Atomistry » Zinc » PDB 6ezu-6f8w » 6f2v
Atomistry »
  Zinc »
    PDB 6ezu-6f8w »
      6f2v »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy