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Calcium 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
Chlorine (Cl) 3 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6c02

Go back to Calcium Binding Sites List in 6c02
Calcium 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 Calcium with other atoms in the Ca 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:Ca903

b:52.5
occ:1.00
 OD1 A:ASN754 2.3 21.9 1.0
OD1 A:ASP760 2.3 13.6 1.0
OD1 A:ASP752 2.4 15.7 1.0
O A:HIS758 2.4 18.4 1.0
OD1 A:ASP756 2.4 18.4 1.0
O A:HOH1302 2.5 20.7 1.0
HA A:ASP752 3.0 16.7 1.0
HD21 A:ASN754 3.2 29.1 1.0
CG A:ASN754 3.3 21.4 1.0
CG A:ASP756 3.3 19.3 1.0
H A:HIS758 3.4 14.8 1.0
CG A:ASP752 3.4 12.8 1.0
H A:ASP756 3.4 20.8 1.0
C A:HIS758 3.5 13.3 1.0
CG A:ASP760 3.6 17.0 1.0
HA A:ASP760 3.6 22.8 1.0
ND2 A:ASN754 3.6 24.3 1.0
HB2 A:HIS758 3.7 21.1 1.0
OD2 A:ASP756 3.8 20.4 1.0
CA A:ASP752 3.8 13.9 1.0
H A:ASN754 3.8 26.8 1.0
N A:ASP760 3.9 18.5 1.0
C A:PHE759 3.9 19.2 1.0
O A:PHE759 4.0 16.8 1.0
CB A:ASP752 4.0 13.4 1.0
N A:HIS758 4.1 12.4 1.0
HB2 A:ASP752 4.1 16.1 1.0
CA A:ASP760 4.2 19.0 1.0
H A:ASP760 4.2 22.2 1.0
CA A:HIS758 4.2 15.4 1.0
N A:ASP756 4.3 17.3 1.0
OD2 A:ASP752 4.3 12.0 1.0
OD2 A:ASP760 4.4 17.8 1.0
H A:TYR755 4.4 23.4 1.0
C A:ASP752 4.4 16.1 1.0
O A:PHE751 4.4 17.2 1.0
CB A:HIS758 4.4 17.6 1.0
N A:PHE759 4.5 16.2 1.0
CB A:ASP760 4.5 18.2 1.0
CB A:ASP756 4.5 19.1 1.0
H A:TYR753 4.5 19.9 1.0
HD22 A:ASN754 4.5 29.1 1.0
HA A:PHE759 4.5 21.0 1.0
H A:GLY757 4.5 16.8 1.0
N A:ASN754 4.6 22.4 1.0
HB3 A:ASP756 4.6 22.9 1.0
CA A:PHE759 4.6 17.5 1.0
N A:TYR755 4.6 19.5 1.0
CB A:ASN754 4.6 21.6 1.0
N A:TYR753 4.7 16.6 1.0
CA A:ASP756 4.8 15.7 1.0
N A:GLY757 4.8 14.0 1.0
C A:ASN754 4.9 17.7 1.0
HB3 A:HIS758 4.9 21.1 1.0
OE1 A:GLU764 4.9 31.0 1.0
CA A:ASN754 4.9 20.0 1.0
O A:HOH1325 4.9 36.0 1.0
N A:ASP752 5.0 14.4 1.0
HB3 A:ASP752 5.0 16.1 1.0

Calcium binding site 2 out of 2 in 6c02

Go back to Calcium Binding Sites List in 6c02
Calcium 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 Calcium with other atoms in the Ca 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:Ca903

b:22.1
occ:1.00
 OD1 B:ASN754 2.3 25.1 1.0
OD1 B:ASP760 2.3 23.4 1.0
OD1 B:ASP752 2.3 19.2 1.0
O B:HOH1123 2.4 24.3 1.0
OD1 B:ASP756 2.4 25.1 1.0
O B:HIS758 2.4 20.9 1.0
HD21 B:ASN754 2.9 32.7 1.0
HA B:ASP752 3.1 25.6 1.0
CG B:ASN754 3.2 25.8 1.0
H B:HIS758 3.4 22.5 1.0
ND2 B:ASN754 3.4 27.2 1.0
CG B:ASP756 3.4 24.6 1.0
CG B:ASP752 3.4 20.4 1.0
C B:HIS758 3.5 22.2 1.0
H B:ASP756 3.5 28.3 1.0
HA B:ASP760 3.6 29.2 1.0
CG B:ASP760 3.6 25.1 1.0
HB2 B:HIS758 3.7 24.8 1.0
OD2 B:ASP756 3.8 24.9 1.0
H B:ASN754 3.9 29.4 1.0
CA B:ASP752 4.0 21.3 1.0
C B:PHE759 4.0 23.6 1.0
N B:HIS758 4.0 18.7 1.0
O B:PHE759 4.1 21.8 1.0
N B:ASP760 4.1 23.6 1.0
CB B:ASP752 4.1 22.0 1.0
CA B:ASP760 4.2 24.3 1.0
CA B:HIS758 4.2 20.0 1.0
HD22 B:ASN754 4.2 32.7 1.0
HB2 B:ASP752 4.2 26.4 1.0
N B:ASP756 4.3 23.6 1.0
OD2 B:ASP760 4.4 25.1 1.0
OD2 B:ASP752 4.4 18.8 1.0
CB B:HIS758 4.4 20.6 1.0
H B:TYR755 4.4 28.0 1.0
H B:ASP760 4.4 28.3 1.0
CB B:ASP760 4.5 22.8 1.0
OE1 B:GLU764 4.5 30.9 1.0
N B:PHE759 4.5 20.8 1.0
O B:PHE751 4.5 22.8 1.0
CB B:ASN754 4.6 27.0 1.0
CB B:ASP756 4.6 23.2 1.0
O B:HOH1170 4.6 33.7 1.0
C B:ASP752 4.6 21.5 1.0
H B:GLY757 4.6 21.8 1.0
HA B:PHE759 4.7 27.9 1.0
N B:ASN754 4.7 24.5 1.0
CA B:PHE759 4.7 23.2 1.0
N B:TYR755 4.7 23.3 1.0
H B:TYR753 4.7 27.3 1.0
HB3 B:ASP756 4.7 27.9 1.0
N B:GLY757 4.8 18.1 1.0
CA B:ASP756 4.9 21.9 1.0
N B:TYR753 4.9 22.8 1.0
HB3 B:HIS758 4.9 24.8 1.0
HB3 B:ASN754 4.9 32.4 1.0
C B:ASN754 5.0 23.2 1.0
CA B:ASN754 5.0 25.5 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: Wed Jul 9 13:01:14 2025

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