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Zinc in PDB 6f2y: Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A

Enzymatic activity of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A

All present enzymatic activity of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A:
3.1.4.1; 3.6.1.9;

Protein crystallography data

The structure of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A, PDB code: 6f2y was solved by C.Dohler, M.Zebisch, N.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.24 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.940, 126.850, 114.480, 90.00, 97.54, 90.00
R / Rfree (%) 20.4 / 21.7

Other elements in 6f2y:

The structure of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A (pdb code 6f2y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A, PDB code: 6f2y:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6f2y

Go back to Zinc Binding Sites List in 6f2y
Zinc binding site 1 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:55.4
occ:1.00
 OD1 A:ASP168 1.9 43.8 1.0
NE2 A:HIS374 2.0 37.4 1.0
O1A A:B4P1001 2.1 61.5 1.0
OD2 A:ASP373 2.1 46.5 1.0
CE1 A:HIS374 2.7 37.0 1.0
CG A:ASP168 2.7 42.8 1.0
OD2 A:ASP168 2.9 47.0 1.0
CG A:ASP373 3.0 38.4 1.0
CD2 A:HIS374 3.1 37.3 1.0
OD1 A:ASP373 3.2 36.1 1.0
PA A:B4P1001 3.3 61.0 1.0
CB A:ALA206 3.3 36.3 1.0
O5E A:B4P1001 3.7 59.2 1.0
CA A:ALA206 3.7 35.2 1.0
OD1 A:ASP326 3.7 40.2 1.0
ND1 A:HIS374 3.8 37.4 1.0
N A:ALA206 4.0 35.9 1.0
O3A A:B4P1001 4.0 64.6 1.0
CG A:HIS374 4.0 35.6 1.0
CG A:ASP326 4.1 40.6 1.0
CB A:ASP168 4.1 33.6 1.0
CE1 A:HIS483 4.2 37.2 1.0
N A:GLY169 4.2 32.5 1.0
NE2 A:HIS483 4.2 37.7 1.0
ZN A:ZN1003 4.2 44.0 1.0
CB A:ASP373 4.3 33.6 1.0
C5E A:B4P1001 4.4 57.8 1.0
OD2 A:ASP326 4.5 46.9 1.0
O2A A:B4P1001 4.5 60.7 1.0
CA A:ASP168 4.5 31.5 1.0
CB A:ASP326 4.7 32.5 1.0
C A:ASP168 4.7 36.3 1.0
CE1 A:HIS210 4.8 38.0 1.0
CA A:GLY169 4.8 32.5 1.0
ND1 A:HIS483 4.9 37.7 1.0
C A:LYS205 4.9 39.4 1.0

Zinc binding site 2 out of 4 in 6f2y

Go back to Zinc Binding Sites List in 6f2y
Zinc binding site 2 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:44.0
occ:1.00
 NE2 A:HIS483 1.9 37.7 1.0
O2A A:B4P1001 2.0 60.7 1.0
NE2 A:HIS330 2.0 38.3 1.0
OD1 A:ASP326 2.3 40.2 1.0
O1A A:B4P1001 2.4 61.5 1.0
OD2 A:ASP326 2.5 46.9 1.0
PA A:B4P1001 2.6 61.0 1.0
CG A:ASP326 2.7 40.6 1.0
CD2 A:HIS483 2.9 38.0 1.0
CD2 A:HIS330 2.9 38.9 1.0
CE1 A:HIS483 3.0 37.2 1.0
CE1 A:HIS330 3.1 38.4 1.0
O3A A:B4P1001 3.3 64.6 1.0
O5E A:B4P1001 4.0 59.2 1.0
CG A:HIS483 4.0 36.2 1.0
ND1 A:HIS483 4.1 37.7 1.0
CE1 A:HIS374 4.1 37.0 1.0
CG A:HIS330 4.1 38.0 1.0
ND1 A:HIS330 4.2 39.7 1.0
CB A:ASP326 4.2 32.5 1.0
ZN A:ZN1002 4.2 55.4 1.0
NE2 A:HIS374 4.4 37.4 1.0
CE A:MET376 4.4 38.0 1.0
OD1 A:ASP168 4.6 43.8 1.0
O A:ASP326 4.8 35.7 1.0
C5E A:B4P1001 4.8 57.8 1.0
PB A:B4P1001 4.8 68.5 1.0
O3G A:B4P1001 4.8 76.2 1.0

Zinc binding site 3 out of 4 in 6f2y

Go back to Zinc Binding Sites List in 6f2y
Zinc binding site 3 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:67.4
occ:1.00
 O1A B:B4P1001 1.9 79.1 1.0
OD1 B:ASP168 1.9 48.6 1.0
NE2 B:HIS374 2.1 47.3 1.0
OD2 B:ASP373 2.2 61.0 1.0
CG B:ASP168 2.7 47.5 1.0
CE1 B:HIS374 2.8 46.9 1.0
OD2 B:ASP168 2.8 51.4 1.0
PA B:B4P1001 3.0 79.2 1.0
CG B:ASP373 3.1 53.5 1.0
CB B:ALA206 3.1 44.6 1.0
CD2 B:HIS374 3.2 46.9 1.0
OD1 B:ASP373 3.4 53.4 1.0
O5E B:B4P1001 3.5 76.2 1.0
CA B:ALA206 3.6 43.1 1.0
O3A B:B4P1001 3.6 83.3 1.0
OD1 B:ASP326 3.8 48.7 1.0
N B:ALA206 3.9 43.1 1.0
ND1 B:HIS374 4.0 46.9 1.0
CG B:ASP326 4.1 49.4 1.0
CB B:ASP168 4.1 38.6 1.0
ZN B:ZN1003 4.1 44.0 1.0
CE1 B:HIS483 4.2 46.8 1.0
CG B:HIS374 4.2 44.8 1.0
NE2 B:HIS483 4.3 47.5 1.0
O2A B:B4P1001 4.3 79.5 1.0
N B:GLY169 4.3 36.2 1.0
OD2 B:ASP326 4.3 56.5 1.0
C5E B:B4P1001 4.4 73.4 1.0
CB B:ASP373 4.4 43.1 1.0
CA B:ASP168 4.6 36.3 1.0
CB B:ASP326 4.7 41.1 1.0
C B:ASP168 4.8 40.3 1.0
C B:LYS205 4.8 46.2 1.0
CE1 B:HIS210 4.8 43.6 1.0
ND1 B:HIS483 4.9 46.9 1.0
CA B:GLY169 5.0 35.8 1.0

Zinc binding site 4 out of 4 in 6f2y

Go back to Zinc Binding Sites List in 6f2y
Zinc binding site 4 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with AP4A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:44.0
occ:1.00
 NE2 B:HIS483 1.9 47.5 1.0
O2A B:B4P1001 1.9 79.5 1.0
NE2 B:HIS330 2.1 49.1 1.0
OD1 B:ASP326 2.3 48.7 1.0
O1A B:B4P1001 2.4 79.1 1.0
OD2 B:ASP326 2.5 56.5 1.0
PA B:B4P1001 2.6 79.2 1.0
CG B:ASP326 2.7 49.4 1.0
CD2 B:HIS330 2.9 49.9 1.0
CE1 B:HIS483 2.9 46.8 1.0
CD2 B:HIS483 2.9 47.4 1.0
CE1 B:HIS330 3.2 49.1 1.0
O3A B:B4P1001 3.4 83.3 1.0
O B:HOH1198 3.7 53.3 1.0
O5E B:B4P1001 4.0 76.2 1.0
CG B:HIS483 4.1 45.2 1.0
ND1 B:HIS483 4.1 46.9 1.0
CE1 B:HIS374 4.1 46.9 1.0
CG B:HIS330 4.1 48.9 1.0
ZN B:ZN1002 4.1 67.4 1.0
CB B:ASP326 4.2 41.1 1.0
ND1 B:HIS330 4.2 50.5 1.0
NE2 B:HIS374 4.3 47.3 1.0
CE B:MET376 4.5 44.3 1.0
O3B B:B4P1001 4.6 92.5 1.0
OD1 B:ASP168 4.6 48.6 1.0
PB B:B4P1001 4.6 88.1 1.0
C5E B:B4P1001 4.7 73.4 1.0
O B:ASP326 4.8 44.1 1.0

Reference:

C.Dohler, M.Zebisch, N.Strater. Crystal Structure and Substrate Binding Mode of Ectonucleotide Phosphodiesterase/Pyrophosphatase-3 (NPP3). Sci Rep V. 8 10874 2018.
ISSN: ESSN 2045-2322
PubMed: 30022031
DOI: 10.1038/S41598-018-28814-Y
Page generated: Mon Oct 28 20:36:29 2024

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