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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 / Rfree (%) 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

Go back to 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

Go back to 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 Dec 15 12:00:27 2020

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