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Zinc in PDB 6c01: Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C)

Enzymatic activity of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C)

All present enzymatic activity of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C):
3.1.4.1; 3.6.1.9;

Protein crystallography data

The structure of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C), PDB code: 6c01 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) 48.27 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.184, 133.640, 167.430, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.4

Other elements in 6c01:

The structure of Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C) also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C) (pdb code 6c01). 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), PDB code: 6c01:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6c01

Go back to Zinc Binding Sites List in 6c01
Zinc binding site 1 out of 4 in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:28.5
occ:1.00
 OD2 A:ASP325 2.0 27.8 1.0
NE2 A:HIS329 2.1 25.7 1.0
NE2 A:HIS483 2.1 24.1 1.0
CG A:ASP325 2.7 30.0 1.0
OD1 A:ASP325 2.8 26.8 1.0
CD2 A:HIS329 3.0 27.6 1.0
CD2 A:HIS483 3.0 22.0 1.0
HD2 A:HIS329 3.1 33.1 1.0
HD2 A:HIS483 3.1 26.4 1.0
CE1 A:HIS329 3.2 30.6 1.0
CE1 A:HIS483 3.2 23.1 1.0
HE1 A:HIS329 3.4 36.7 1.0
HE1 A:HIS483 3.4 27.7 1.0
HE1 A:MET375 3.5 35.5 1.0
HE1 A:HIS373 3.5 34.6 1.0
CE1 A:HIS373 4.2 28.8 1.0
CG A:HIS329 4.2 28.1 1.0
CG A:HIS483 4.2 23.2 1.0
CB A:ASP325 4.2 31.3 1.0
ND1 A:HIS329 4.2 32.1 1.0
ND1 A:HIS483 4.3 26.3 1.0
ZN A:ZN902 4.4 34.4 1.0
CE A:MET375 4.4 29.6 1.0
NE2 A:HIS373 4.4 28.9 1.0
HB2 A:ASP325 4.5 37.5 1.0
HE2 A:MET375 4.5 35.5 1.0
OG1 A:THR205 4.5 25.8 1.0
OD1 A:ASP167 4.7 26.2 1.0
HB3 A:ASP325 4.7 37.5 1.0
HE3 A:MET375 4.9 35.5 1.0
HA A:ASP325 4.9 34.4 1.0
O A:ASP325 4.9 27.2 1.0
O A:HOH1024 5.0 34.9 1.0

Zinc binding site 2 out of 4 in 6c01

Go back to Zinc Binding Sites List in 6c01
Zinc binding site 2 out of 4 in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:34.4
occ:1.00
 OD1 A:ASP167 2.0 26.2 1.0
OG1 A:THR205 2.0 25.8 1.0
OD2 A:ASP372 2.1 25.2 1.0
NE2 A:HIS373 2.2 28.9 1.0
CG A:ASP167 2.6 24.8 1.0
OD2 A:ASP167 2.7 23.7 1.0
HG23 A:THR205 3.0 25.1 1.0
CG A:ASP372 3.0 28.7 1.0
CE1 A:HIS373 3.0 28.8 1.0
HA A:THR205 3.1 26.5 1.0
CB A:THR205 3.1 19.7 1.0
CD2 A:HIS373 3.1 28.2 1.0
HE1 A:HIS373 3.2 34.6 1.0
HD2 A:HIS373 3.4 33.8 1.0
OD1 A:ASP372 3.4 27.7 1.0
CG2 A:THR205 3.4 20.9 1.0
CA A:THR205 3.5 22.1 1.0
HG21 A:THR205 3.6 25.1 1.0
HE1 A:HIS209 3.8 38.5 1.0
HE1 A:HIS483 3.9 27.7 1.0
OD2 A:ASP325 3.9 27.8 1.0
HB A:THR205 3.9 23.7 1.0
N A:THR205 4.1 23.4 1.0
CB A:ASP167 4.1 23.2 1.0
ND1 A:HIS373 4.1 28.3 1.0
H A:GLY168 4.1 27.7 1.0
CG A:HIS373 4.2 27.2 1.0
H A:THR205 4.2 28.1 1.0
HB2 A:ASP325 4.2 37.5 1.0
CE1 A:HIS483 4.2 23.1 1.0
CG A:ASP325 4.3 30.0 1.0
HA A:ASP167 4.3 31.6 1.0
HG22 A:THR205 4.3 25.1 1.0
ZN A:ZN901 4.4 28.5 1.0
CB A:ASP372 4.4 26.8 1.0
N A:GLY168 4.4 23.1 1.0
NE2 A:HIS483 4.4 24.1 1.0
HH A:TYR320 4.4 37.5 1.0
HB2 A:ASP372 4.5 32.1 1.0
HB3 A:ASP167 4.6 27.8 1.0
HB2 A:ASP167 4.6 27.8 1.0
CE1 A:HIS209 4.6 32.1 1.0
CA A:ASP167 4.6 26.4 1.0
HD1 A:HIS209 4.6 39.1 1.0
CB A:ASP325 4.7 31.3 1.0
HB3 A:ASP372 4.8 32.1 1.0
C A:ASP167 4.8 26.8 1.0
C A:LYS204 4.8 26.0 1.0
HA2 A:GLY168 4.8 29.3 1.0
HD1 A:HIS373 4.8 34.0 1.0
OD1 A:ASP325 4.9 26.8 1.0
C A:THR205 4.9 23.9 1.0
HB3 A:ASP325 5.0 37.5 1.0
ND1 A:HIS209 5.0 32.5 1.0

Zinc binding site 3 out of 4 in 6c01

Go back to Zinc Binding Sites List in 6c01
Zinc binding site 3 out of 4 in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:29.0
occ:1.00
 OD2 B:ASP325 2.1 25.6 1.0
NE2 B:HIS483 2.1 24.5 1.0
NE2 B:HIS329 2.2 31.7 1.0
OD1 B:ASP325 2.7 25.1 1.0
CG B:ASP325 2.7 26.9 1.0
CD2 B:HIS329 3.0 31.6 1.0
CD2 B:HIS483 3.0 22.8 1.0
HD2 B:HIS329 3.1 38.0 1.0
HD2 B:HIS483 3.1 27.4 1.0
CE1 B:HIS483 3.2 24.1 1.0
CE1 B:HIS329 3.2 35.6 1.0
HE1 B:HIS483 3.4 28.9 1.0
HE1 B:MET375 3.5 45.6 1.0
HE1 B:HIS329 3.5 42.8 1.0
HE1 B:HIS373 3.6 27.6 1.0
CE1 B:HIS373 4.2 23.0 1.0
CB B:ASP325 4.2 28.9 1.0
CG B:HIS483 4.2 24.1 1.0
CG B:HIS329 4.2 32.4 1.0
ND1 B:HIS483 4.2 25.4 1.0
ND1 B:HIS329 4.3 34.6 1.0
ZN B:ZN902 4.4 33.7 1.0
OG1 B:THR205 4.4 38.2 1.0
NE2 B:HIS373 4.4 24.1 1.0
CE B:MET375 4.4 38.0 1.0
HB2 B:ASP325 4.4 34.7 1.0
HE2 B:MET375 4.6 45.6 1.0
OD2 B:ASP167 4.6 35.7 1.0
HB3 B:ASP325 4.7 34.7 1.0
O B:ASP325 4.8 33.0 1.0
HE3 B:MET375 4.9 45.6 1.0
HA B:ASP325 5.0 35.5 1.0
O B:HOH1057 5.0 37.7 1.0

Zinc binding site 4 out of 4 in 6c01

Go back to Zinc Binding Sites List in 6c01
Zinc binding site 4 out of 4 in the Human Ectonucleotide Pyrophosphatase / Phosphodiesterase 3 (ENPP3, NPP3, CD203C)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:33.7
occ:1.00
 OD2 B:ASP167 2.0 35.7 1.0
OD2 B:ASP372 2.0 25.1 1.0
OG1 B:THR205 2.0 38.2 1.0
NE2 B:HIS373 2.1 24.1 1.0
CG B:ASP167 2.6 34.5 1.0
OD1 B:ASP167 2.7 35.1 1.0
HG23 B:THR205 2.9 40.3 1.0
HA B:THR205 2.9 35.2 1.0
CB B:THR205 3.0 33.0 1.0
CG B:ASP372 3.0 26.2 1.0
CE1 B:HIS373 3.0 23.0 1.0
CD2 B:HIS373 3.1 23.6 1.0
HE1 B:HIS373 3.2 27.6 1.0
HD2 B:HIS373 3.3 28.3 1.0
OD1 B:ASP372 3.3 27.9 1.0
CG2 B:THR205 3.3 33.6 1.0
CA B:THR205 3.4 29.3 1.0
HG21 B:THR205 3.6 40.3 1.0
HE1 B:HIS209 3.7 37.3 1.0
HB B:THR205 3.8 39.5 1.0
HE1 B:HIS483 3.9 28.9 1.0
H B:GLY168 3.9 31.4 1.0
OD2 B:ASP325 3.9 25.6 1.0
N B:THR205 3.9 29.0 1.0
H B:THR205 4.0 34.8 1.0
ND1 B:HIS373 4.1 26.1 1.0
CB B:ASP167 4.1 28.8 1.0
CG B:HIS373 4.1 25.4 1.0
CE1 B:HIS483 4.2 24.1 1.0
HA B:ASP167 4.2 29.3 1.0
HG22 B:THR205 4.2 40.3 1.0
HB2 B:ASP325 4.2 34.7 1.0
CG B:ASP325 4.3 26.9 1.0
N B:GLY168 4.3 26.1 1.0
CB B:ASP372 4.3 22.3 1.0
ZN B:ZN901 4.4 29.0 1.0
HB2 B:ASP372 4.4 26.8 1.0
NE2 B:HIS483 4.4 24.5 1.0
HH B:TYR320 4.5 38.2 1.0
CE1 B:HIS209 4.5 31.1 1.0
HB3 B:ASP167 4.5 34.6 1.0
HB2 B:ASP167 4.6 34.6 1.0
CA B:ASP167 4.6 24.4 1.0
HD1 B:HIS209 4.7 38.8 1.0
HB3 B:ASP372 4.7 26.8 1.0
CB B:ASP325 4.7 28.9 1.0
C B:LYS204 4.7 29.6 1.0
C B:THR205 4.8 26.8 1.0
C B:ASP167 4.8 22.4 1.0
OD1 B:ASP325 4.8 25.1 1.0
HD1 B:HIS373 4.8 31.3 1.0
HA2 B:GLY168 4.8 32.9 1.0
HB3 B:ASP325 4.9 34.7 1.0
HA3 B:GLY168 5.0 32.9 1.0
ND1 B:HIS209 5.0 32.3 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 18:24:35 2024

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