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Calcium in PDB 7pd9: Crystal Structure of CD73 in Complex with Riboflavin in the Open Form

Enzymatic activity of Crystal Structure of CD73 in Complex with Riboflavin in the Open Form

All present enzymatic activity of Crystal Structure of CD73 in Complex with Riboflavin in the Open Form:
3.1.3.5;

Protein crystallography data

The structure of Crystal Structure of CD73 in Complex with Riboflavin in the Open Form, PDB code: 7pd9 was solved by E.R.Scaletti, N.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.16 / 1.39
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.396, 131.782, 66.517, 90, 90, 90
R / Rfree (%) 12 / 14.9

Other elements in 7pd9:

The structure of Crystal Structure of CD73 in Complex with Riboflavin in the Open Form also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of CD73 in Complex with Riboflavin in the Open Form (pdb code 7pd9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of CD73 in Complex with Riboflavin in the Open Form, PDB code: 7pd9:

Calcium binding site 1 out of 1 in 7pd9

Go back to Calcium Binding Sites List in 7pd9
Calcium binding site 1 out of 1 in the Crystal Structure of CD73 in Complex with Riboflavin in the Open Form


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 CD73 in Complex with Riboflavin in the Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:16.1
occ:1.00
 O A:ASN213 2.3 16.8 1.0
O A:HOH997 2.4 35.0 1.0
O A:GLY298 2.4 17.0 1.0
OD1 A:ASP237 2.4 15.0 1.0
O A:HOH885 2.4 18.6 1.0
O A:HOH744 2.5 22.4 1.0
OD2 A:ASP237 2.5 13.6 1.0
CG A:ASP237 2.8 12.5 1.0
C A:GLY298 3.4 15.2 1.0
C A:ASN213 3.5 16.7 1.0
CA A:GLY298 4.1 17.4 1.0
O A:GLY235 4.3 14.3 1.0
CB A:ASP237 4.3 12.2 1.0
N A:LYS214 4.3 13.5 1.0
CA A:LYS214 4.3 13.8 1.0
O A:HOH751 4.3 18.4 1.0
N A:ASN299 4.3 18.3 1.0
CA A:ASN213 4.4 17.1 1.0
CA A:ASN299 4.6 17.2 1.0
O A:ARG297 4.7 20.5 1.0
O A:HOH1002 4.7 22.9 1.0
NH2 A:ARG273 4.8 37.3 1.0
N A:ILE215 4.8 11.2 1.0
ND2 A:ASN299 4.8 23.2 1.0
CB A:ASN213 4.9 19.7 1.0

Reference:

E.Scaletti, F.U.Huschmann, U.Mueller, M.S.Weiss, N.Strater. Substrate Binding Modes of Purine and Pyrimidine Nucleotides to Human Ecto-5'-Nucleotidase (CD73) and Inhibition By Their Bisphosphonic Acid Derivatives. Purinergic Signal 2021.
ISSN: ISSN 1573-9546
PubMed: 34403084
DOI: 10.1007/S11302-021-09802-W
Page generated: Thu Jul 10 00:08:40 2025

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