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: Wed Dec 16 11:33:54 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy