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Zinc in PDB 6f2t: Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3)

Enzymatic activity of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3)

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

Protein crystallography data

The structure of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3), PDB code: 6f2t 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) 47.35 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.843, 124.063, 110.673, 90.00, 97.03, 90.00
R / Rfree (%) 21.5 / 22.9

Other elements in 6f2t:

The structure of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) 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) (pdb code 6f2t). 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), PDB code: 6f2t:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6f2t

Go back to Zinc Binding Sites List in 6f2t
Zinc binding site 1 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3)


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

b:43.2
occ:1.00
 OD1 A:ASP168 1.9 41.1 1.0
OD2 A:ASP373 1.9 49.4 1.0
OG1 A:THR206 2.0 42.0 1.0
NE2 A:HIS374 2.0 40.1 1.0
CG A:ASP168 2.6 41.7 1.0
OD2 A:ASP168 2.7 44.8 1.0
CE1 A:HIS374 2.8 39.7 1.0
CG A:ASP373 2.9 44.3 1.0
CB A:THR206 3.0 43.9 1.0
CD2 A:HIS374 3.1 40.4 1.0
OD1 A:ASP373 3.2 45.2 1.0
CA A:THR206 3.3 38.3 1.0
CG2 A:THR206 3.5 41.4 1.0
O4 A:PO41001 3.5 67.1 1.0
N A:THR206 3.8 38.7 1.0
ND1 A:HIS374 3.9 40.3 1.0
CB A:ASP168 4.0 37.1 1.0
CG A:HIS374 4.0 38.7 1.0
OD1 A:ASP326 4.1 45.5 1.0
CB A:ASP373 4.2 37.5 1.0
CE1 A:HIS483 4.2 41.9 1.0
CG A:ASP326 4.4 46.5 1.0
NE2 A:HIS483 4.4 42.3 1.0
N A:GLY169 4.4 36.4 1.0
ZN A:ZN1003 4.5 44.9 1.0
O2 A:PO41001 4.5 68.0 1.0
CA A:ASP168 4.5 35.8 1.0
P A:PO41001 4.6 67.2 1.0
CE1 A:HIS210 4.6 42.2 1.0
C A:LYS205 4.6 42.0 1.0
OD2 A:ASP326 4.6 52.5 1.0
C A:THR206 4.7 42.0 1.0
C A:ASP168 4.8 40.2 1.0
O A:HOH1227 4.8 38.0 1.0
ND1 A:HIS210 4.9 42.7 1.0
ND1 A:HIS483 4.9 42.5 1.0
CB A:ASP326 4.9 40.4 1.0
O3 A:PO41001 4.9 67.4 1.0

Zinc binding site 2 out of 4 in 6f2t

Go back to Zinc Binding Sites List in 6f2t
Zinc binding site 2 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3)


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

b:44.9
occ:1.00
 O4 A:PO41001 1.9 67.1 1.0
NE2 A:HIS483 1.9 42.3 1.0
NE2 A:HIS330 2.0 48.3 1.0
OD1 A:ASP326 2.3 45.5 1.0
OD2 A:ASP326 2.4 52.5 1.0
CG A:ASP326 2.7 46.5 1.0
CD2 A:HIS483 2.8 42.6 1.0
CD2 A:HIS330 2.9 48.9 1.0
CE1 A:HIS483 3.0 41.9 1.0
P A:PO41001 3.1 67.2 1.0
CE1 A:HIS330 3.2 48.1 1.0
O1 A:PO41001 3.3 67.8 1.0
CG A:HIS483 4.0 41.0 1.0
ND1 A:HIS483 4.1 42.5 1.0
O2 A:PO41001 4.1 68.0 1.0
CG A:HIS330 4.1 47.6 1.0
CB A:ASP326 4.2 40.4 1.0
CE1 A:HIS374 4.2 39.7 1.0
ND1 A:HIS330 4.2 49.4 1.0
O3 A:PO41001 4.3 67.4 1.0
OG1 A:THR206 4.3 42.0 1.0
NE2 A:HIS374 4.4 40.1 1.0
ZN A:ZN1002 4.5 43.2 1.0
OD1 A:ASP168 4.5 41.1 1.0
CE A:MET376 4.6 42.4 1.0
O A:HOH1227 4.7 38.0 1.0
O A:ASP326 4.8 43.9 1.0

Zinc binding site 3 out of 4 in 6f2t

Go back to Zinc Binding Sites List in 6f2t
Zinc binding site 3 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3)


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

b:48.2
occ:1.00
 OD1 B:ASP168 1.9 52.3 1.0
OG1 B:THR206 2.0 50.4 1.0
NE2 B:HIS374 2.0 47.7 1.0
OD2 B:ASP373 2.0 60.0 1.0
CG B:ASP168 2.6 51.7 1.0
OD2 B:ASP168 2.7 57.3 1.0
CE1 B:HIS374 2.8 47.5 1.0
CG B:ASP373 2.9 52.2 1.0
CB B:THR206 3.0 50.0 1.0
CD2 B:HIS374 3.0 47.5 1.0
OD1 B:ASP373 3.2 51.7 1.0
CA B:THR206 3.3 43.8 1.0
CG2 B:THR206 3.6 47.3 1.0
N B:THR206 3.8 44.1 1.0
ND1 B:HIS374 3.9 47.9 1.0
O4 B:PO41001 4.0 63.5 1.0
CG B:HIS374 4.0 45.7 1.0
CB B:ASP168 4.0 42.0 1.0
OD1 B:ASP326 4.1 47.6 1.0
O2 B:PO41001 4.1 63.6 1.0
CE1 B:HIS483 4.2 50.8 1.0
CB B:ASP373 4.3 43.7 1.0
NE2 B:HIS483 4.3 51.5 1.0
CG B:ASP326 4.3 48.8 1.0
N B:GLY169 4.4 39.9 1.0
ZN B:ZN1003 4.4 50.0 1.0
CA B:ASP168 4.5 40.0 1.0
P B:PO41001 4.6 64.3 1.0
OD2 B:ASP326 4.6 55.8 1.0
O B:HOH1198 4.6 41.1 1.0
C B:LYS205 4.6 47.5 1.0
CE1 B:HIS210 4.6 47.3 1.0
C B:THR206 4.7 47.1 1.0
C B:ASP168 4.8 44.3 1.0
ND1 B:HIS483 4.8 51.1 1.0
CB B:ASP326 4.9 43.8 1.0
O1 B:PO41001 4.9 64.5 1.0
ND1 B:HIS210 4.9 47.9 1.0

Zinc binding site 4 out of 4 in 6f2t

Go back to Zinc Binding Sites List in 6f2t
Zinc binding site 4 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3)


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

b:50.0
occ:1.00
 O2 B:PO41001 1.9 63.6 1.0
NE2 B:HIS483 1.9 51.5 1.0
NE2 B:HIS330 2.0 50.2 1.0
OD1 B:ASP326 2.2 47.6 1.0
OD2 B:ASP326 2.3 55.8 1.0
CG B:ASP326 2.6 48.8 1.0
CD2 B:HIS483 2.8 51.6 1.0
CD2 B:HIS330 2.9 50.9 1.0
CE1 B:HIS483 3.0 50.8 1.0
CE1 B:HIS330 3.2 50.1 1.0
P B:PO41001 3.3 64.3 1.0
O3 B:PO41001 3.9 65.8 1.0
O4 B:PO41001 4.0 63.5 1.0
CG B:HIS483 4.0 49.5 1.0
CG B:HIS330 4.1 49.8 1.0
CB B:ASP326 4.1 43.8 1.0
ND1 B:HIS483 4.1 51.1 1.0
CE1 B:HIS374 4.2 47.5 1.0
ND1 B:HIS330 4.2 51.3 1.0
OG1 B:THR206 4.4 50.4 1.0
ZN B:ZN1002 4.4 48.2 1.0
NE2 B:HIS374 4.4 47.7 1.0
O1 B:PO41001 4.5 64.5 1.0
O B:HOH1198 4.5 41.1 1.0
OD1 B:ASP168 4.5 52.3 1.0
CE B:MET376 4.5 46.9 1.0
O B:HOH1226 4.7 59.0 1.0
O B:ASP326 4.7 47.7 1.0
C B:ASP326 5.0 47.8 1.0
CA B:ASP326 5.0 42.8 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 20:34:38 2024

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