ampcpp)

Enzymatic activity of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), Inactive (T205A), N594S, with Alpha,Beta-Methylene-Atp (Ampcpp)

All present enzymatic activity of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), Inactive (T205A), N594S, with Alpha,Beta-Methylene-Atp (Ampcpp):
3.1.4.1; 3.6.1.9;

Protein crystallography data

The structure of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), Inactive (T205A), N594S, with Alpha,Beta-Methylene-Atp (Ampcpp), PDB code: 6c02 was solved by A.Gorelik, A.Randriamihaja, K.Illes, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	48.62 / 1.94
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	78.656, 169.457, 79.062, 90.00, 103.87, 90.00
*R / R_free (%)*	16.6 / 19.7

Other elements in 6c02:

The structure of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), Inactive (T205A), N594S, with Alpha,Beta-Methylene-Atp (Ampcpp) also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Calcium	(Ca)	2 atoms
Chlorine	(Cl)	3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), Inactive (T205A), N594S, with Alpha,Beta-Methylene-Atp (Ampcpp) (pdb code 6c02). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), Inactive (T205A), N594S, with Alpha,Beta-Methylene-Atp (Ampcpp), PDB code: 6c02:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6c02

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Sodium Binding Sites List in 6c02

Sodium binding site 1 out of 2 in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), Inactive (T205A), N594S, with Alpha,Beta-Methylene-Atp (Ampcpp)

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), Inactive (T205A), N594S, with Alpha,Beta-Methylene-Atp (Ampcpp) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na921 b:40.6 occ:1.00	O	A:HOH1138	2.4	39.0	1.0
	O	A:ASP685	2.5	33.5	1.0
	O	A:TYR682	2.7	37.7	1.0
	O	A:ILE688	2.7	39.7	1.0
	HA	A:LYS686	3.4	42.3	1.0
	CL	A:CL922	3.5	65.9	1.0
	HA	A:THR689	3.5	38.0	1.0
	C	A:ILE688	3.7	37.9	1.0
	C	A:ASP685	3.7	34.0	1.0
	C	A:TYR682	3.7	37.6	1.0
	H	A:ILE688	3.8	46.8	1.0
	HB	A:THR689	3.8	37.3	1.0
	HA	A:LEU683	4.0	48.7	1.0
	HB3	A:TYR682	4.1	39.9	1.0
	O	A:HOH1598	4.1	39.7	1.0
	CA	A:LYS686	4.2	35.3	1.0
	CA	A:THR689	4.2	31.7	1.0
	N	A:THR689	4.3	34.0	1.0
	C	A:LYS686	4.4	33.0	1.0
	N	A:LYS686	4.4	34.2	1.0
	HG1	A:THR689	4.4	39.5	1.0
	HA	A:TYR682	4.4	42.1	1.0
	N	A:ILE688	4.4	39.0	1.0
	CB	A:THR689	4.4	31.1	1.0
	HB3	A:ASP685	4.5	42.0	1.0
	O	A:LYS686	4.5	30.1	1.0
	N	A:LEU683	4.6	38.6	1.0
	CA	A:TYR682	4.6	35.1	1.0
	O	A:LEU683	4.6	41.4	1.0
	CA	A:LEU683	4.6	40.6	1.0
	HD3	A:LYS686	4.6	50.1	1.0
	CA	A:ILE688	4.7	39.0	1.0
	C	A:LEU683	4.8	40.2	1.0
	H	A:ASP685	4.8	42.6	1.0
	CA	A:ASP685	4.8	34.4	1.0
	CB	A:TYR682	4.8	33.3	1.0
	OG1	A:THR689	4.9	32.9	1.0
	N	A:ASP685	4.9	35.5	1.0
	N	A:ASN687	4.9	37.3	1.0
	HD1	A:TYR682	5.0	37.0	1.0

Sodium binding site 2 out of 2 in 6c02

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Sodium Binding Sites List in 6c02

Sodium binding site 2 out of 2 in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), Inactive (T205A), N594S, with Alpha,Beta-Methylene-Atp (Ampcpp)

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), Inactive (T205A), N594S, with Alpha,Beta-Methylene-Atp (Ampcpp) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na916 b:38.9 occ:1.00	O	B:TYR682	2.3	46.9	1.0
	O	B:HOH1476	2.8	40.9	1.0
	O	B:HOH1510	2.9	39.7	1.0
	O	B:ILE688	3.0	44.5	1.0
	O	B:ASP685	3.0	46.4	1.0
	O	B:HOH1495	3.0	45.1	1.0
	HA	B:THR689	3.3	50.0	1.0
	C	B:TYR682	3.3	45.7	1.0
	HB3	B:TYR682	3.5	51.6	1.0
	HB	B:THR689	3.7	52.2	1.0
	HA	B:LEU683	3.7	59.4	1.0
	C	B:ILE688	3.9	41.7	1.0
	CA	B:THR689	4.0	41.6	1.0
	HA	B:TYR682	4.0	51.4	1.0
	CA	B:TYR682	4.1	42.8	1.0
	N	B:LEU683	4.2	46.9	1.0
	C	B:ASP685	4.2	47.5	1.0
	CB	B:THR689	4.2	43.5	1.0
	HA	B:LYS686	4.2	65.8	1.0
	H	B:ILE688	4.2	51.4	1.0
	CB	B:TYR682	4.3	43.0	1.0
	N	B:THR689	4.3	39.6	1.0
	CA	B:LEU683	4.3	49.5	1.0
	OG1	B:THR689	4.5	45.0	1.0
	HB3	B:ASP685	4.5	51.6	1.0
	HD1	B:TYR682	4.5	48.2	1.0
	O	B:LEU683	4.6	46.3	1.0
	C	B:LEU683	4.7	47.8	1.0
	HD23	B:LEU683	4.7	69.8	1.0
	HB2	B:TYR682	4.8	51.6	1.0
	HG1	B:THR689	4.9	54.0	1.0
	H	B:ASP685	4.9	56.7	1.0
	N	B:ILE688	4.9	42.8	1.0
	H	B:LEU683	4.9	56.3	1.0
	CA	B:LYS686	4.9	54.8	1.0

Reference:

A.Gorelik, A.Randriamihaja, K.Illes, B.Nagar. Structural Basis For Nucleotide Recognition By the Ectoenzyme CD203C. Febs J. V. 285 2481 2018.
ISSN: ISSN 1742-4658
PubMed: 29717535
DOI: 10.1111/FEBS.14489

Page generated: Tue Oct 8 02:16:49 2024

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