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Calcium in PDB 6ye2: Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A1202 (Compound 4A in Publication) in the Closed Form (Crystal Form IV)

Enzymatic activity of Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A1202 (Compound 4A in Publication) in the Closed Form (Crystal Form IV)

All present enzymatic activity of Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A1202 (Compound 4A in Publication) in the Closed Form (Crystal Form IV):
3.1.3.5;

Protein crystallography data

The structure of Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A1202 (Compound 4A in Publication) in the Closed Form (Crystal Form IV), PDB code: 6ye2 was solved by E.Scaletti, N.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.73 / 2.44
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.36, 230.94, 53.97, 90, 90, 90
R / Rfree (%) 17.5 / 23

Other elements in 6ye2:

The structure of Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A1202 (Compound 4A in Publication) in the Closed Form (Crystal Form IV) also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A1202 (Compound 4A in Publication) in the Closed Form (Crystal Form IV) (pdb code 6ye2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A1202 (Compound 4A in Publication) in the Closed Form (Crystal Form IV), PDB code: 6ye2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6ye2

Go back to Calcium Binding Sites List in 6ye2
Calcium binding site 1 out of 2 in the Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A1202 (Compound 4A in Publication) in the Closed Form (Crystal Form IV)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A1202 (Compound 4A in Publication) in the Closed Form (Crystal Form IV) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:84.1
occ:1.00
 O A:ASN213 2.2 39.8 1.0
OD2 A:ASP237 2.5 37.5 1.0
OD1 A:ASP237 2.6 33.3 1.0
O A:GLY298 2.7 40.9 1.0
O A:HOH720 2.7 33.7 1.0
CG A:ASP237 2.9 33.3 1.0
C A:GLY298 3.4 41.7 1.0
C A:ASN213 3.4 41.0 1.0
NZ A:LYS208 3.4 84.6 1.0
O A:HOH926 3.7 48.8 1.0
ND2 A:ASN299 4.0 28.1 1.0
N A:ASN299 4.1 39.2 1.0
CA A:LYS214 4.1 33.0 1.0
CA A:GLY298 4.1 36.7 1.0
N A:LYS214 4.1 34.5 1.0
O A:GLY235 4.2 40.9 1.0
CA A:ASN299 4.3 38.4 1.0
CB A:ASP237 4.3 34.4 1.0
CA A:ASN213 4.4 44.1 1.0
N A:ILE215 4.5 34.1 1.0
O A:ARG297 4.5 40.4 1.0
CE A:LYS208 4.8 88.1 1.0
C A:LYS214 4.8 38.4 1.0
CG A:ASN299 4.8 45.1 1.0
CB A:ASN213 5.0 46.4 1.0

Calcium binding site 2 out of 2 in 6ye2

Go back to Calcium Binding Sites List in 6ye2
Calcium binding site 2 out of 2 in the Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A1202 (Compound 4A in Publication) in the Closed Form (Crystal Form IV)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A1202 (Compound 4A in Publication) in the Closed Form (Crystal Form IV) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:112.5
occ:1.00
 OD2 B:ASP237 2.3 62.9 1.0
OD1 B:ASP237 2.4 56.8 1.0
O B:ASN213 2.4 51.8 1.0
CG B:ASP237 2.6 56.4 1.0
O B:GLY298 2.8 55.4 1.0
O B:HOH709 2.8 51.1 1.0
NZ B:LYS208 3.2 93.2 1.0
C B:ASN213 3.5 51.3 1.0
O B:GLY235 3.7 60.9 1.0
C B:GLY298 3.7 56.4 1.0
CA B:LYS214 4.1 42.4 1.0
CB B:ASP237 4.2 47.7 1.0
N B:LYS214 4.2 44.3 1.0
N B:ILE215 4.3 41.5 1.0
CA B:GLY298 4.4 53.1 1.0
CE B:LYS208 4.5 83.7 1.0
CA B:ASN213 4.6 49.9 1.0
N B:ASN299 4.7 53.2 1.0
C B:LYS214 4.7 46.3 1.0
C B:GLY235 4.7 61.2 1.0
CA B:ASN299 4.9 53.3 1.0
NH2 B:ARG273 4.9 118.2 1.0
ND2 B:ASN299 5.0 59.8 1.0

Reference:

E.U.Sharif, J.Kalisiak, K.V.Lawson, D.H.Miles, E.Newcomb, E.A.Lindsey, B.R.Rosen, L.P.P.Debien, A.Chen, X.Zhao, S.W.Young, N.P.Walker, N.Strater, E.R.Scaletti, L.Jin, G.Xu, M.R.Leleti, J.P.Powers. Discovery of Potent and Selective Methylenephosphonic Acid CD73 Inhibitors. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 33399453
DOI: 10.1021/ACS.JMEDCHEM.0C01835
Page generated: Wed Jul 9 20:21:05 2025

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