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Zinc in PDB 6f30: Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Udpglcnac

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

All present enzymatic activity of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Udpglcnac:
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 Udpglcnac, PDB code: 6f30 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) 37.51 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.270, 127.682, 113.414, 90.00, 97.14, 90.00
R / Rfree (%) 19.6 / 21.3

Other elements in 6f30:

The structure of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Udpglcnac 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 Udpglcnac (pdb code 6f30). 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 Udpglcnac, PDB code: 6f30:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6f30

Go back to Zinc Binding Sites List in 6f30
Zinc binding site 1 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Udpglcnac


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 Udpglcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:47.1
occ:1.00
 OD1 A:ASP168 1.9 38.8 1.0
OD2 A:ASP373 2.0 45.1 1.0
O2A A:UD11001 2.0 54.4 1.0
NE2 A:HIS374 2.0 39.7 1.0
CG A:ASP168 2.6 40.4 1.0
OD2 A:ASP168 2.7 43.7 1.0
CE1 A:HIS374 2.8 39.3 1.0
CG A:ASP373 2.9 40.3 1.0
CD2 A:HIS374 3.1 39.6 1.0
OD1 A:ASP373 3.1 39.6 1.0
PA A:UD11001 3.5 55.0 1.0
CB A:ALA206 3.6 41.8 1.0
OD1 A:ASP326 3.9 49.6 1.0
CA A:ALA206 3.9 40.5 1.0
ND1 A:HIS374 3.9 39.6 1.0
O5B A:UD11001 3.9 56.2 1.0
CB A:ASP168 4.0 37.3 1.0
CG A:HIS374 4.0 37.9 1.0
N A:ALA206 4.1 40.9 1.0
CE1 A:HIS483 4.1 39.7 1.0
CG A:ASP326 4.2 48.9 1.0
N A:GLY169 4.2 36.9 1.0
O1A A:UD11001 4.2 54.1 1.0
CB A:ASP373 4.2 35.5 1.0
NE2 A:HIS483 4.3 40.2 1.0
ZN A:ZN1003 4.3 43.6 1.0
C5B A:UD11001 4.4 60.1 1.0
O3A A:UD11001 4.5 59.0 1.0
CA A:ASP168 4.5 35.4 1.0
OD2 A:ASP326 4.6 54.6 1.0
C A:ASP168 4.7 40.5 1.0
CB A:ASP326 4.7 39.6 1.0
O2B A:UD11001 4.7 61.6 1.0
CE1 A:HIS210 4.7 41.7 1.0
ND1 A:HIS483 4.8 40.1 1.0
CA A:GLY169 4.9 37.1 1.0
C A:LYS205 5.0 44.1 1.0

Zinc binding site 2 out of 4 in 6f30

Go back to Zinc Binding Sites List in 6f30
Zinc binding site 2 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Udpglcnac


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 Udpglcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:43.6
occ:1.00
 O1A A:UD11001 1.9 54.1 1.0
NE2 A:HIS483 1.9 40.2 1.0
NE2 A:HIS330 2.1 44.9 1.0
OD1 A:ASP326 2.1 49.6 1.0
OD2 A:ASP326 2.5 54.6 1.0
CG A:ASP326 2.6 48.9 1.0
CD2 A:HIS483 2.8 40.5 1.0
CD2 A:HIS330 2.9 45.5 1.0
CE1 A:HIS483 3.0 39.7 1.0
PA A:UD11001 3.1 55.0 1.0
CE1 A:HIS330 3.2 45.1 1.0
O2A A:UD11001 3.3 54.4 1.0
C1' A:UD11001 3.9 69.1 1.0
CG A:HIS483 4.0 38.7 1.0
O5B A:UD11001 4.0 56.2 1.0
CB A:ASP326 4.1 39.6 1.0
ND1 A:HIS483 4.1 40.1 1.0
CG A:HIS330 4.1 44.5 1.0
CE1 A:HIS374 4.1 39.3 1.0
O7' A:UD11001 4.1 69.9 1.0
C2' A:UD11001 4.2 70.5 1.0
O3A A:UD11001 4.2 59.0 1.0
ND1 A:HIS330 4.2 46.3 1.0
N2' A:UD11001 4.3 70.1 1.0
C7' A:UD11001 4.3 69.9 1.0
ZN A:ZN1002 4.3 47.1 1.0
NE2 A:HIS374 4.4 39.7 1.0
CE A:MET376 4.4 42.6 1.0
OD1 A:ASP168 4.5 38.8 1.0
O5' A:UD11001 4.5 71.1 1.0
O A:ASP326 4.7 42.9 1.0
O1' A:UD11001 4.7 66.6 1.0
PB A:UD11001 4.8 63.2 1.0
O2B A:UD11001 4.9 61.6 1.0
C A:ASP326 4.9 42.7 1.0
CA A:ASP326 4.9 38.3 1.0

Zinc binding site 3 out of 4 in 6f30

Go back to Zinc Binding Sites List in 6f30
Zinc binding site 3 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Udpglcnac


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 Udpglcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:54.9
occ:1.00
 OD1 B:ASP168 1.9 55.0 1.0
NE2 B:HIS374 2.0 52.0 1.0
O1A B:UD11001 2.0 74.9 1.0
OD2 B:ASP373 2.1 63.4 1.0
CG B:ASP168 2.6 55.0 1.0
OD2 B:ASP168 2.7 60.9 1.0
CE1 B:HIS374 2.7 51.3 1.0
CG B:ASP373 2.9 57.1 1.0
CD2 B:HIS374 3.1 51.1 1.0
OD1 B:ASP373 3.2 56.9 1.0
PA B:UD11001 3.3 75.9 1.0
CB B:ALA206 3.6 48.7 1.0
OD1 B:ASP326 3.8 51.5 1.0
O5B B:UD11001 3.9 76.2 1.0
ND1 B:HIS374 3.9 50.6 1.0
CA B:ALA206 3.9 46.6 1.0
CB B:ASP168 4.0 47.0 1.0
CG B:HIS374 4.0 48.3 1.0
N B:ALA206 4.1 46.2 1.0
CG B:ASP326 4.1 53.3 1.0
CE1 B:HIS483 4.1 49.8 1.0
N B:GLY169 4.2 43.4 1.0
ZN B:ZN1003 4.2 51.0 1.0
O2A B:UD11001 4.2 75.6 1.0
NE2 B:HIS483 4.3 50.6 1.0
CB B:ASP373 4.3 47.9 1.0
C5B B:UD11001 4.4 76.7 1.0
O3A B:UD11001 4.4 80.1 1.0
CA B:ASP168 4.5 44.2 1.0
O2B B:UD11001 4.5 84.0 1.0
OD2 B:ASP326 4.6 61.1 1.0
CB B:ASP326 4.7 46.4 1.0
C B:ASP168 4.7 48.1 1.0
CE1 B:HIS210 4.8 52.0 1.0
ND1 B:HIS483 4.8 49.4 1.0
CA B:GLY169 4.9 42.5 1.0
C B:LYS205 5.0 48.7 1.0

Zinc binding site 4 out of 4 in 6f30

Go back to Zinc Binding Sites List in 6f30
Zinc binding site 4 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Udpglcnac


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 Udpglcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:51.0
occ:1.00
 O2A B:UD11001 1.9 75.6 1.0
NE2 B:HIS483 1.9 50.6 1.0
NE2 B:HIS330 2.1 55.5 1.0
OD1 B:ASP326 2.2 51.5 1.0
OD2 B:ASP326 2.5 61.1 1.0
CG B:ASP326 2.7 53.3 1.0
CD2 B:HIS483 2.9 50.0 1.0
CD2 B:HIS330 2.9 56.6 1.0
PA B:UD11001 2.9 75.9 1.0
O1A B:UD11001 2.9 74.9 1.0
CE1 B:HIS483 3.0 49.8 1.0
CE1 B:HIS330 3.2 55.7 1.0
C1' B:UD11001 3.6 90.3 1.0
O3A B:UD11001 4.0 80.1 1.0
CG B:HIS483 4.0 47.6 1.0
O5B B:UD11001 4.1 76.2 1.0
ND1 B:HIS483 4.1 49.4 1.0
C2' B:UD11001 4.1 91.7 1.0
CE1 B:HIS374 4.1 51.3 1.0
CG B:HIS330 4.1 55.7 1.0
O5' B:UD11001 4.1 91.8 1.0
CB B:ASP326 4.2 46.4 1.0
ZN B:ZN1002 4.2 54.9 1.0
ND1 B:HIS330 4.3 57.4 1.0
O7' B:UD11001 4.3 91.2 1.0
NE2 B:HIS374 4.3 52.0 1.0
N2' B:UD11001 4.4 91.4 1.0
OD1 B:ASP168 4.5 55.0 1.0
O1' B:UD11001 4.5 87.5 1.0
CE B:MET376 4.5 46.4 1.0
C7' B:UD11001 4.5 91.4 1.0
PB B:UD11001 4.6 84.2 1.0
O2B B:UD11001 4.7 84.0 1.0
O B:ASP326 4.8 50.0 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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