Calcium 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:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Amp, PDB code: 6f2v:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6f2v

Go back to Calcium Binding Sites List in 6f2v
Calcium binding site 1 out of 2 in the Crystal Structure of Ectonucleotide Phosphodiesterase/Pyrophosphatase- 3 (NPP3) in Complex with Amp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca1004

b:57.7
occ:1.00
OD1 A:ASN754 2.1 65.7 1.0
OD1 A:ASP756 2.4 50.8 1.0
OD1 A:ASP752 2.4 42.7 1.0
O A:HIS758 2.5 42.9 1.0
OD1 A:ASP760 2.7 53.6 1.0
CG A:ASN754 3.3 70.0 1.0
CG A:ASP756 3.4 49.9 1.0
CG A:ASP752 3.5 43.0 1.0
C A:HIS758 3.6 42.8 1.0
CG A:ASP760 3.8 54.3 1.0
ND2 A:ASN754 3.8 62.0 1.0
N A:ASP760 3.9 42.4 1.0
CA A:ASP752 3.9 36.3 1.0
C A:PHE759 4.0 44.7 1.0
OD2 A:ASP756 4.0 55.5 1.0
O A:PHE759 4.0 44.5 1.0
CA A:ASP760 4.0 43.6 1.0
CB A:ASP752 4.2 36.7 1.0
N A:ASP756 4.3 38.9 1.0
N A:HIS758 4.3 38.8 1.0
CA A:HIS758 4.4 38.8 1.0
O A:PHE751 4.4 39.3 1.0
CB A:ASP756 4.4 40.6 1.0
OD2 A:ASP752 4.5 47.6 1.0
CB A:ASP760 4.5 46.1 1.0
N A:PHE759 4.5 39.1 1.0
N A:ASN754 4.5 43.1 1.0
C A:ASP752 4.5 41.6 1.0
OE2 A:GLU764 4.5 71.9 1.0
CB A:HIS758 4.5 39.9 1.0
CB A:ASN754 4.5 45.9 1.0
CA A:PHE759 4.6 39.3 1.0
OD2 A:ASP760 4.7 59.9 1.0
N A:TYR755 4.7 40.2 1.0
N A:TYR753 4.8 40.0 1.0
CA A:ASP756 4.8 38.4 1.0
C A:ASN754 4.8 45.4 1.0
CA A:ASN754 4.8 43.2 1.0
OE1 A:GLU764 4.8 76.7 1.0
CD A:GLU764 4.9 78.3 1.0
N A:ASP752 5.0 36.8 1.0

Calcium binding site 2 out of 2 in 6f2v

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
B:Ca1004

b:46.7
occ:1.00
OD1 B:ASN754 2.1 58.4 1.0
O B:HOH1163 2.2 38.0 1.0
OD1 B:ASP756 2.4 45.2 1.0
OD1 B:ASP752 2.4 41.7 1.0
O B:HIS758 2.5 35.8 1.0
OD1 B:ASP760 2.7 44.3 1.0
CG B:ASN754 3.3 64.2 1.0
CG B:ASP756 3.4 46.2 1.0
CG B:ASP752 3.5 40.1 1.0
C B:HIS758 3.6 36.0 1.0
CG B:ASP760 3.8 43.5 1.0
ND2 B:ASN754 3.8 58.0 1.0
N B:ASP760 3.9 33.5 1.0
CA B:ASP752 3.9 30.4 1.0
C B:PHE759 4.0 37.0 1.0
OD2 B:ASP756 4.0 52.6 1.0
O B:PHE759 4.0 37.8 1.0
CA B:ASP760 4.0 34.4 1.0
CB B:ASP752 4.2 31.3 1.0
N B:ASP756 4.3 34.6 1.0
N B:HIS758 4.3 32.3 1.0
CA B:HIS758 4.4 32.0 1.0
O B:PHE751 4.4 33.4 1.0
O B:HOH1187 4.4 60.8 1.0
CB B:ASP756 4.4 38.0 1.0
OD2 B:ASP752 4.5 44.6 1.0
N B:PHE759 4.5 32.3 1.0
CB B:ASP760 4.5 35.8 1.0
N B:ASN754 4.5 35.1 1.0
C B:ASP752 4.5 35.7 1.0
OE2 B:GLU764 4.5 48.0 1.0
CB B:ASN754 4.5 39.2 1.0
CB B:HIS758 4.5 33.9 1.0
CA B:PHE759 4.6 31.6 1.0
N B:TYR755 4.7 34.4 1.0
OD2 B:ASP760 4.7 47.2 1.0
N B:TYR753 4.8 32.5 1.0
CA B:ASP756 4.8 35.0 1.0
C B:ASN754 4.8 39.7 1.0
CA B:ASN754 4.8 36.6 1.0
OE1 B:GLU764 4.8 70.0 1.0
CD B:GLU764 4.9 62.1 1.0
N B:ASP752 5.0 29.8 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: Sat Dec 12 06:05:53 2020

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