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Zinc in PDB 6f2v: Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Amp

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

All present enzymatic activity of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Amp:
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 Amp, PDB code: 6f2v 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) 37.81 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.918, 125.327, 112.248, 90.00, 96.91, 90.00
R / Rfree (%) 19.4 / 20.9

Other elements in 6f2v:

The structure of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Amp 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 Amp (pdb code 6f2v). 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 Amp, PDB code: 6f2v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6f2v

Go back to Zinc Binding Sites List in 6f2v
Zinc binding site 1 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Amp


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

b:32.3
occ:1.00
 OD1 A:ASP168 1.9 32.0 1.0
OG1 A:THR206 1.9 43.7 1.0
NE2 A:HIS374 1.9 30.2 1.0
OD2 A:ASP373 2.0 43.2 1.0
CG A:ASP168 2.7 32.9 1.0
CE1 A:HIS374 2.7 29.9 1.0
O3P A:AMP1001 2.9 51.8 1.0
OD2 A:ASP168 2.9 37.0 1.0
CG A:ASP373 2.9 34.8 1.0
CD2 A:HIS374 3.0 30.4 1.0
CB A:THR206 3.1 41.0 1.0
OD1 A:ASP373 3.2 33.8 1.0
CA A:THR206 3.5 31.0 1.0
N A:THR206 3.7 31.6 1.0
ND1 A:HIS374 3.8 30.4 1.0
OD1 A:ASP326 3.9 34.8 1.0
CG A:HIS374 3.9 28.8 1.0
CG2 A:THR206 3.9 37.5 1.0
P A:AMP1001 3.9 51.3 1.0
CB A:ASP168 4.1 27.1 1.0
CE1 A:HIS483 4.1 32.6 1.0
O2P A:AMP1001 4.2 51.7 1.0
N A:GLY169 4.2 27.4 1.0
CG A:ASP326 4.3 36.0 1.0
CB A:ASP373 4.3 26.9 1.0
NE2 A:HIS483 4.3 33.1 1.0
ZN A:ZN1003 4.3 35.0 1.0
O5' A:AMP1001 4.3 49.9 1.0
C5' A:AMP1001 4.4 48.3 1.0
C A:LYS205 4.5 34.8 1.0
CA A:ASP168 4.5 25.5 1.0
OD2 A:ASP326 4.7 42.4 1.0
C A:ASP168 4.7 30.9 1.0
ND1 A:HIS483 4.8 33.2 1.0
CB A:ASP326 4.8 30.3 1.0
CE1 A:HIS210 4.8 31.4 1.0
C A:THR206 4.9 34.5 1.0
CA A:GLY169 4.9 27.6 1.0

Zinc binding site 2 out of 4 in 6f2v

Go back to Zinc Binding Sites List in 6f2v
Zinc binding site 2 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Amp


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

b:35.0
occ:1.00
 NE2 A:HIS483 1.9 33.1 1.0
O3P A:AMP1001 2.0 51.8 1.0
NE2 A:HIS330 2.1 37.0 1.0
OD1 A:ASP326 2.1 34.8 1.0
OD2 A:ASP326 2.4 42.4 1.0
CG A:ASP326 2.6 36.0 1.0
O1P A:AMP1001 2.7 52.3 1.0
P A:AMP1001 2.8 51.3 1.0
CD2 A:HIS483 2.9 33.6 1.0
CD2 A:HIS330 2.9 37.5 1.0
CE1 A:HIS483 3.0 32.6 1.0
CE1 A:HIS330 3.2 37.4 1.0
O2P A:AMP1001 3.8 51.7 1.0
CG A:HIS483 4.0 32.0 1.0
ND1 A:HIS483 4.1 33.2 1.0
CB A:ASP326 4.1 30.3 1.0
O5' A:AMP1001 4.1 49.9 1.0
CG A:HIS330 4.1 36.8 1.0
CE1 A:HIS374 4.2 29.9 1.0
O A:HOH1233 4.2 43.5 1.0
ND1 A:HIS330 4.3 38.8 1.0
ZN A:ZN1002 4.3 32.3 1.0
C5' A:AMP1001 4.4 48.3 1.0
NE2 A:HIS374 4.4 30.2 1.0
OD1 A:ASP168 4.5 32.0 1.0
CE A:MET376 4.5 33.6 1.0
O A:HOH1139 4.6 44.8 1.0
OG1 A:THR206 4.7 43.7 1.0
O A:ASP326 4.7 35.0 1.0
CA A:ASP326 5.0 29.1 1.0
C A:ASP326 5.0 34.4 1.0

Zinc binding site 3 out of 4 in 6f2v

Go back to Zinc Binding Sites List in 6f2v
Zinc binding site 3 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Amp


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

b:43.4
occ:1.00
 OD1 B:ASP168 1.9 45.5 1.0
OG1 B:THR206 1.9 53.5 1.0
NE2 B:HIS374 1.9 41.5 1.0
OD2 B:ASP373 2.0 49.6 1.0
CG B:ASP168 2.7 45.8 1.0
CE1 B:HIS374 2.7 40.8 1.0
O2P B:AMP1001 2.8 56.7 1.0
OD2 B:ASP168 2.9 51.6 1.0
CG B:ASP373 2.9 43.0 1.0
CD2 B:HIS374 3.0 40.6 1.0
CB B:THR206 3.2 51.1 1.0
OD1 B:ASP373 3.2 42.4 1.0
CA B:THR206 3.5 40.9 1.0
N B:THR206 3.7 40.7 1.0
ND1 B:HIS374 3.8 40.2 1.0
OD1 B:ASP326 3.9 48.3 1.0
CG B:HIS374 3.9 37.9 1.0
CG2 B:THR206 3.9 49.1 1.0
P B:AMP1001 3.9 57.3 1.0
CB B:ASP168 4.1 37.8 1.0
CE1 B:HIS483 4.1 46.1 1.0
O1P B:AMP1001 4.2 57.7 1.0
N B:GLY169 4.2 35.2 1.0
CG B:ASP326 4.2 49.0 1.0
CB B:ASP373 4.3 35.6 1.0
NE2 B:HIS483 4.3 47.1 1.0
ZN B:ZN1003 4.3 44.7 1.0
O5' B:AMP1001 4.3 58.0 1.0
C5' B:AMP1001 4.4 58.3 1.0
C B:LYS205 4.5 43.1 1.0
CA B:ASP168 4.5 35.0 1.0
OD2 B:ASP326 4.7 56.0 1.0
C B:ASP168 4.7 39.2 1.0
ND1 B:HIS483 4.8 45.5 1.0
CB B:ASP326 4.8 40.3 1.0
CE1 B:HIS210 4.8 43.2 1.0
C B:THR206 4.9 44.3 1.0
CA B:GLY169 4.9 34.7 1.0

Zinc binding site 4 out of 4 in 6f2v

Go back to Zinc Binding Sites List in 6f2v
Zinc binding site 4 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Amp


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

b:44.7
occ:1.00
 NE2 B:HIS483 1.9 47.1 1.0
O2P B:AMP1001 2.0 56.7 1.0
NE2 B:HIS330 2.1 45.8 1.0
OD1 B:ASP326 2.1 48.3 1.0
OD2 B:ASP326 2.4 56.0 1.0
CG B:ASP326 2.6 49.0 1.0
O3P B:AMP1001 2.7 57.6 1.0
P B:AMP1001 2.8 57.3 1.0
CD2 B:HIS483 2.9 46.4 1.0
CD2 B:HIS330 2.9 47.0 1.0
CE1 B:HIS483 3.0 46.1 1.0
CE1 B:HIS330 3.2 46.0 1.0
O1P B:AMP1001 3.8 57.7 1.0
CG B:HIS483 4.0 43.7 1.0
CB B:ASP326 4.1 40.3 1.0
ND1 B:HIS483 4.1 45.5 1.0
O5' B:AMP1001 4.1 58.0 1.0
CG B:HIS330 4.1 46.2 1.0
CE1 B:HIS374 4.2 40.8 1.0
ND1 B:HIS330 4.3 47.7 1.0
ZN B:ZN1002 4.3 43.4 1.0
O B:HOH1323 4.3 60.2 1.0
C5' B:AMP1001 4.4 58.3 1.0
NE2 B:HIS374 4.4 41.5 1.0
OD1 B:ASP168 4.5 45.5 1.0
CE B:MET376 4.5 40.0 1.0
OG1 B:THR206 4.7 53.5 1.0
O B:ASP326 4.7 43.8 1.0
C B:ASP326 4.9 43.7 1.0
CA B:ASP326 4.9 38.5 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 20:35:29 2024

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