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Zinc in PDB 6f33: Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Ampnpp

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

All present enzymatic activity of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Ampnpp:
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 Ampnpp, PDB code: 6f33 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) 47.26 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.492, 126.935, 112.245, 90.00, 96.75, 90.00
R / Rfree (%) 24.5 / 26.8

Other elements in 6f33:

The structure of Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Ampnpp 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 Ampnpp (pdb code 6f33). 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 Ampnpp, PDB code: 6f33:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6f33

Go back to Zinc Binding Sites List in 6f33
Zinc binding site 1 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Ampnpp


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

b:52.9
occ:1.00
 OD1 A:ASP168 1.9 60.4 1.0
NE2 A:HIS374 1.9 55.8 1.0
OD2 A:ASP373 2.1 67.4 1.0
CG A:ASP168 2.4 59.7 1.0
OD2 A:ASP168 2.5 65.8 1.0
CE1 A:HIS374 2.7 56.0 1.0
CD2 A:HIS374 2.9 55.4 1.0
CG A:ASP373 3.0 61.1 1.0
O2A A:ZAN1001 3.1 70.8 1.0
CB A:ALA206 3.2 40.7 1.0
OD1 A:ASP373 3.3 62.5 1.0
CA A:ALA206 3.5 39.4 1.0
N A:ALA206 3.6 40.1 1.0
ND1 A:HIS374 3.8 56.4 1.0
CB A:ASP168 3.9 49.6 1.0
CG A:HIS374 3.9 53.8 1.0
CE1 A:HIS483 4.0 51.6 1.0
ZN A:ZN1003 4.1 36.7 1.0
PA A:ZAN1001 4.1 70.5 1.0
O1A A:ZAN1001 4.2 69.8 1.0
NE2 A:HIS483 4.3 52.7 1.0
OD1 A:ASP326 4.3 58.5 1.0
N A:GLY169 4.3 48.8 1.0
CG A:ASP326 4.4 58.0 1.0
CB A:ASP373 4.4 49.1 1.0
C A:LYS205 4.4 43.7 1.0
CA A:ASP168 4.4 47.4 1.0
OD2 A:ASP326 4.5 64.5 1.0
C5' A:ZAN1001 4.6 63.8 1.0
O5' A:ZAN1001 4.6 67.3 1.0
ND1 A:HIS483 4.6 52.1 1.0
CE1 A:HIS210 4.7 44.4 1.0
C A:ASP168 4.7 52.2 1.0
CB A:ASP326 4.9 47.6 1.0

Zinc binding site 2 out of 4 in 6f33

Go back to Zinc Binding Sites List in 6f33
Zinc binding site 2 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Ampnpp


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

b:36.7
occ:1.00
 NE2 A:HIS483 2.0 52.7 1.0
OD2 A:ASP326 2.1 64.5 1.0
O2A A:ZAN1001 2.2 70.8 1.0
O1B A:ZAN1001 2.3 76.1 1.0
OD1 A:ASP326 2.5 58.5 1.0
CG A:ASP326 2.6 58.0 1.0
NE2 A:HIS330 2.6 54.5 1.0
CD2 A:HIS483 2.9 53.4 1.0
CE1 A:HIS483 3.0 51.6 1.0
PB A:ZAN1001 3.3 75.8 1.0
PA A:ZAN1001 3.3 70.5 1.0
N3A A:ZAN1001 3.5 73.2 1.0
CD2 A:HIS330 3.6 55.8 1.0
CE1 A:HIS330 3.7 54.9 1.0
O3B A:ZAN1001 4.0 77.7 1.0
OD1 A:ASP168 4.0 60.4 1.0
CB A:ASP326 4.0 47.6 1.0
CG A:HIS483 4.0 51.2 1.0
ND1 A:HIS483 4.1 52.1 1.0
CE1 A:HIS374 4.1 56.0 1.0
ZN A:ZN1002 4.1 52.9 1.0
NE2 A:HIS374 4.2 55.8 1.0
O1A A:ZAN1001 4.4 69.8 1.0
O5' A:ZAN1001 4.4 67.3 1.0
C5' A:ZAN1001 4.5 63.8 1.0
O2G A:ZAN1001 4.6 79.2 1.0
O2B A:ZAN1001 4.7 75.7 1.0
CG A:HIS330 4.7 55.7 1.0
ND1 A:HIS330 4.8 57.2 1.0
PG A:ZAN1001 4.8 79.2 1.0
CE A:MET376 4.8 60.7 1.0
CG A:ASP168 4.9 59.7 1.0

Zinc binding site 3 out of 4 in 6f33

Go back to Zinc Binding Sites List in 6f33
Zinc binding site 3 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Ampnpp


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

b:0.1
occ:1.00
 OD1 B:ASP168 1.9 68.5 1.0
NE2 B:HIS374 2.2 70.7 1.0
CG B:ASP168 2.6 68.4 1.0
OD2 B:ASP168 2.6 73.5 1.0
CE1 B:HIS374 2.9 70.6 1.0
O1A B:ZAN1001 2.9 0.3 1.0
OD2 B:ASP373 2.9 83.4 1.0
CB B:ALA206 3.3 58.2 1.0
CD2 B:HIS374 3.4 69.9 1.0
O2A B:ZAN1001 3.5 0.5 1.0
PA B:ZAN1001 3.5 0.6 1.0
CE1 B:HIS483 3.6 66.5 1.0
O5' B:ZAN1001 3.6 0.1 1.0
ZN B:ZN1003 3.7 72.9 1.0
NE2 B:HIS483 3.7 67.7 1.0
N B:ALA206 3.8 56.5 1.0
CA B:ALA206 3.8 56.3 1.0
CG B:ASP373 3.8 76.9 1.0
OD2 B:ASP326 3.8 75.6 1.0
OD1 B:ASP326 3.8 69.4 1.0
CG B:ASP326 3.8 69.6 1.0
OD1 B:ASP373 4.0 77.2 1.0
CB B:ASP168 4.0 60.5 1.0
ND1 B:HIS374 4.1 70.4 1.0
CG B:HIS374 4.3 67.9 1.0
ND1 B:HIS483 4.4 66.1 1.0
CB B:ASP326 4.6 59.8 1.0
N B:GLY169 4.6 59.2 1.0
CD2 B:HIS483 4.6 67.6 1.0
C B:LYS205 4.6 59.3 1.0
CA B:ASP168 4.8 58.2 1.0
C5' B:ZAN1001 4.8 99.4 1.0
CG B:HIS483 4.9 64.7 1.0
C B:ASP168 5.0 62.8 1.0
OH B:TYR321 5.0 78.8 1.0

Zinc binding site 4 out of 4 in 6f33

Go back to Zinc Binding Sites List in 6f33
Zinc binding site 4 out of 4 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Ampnpp


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

b:72.9
occ:1.00
 NE2 B:HIS483 1.9 67.7 1.0
O1A B:ZAN1001 1.9 0.3 1.0
OD2 B:ASP326 2.1 75.6 1.0
NE2 B:HIS330 2.3 74.3 1.0
OD1 B:ASP326 2.4 69.4 1.0
CG B:ASP326 2.5 69.6 1.0
CD2 B:HIS483 2.8 67.6 1.0
O2B B:ZAN1001 2.8 0.9 1.0
CE1 B:HIS483 3.0 66.5 1.0
CD2 B:HIS330 3.2 75.7 1.0
CE1 B:HIS330 3.3 74.2 1.0
PA B:ZAN1001 3.4 0.6 1.0
ZN B:ZN1002 3.7 0.1 1.0
PB B:ZAN1001 3.9 0.1 1.0
CG B:HIS483 4.0 64.7 1.0
N3A B:ZAN1001 4.0 0.4 1.0
O2A B:ZAN1001 4.1 0.5 1.0
CB B:ASP326 4.1 59.8 1.0
ND1 B:HIS483 4.1 66.1 1.0
CE1 B:HIS374 4.2 70.6 1.0
OD1 B:ASP168 4.3 68.5 1.0
O3B B:ZAN1001 4.3 0.9 1.0
O5' B:ZAN1001 4.4 0.1 1.0
NE2 B:HIS374 4.4 70.7 1.0
CG B:HIS330 4.4 74.9 1.0
ND1 B:HIS330 4.4 76.1 1.0
CE B:MET376 4.5 75.0 1.0
O3G B:ZAN1001 4.8 1.0 1.0
O B:ASP326 4.8 64.4 1.0
C B:ASP326 4.9 64.5 1.0
PG B:ZAN1001 5.0 0.9 1.0
CA B:ASP326 5.0 58.6 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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