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Zinc 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:

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

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6c02

Go back to Zinc Binding Sites List in 6c02
Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn901

b:41.2
occ:1.00
 NE2 A:HIS483 1.9 28.8 1.0
O2A A:APC927 1.9 44.6 1.0
NE2 A:HIS329 2.1 18.8 1.0
OD2 A:ASP325 2.3 16.7 1.0
OD1 A:ASP325 2.5 16.2 1.0
CG A:ASP325 2.7 15.8 1.0
CE1 A:HIS483 2.9 19.6 1.0
CD2 A:HIS483 3.0 19.6 1.0
CD2 A:HIS329 3.0 17.5 1.0
HE1 A:HIS483 3.0 23.6 1.0
CE1 A:HIS329 3.1 17.9 1.0
HD2 A:HIS329 3.2 21.0 1.0
HD2 A:HIS483 3.2 23.5 1.0
HE1 A:HIS373 3.3 18.3 1.0
HE1 A:HIS329 3.3 21.4 1.0
PA A:APC927 3.4 38.0 1.0
H5'1 A:APC927 3.4 36.5 1.0
HE1 A:MET375 3.6 21.5 1.0
ZN A:ZN902 3.7 19.0 0.3
O1A A:APC927 3.9 32.3 1.0
O A:HOH1495 3.9 39.2 1.0
CE1 A:HIS373 4.0 15.3 1.0
ND1 A:HIS483 4.0 17.8 1.0
O2B A:APC927 4.0 40.3 1.0
CG A:HIS483 4.1 16.7 1.0
C5' A:APC927 4.1 30.4 1.0
O5' A:APC927 4.2 32.8 1.0
CG A:HIS329 4.2 18.8 1.0
O A:HOH1496 4.2 38.5 1.0
ND1 A:HIS329 4.2 19.8 1.0
NE2 A:HIS373 4.2 14.7 1.0
CB A:ASP325 4.2 15.4 1.0
H5'2 A:APC927 4.4 36.5 1.0
CE A:MET375 4.5 17.9 1.0
HB2 A:ASP325 4.6 18.5 1.0
OD1 A:ASP167 4.6 18.9 1.0
HE2 A:MET375 4.6 21.5 1.0
HB3 A:ASP325 4.7 18.5 1.0
C3A A:APC927 4.7 38.5 1.0
H3A1 A:APC927 4.7 46.3 1.0
HD1 A:HIS483 4.8 21.4 1.0
HB2 A:ALA205 4.8 16.1 1.0
O A:ASP325 4.8 16.9 1.0
HA A:ASP325 4.9 18.5 1.0
O A:HOH1164 5.0 29.5 1.0

Zinc binding site 2 out of 4 in 6c02

Go back to Zinc Binding Sites List in 6c02
Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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
A:Zn902

b:19.0
occ:0.31
 OD1 A:ASP167 1.8 18.9 1.0
NE2 A:HIS373 2.0 14.7 1.0
OD2 A:ASP372 2.3 16.1 1.0
HB2 A:ALA205 2.5 16.1 1.0
CE1 A:HIS373 2.7 15.3 1.0
CG A:ASP167 2.7 17.6 1.0
HE1 A:HIS373 2.7 18.3 1.0
OD2 A:ASP167 2.9 19.8 1.0
CD2 A:HIS373 3.1 13.4 1.0
CG A:ASP372 3.3 15.1 1.0
CB A:ALA205 3.3 13.4 1.0
HA A:ALA205 3.4 16.2 1.0
HD2 A:HIS373 3.4 16.1 1.0
OD2 A:ASP325 3.5 16.7 1.0
HB1 A:ALA205 3.6 16.1 1.0
H5'2 A:APC927 3.6 36.5 1.0
OD1 A:ASP372 3.6 12.4 1.0
CG A:ASP325 3.6 15.8 1.0
ZN A:ZN901 3.7 41.2 1.0
HE1 A:HIS483 3.7 23.6 1.0
CA A:ALA205 3.8 13.5 1.0
ND1 A:HIS373 3.8 14.2 1.0
OD1 A:ASP325 3.8 16.2 1.0
CE1 A:HIS483 3.9 19.6 1.0
H A:GLY168 3.9 16.5 1.0
NE2 A:HIS483 3.9 28.8 1.0
HB2 A:ASP325 4.0 18.5 1.0
O5' A:APC927 4.0 32.8 1.0
O2A A:APC927 4.0 44.6 1.0
H A:ALA205 4.0 17.8 1.0
CG A:HIS373 4.0 10.9 1.0
N A:ALA205 4.0 14.8 1.0
HB3 A:ALA205 4.1 16.1 1.0
O1A A:APC927 4.1 32.3 1.0
CB A:ASP167 4.1 16.4 1.0
C5' A:APC927 4.1 30.4 1.0
H5'1 A:APC927 4.2 36.5 1.0
HE1 A:HIS209 4.2 16.5 1.0
N A:GLY168 4.3 13.8 1.0
HA A:ASP167 4.3 17.5 1.0
PA A:APC927 4.3 38.0 1.0
CB A:ASP325 4.4 15.4 1.0
HB3 A:ASP167 4.5 19.7 1.0
HD1 A:HIS373 4.5 17.0 1.0
CA A:ASP167 4.6 14.6 1.0
CB A:ASP372 4.6 14.3 1.0
HB2 A:ASP372 4.6 17.2 1.0
HA2 A:GLY168 4.6 18.3 1.0
ND1 A:HIS483 4.7 17.8 1.0
HB3 A:ASP325 4.7 18.5 1.0
HB2 A:ASP167 4.7 19.7 1.0
C A:ASP167 4.8 13.7 1.0
CD2 A:HIS483 4.8 19.6 1.0
HA3 A:GLY168 4.8 18.3 1.0
C A:LYS204 4.8 13.3 1.0
HH A:TYR320 4.8 21.1 1.0
CA A:GLY168 4.9 15.2 1.0
HA A:LYS204 4.9 19.0 1.0

Zinc binding site 3 out of 4 in 6c02

Go back to Zinc Binding Sites List in 6c02
Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn binding site number 3 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:Zn901

b:31.1
occ:1.00
 O2A B:APC919 1.8 41.2 1.0
NE2 B:HIS483 1.9 26.6 1.0
NE2 B:HIS329 2.1 22.1 1.0
OD1 B:ASP325 2.4 16.9 1.0
OD2 B:ASP325 2.4 17.7 1.0
CG B:ASP325 2.7 16.5 1.0
CE1 B:HIS483 2.8 19.1 1.0
CD2 B:HIS483 3.0 21.0 1.0
HE1 B:HIS483 3.0 23.0 1.0
CD2 B:HIS329 3.0 18.1 1.0
CE1 B:HIS329 3.1 20.3 1.0
HD2 B:HIS329 3.2 21.7 1.0
HD2 B:HIS483 3.2 25.2 1.0
PA B:APC919 3.2 38.1 1.0
HE1 B:HIS329 3.3 24.4 1.0
HE1 B:HIS373 3.3 18.0 1.0
ZN B:ZN902 3.4 29.1 0.4
H5'1 B:APC919 3.4 38.9 1.0
HE1 B:MET375 3.5 20.3 1.0
O1A B:APC919 3.8 36.2 1.0
ND1 B:HIS483 4.0 17.2 1.0
CE1 B:HIS373 4.0 15.0 1.0
O B:HOH1450 4.1 40.5 1.0
O5' B:APC919 4.1 34.5 1.0
CG B:HIS483 4.1 15.3 1.0
C5' B:APC919 4.1 32.4 1.0
O2B B:APC919 4.1 44.1 1.0
ND1 B:HIS329 4.2 23.0 1.0
CG B:HIS329 4.2 18.9 1.0
CB B:ASP325 4.2 15.0 1.0
NE2 B:HIS373 4.3 19.2 1.0
H5'2 B:APC919 4.3 38.9 1.0
CE B:MET375 4.5 16.9 1.0
OD1 B:ASP167 4.5 20.5 1.0
C3A B:APC919 4.5 42.7 1.0
HB2 B:ASP325 4.5 18.0 1.0
HB3 B:ASP325 4.6 18.0 1.0
H3A1 B:APC919 4.6 51.2 1.0
HE2 B:MET375 4.6 20.3 1.0
HB2 B:ALA205 4.7 18.4 1.0
HD1 B:HIS483 4.7 20.7 1.0
O B:ASP325 4.8 13.0 1.0
HA B:ASP325 4.9 18.1 1.0
HD1 B:HIS329 5.0 27.6 1.0
HE3 B:MET375 5.0 20.3 1.0
PB B:APC919 5.0 46.4 1.0

Zinc binding site 4 out of 4 in 6c02

Go back to Zinc Binding Sites List in 6c02
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn binding site number 4 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:Zn902

b:29.1
occ:0.42
 OD1 B:ASP167 2.0 20.5 1.0
NE2 B:HIS373 2.2 19.2 1.0
HB2 B:ALA205 2.4 18.4 1.0
OD2 B:ASP372 2.6 11.3 1.0
HE1 B:HIS373 2.7 18.0 1.0
CE1 B:HIS373 2.8 15.0 1.0
CG B:ASP167 2.9 17.7 1.0
OD2 B:ASP167 3.1 17.1 1.0
CB B:ALA205 3.3 15.3 1.0
HE1 B:HIS483 3.3 23.0 1.0
H5'2 B:APC919 3.4 38.9 1.0
ZN B:ZN901 3.4 31.1 1.0
HA B:ALA205 3.4 17.8 1.0
OD2 B:ASP325 3.4 17.7 1.0
CD2 B:HIS373 3.5 15.9 1.0
O5' B:APC919 3.5 34.5 1.0
O2A B:APC919 3.5 41.2 1.0
HB1 B:ALA205 3.6 18.4 1.0
CG B:ASP325 3.6 16.5 1.0
CE1 B:HIS483 3.6 19.1 1.0
CG B:ASP372 3.6 12.2 1.0
O1A B:APC919 3.6 36.2 1.0
NE2 B:HIS483 3.7 26.6 1.0
CA B:ALA205 3.7 14.8 1.0
C5' B:APC919 3.8 32.4 1.0
OD1 B:ASP325 3.8 16.9 1.0
PA B:APC919 3.8 38.1 1.0
H5'1 B:APC919 3.8 38.9 1.0
HD2 B:HIS373 3.9 19.1 1.0
H B:ALA205 3.9 19.5 1.0
OD1 B:ASP372 3.9 10.7 1.0
ND1 B:HIS373 4.0 13.1 1.0
HB3 B:ALA205 4.0 18.4 1.0
N B:ALA205 4.0 16.3 1.0
HB2 B:ASP325 4.1 18.0 1.0
H B:GLY168 4.2 13.8 1.0
HE1 B:HIS209 4.3 19.5 1.0
CB B:ASP167 4.3 17.3 1.0
CG B:HIS373 4.3 14.6 1.0
CB B:ASP325 4.4 15.0 1.0
N B:GLY168 4.5 11.5 1.0
ND1 B:HIS483 4.5 17.2 1.0
HB3 B:ASP167 4.5 20.8 1.0
HA B:ASP167 4.6 17.6 1.0
CD2 B:HIS483 4.6 21.0 1.0
HD1 B:HIS373 4.6 15.7 1.0
HB3 B:ASP325 4.7 18.0 1.0
HA2 B:GLY168 4.8 13.8 1.0
C B:LYS204 4.8 14.0 1.0
CA B:ASP167 4.8 14.7 1.0
HA B:LYS204 4.9 16.3 1.0
HA3 B:GLY168 4.9 13.8 1.0
HD1 B:HIS483 4.9 20.7 1.0
HB2 B:ASP167 4.9 20.8 1.0
HB2 B:ASP372 4.9 11.4 1.0
CB B:ASP372 4.9 9.5 1.0
C B:ASP167 5.0 14.3 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: Mon Oct 28 18:24:34 2024

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