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Calcium in PDB 7qgm: Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4598 (A 3-Methyl- Cmpcp Derivative, Compound 16 in Paper) in the Open State

Enzymatic activity of Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4598 (A 3-Methyl- Cmpcp Derivative, Compound 16 in Paper) in the Open State

All present enzymatic activity of Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4598 (A 3-Methyl- Cmpcp Derivative, Compound 16 in Paper) in the Open State:
3.1.3.5;

Protein crystallography data

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4598 (A 3-Methyl- Cmpcp Derivative, Compound 16 in Paper) in the Open State, PDB code: 7qgm was solved by N.S.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.98 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 54.989, 98.185, 234.902, 90, 90, 90
R / Rfree (%) 26.1 / 29.4

Other elements in 7qgm:

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4598 (A 3-Methyl- Cmpcp Derivative, Compound 16 in Paper) in the Open State also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4598 (A 3-Methyl- Cmpcp Derivative, Compound 16 in Paper) in the Open State (pdb code 7qgm). 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 Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4598 (A 3-Methyl- Cmpcp Derivative, Compound 16 in Paper) in the Open State, PDB code: 7qgm:

Calcium binding site 1 out of 1 in 7qgm

Go back to Calcium Binding Sites List in 7qgm
Calcium binding site 1 out of 1 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4598 (A 3-Methyl- Cmpcp Derivative, Compound 16 in Paper) in the Open State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4598 (A 3-Methyl- Cmpcp Derivative, Compound 16 in Paper) in the Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:85.6
occ:1.00
 O A:GLY298 2.9 82.4 1.0
OD2 A:ASP237 2.9 81.3 1.0
O A:ASN213 3.2 83.5 1.0
OD1 A:ASP237 3.2 83.3 1.0
HE2 A:LYS208 3.3 93.5 1.0
HE3 A:LYS208 3.3 93.5 1.0
CG A:ASP237 3.4 81.4 1.0
HB2 A:ASN213 3.6 96.8 1.0
CE A:LYS208 3.8 76.6 1.0
C A:ASN213 3.8 80.7 1.0
HB3 A:ASN213 3.9 96.8 1.0
C A:GLY298 3.9 83.4 1.0
O A:GLY235 4.0 85.0 1.0
HA A:ASN213 4.0 91.2 1.0
CB A:ASN213 4.1 79.3 1.0
HA A:ASN299 4.1 97.9 1.0
CA A:ASN213 4.2 74.7 1.0
HD22 A:ASN299 4.2 98.4 1.0
HA3 A:GLY298 4.3 100.0 1.0
O A:ARG297 4.3 80.2 1.0
HD2 A:LYS208 4.5 92.4 1.0
HZ2 A:LYS208 4.5 93.0 1.0
ND2 A:ASN299 4.5 80.6 1.0
HA2 A:GLY235 4.6 111.6 1.0
HD21 A:ASN299 4.6 98.4 1.0
HA A:LYS214 4.6 87.8 1.0
HH12 A:ARG273 4.6 105.1 1.0
CA A:GLY298 4.7 81.9 1.0
N A:ASN299 4.7 82.2 1.0
HH11 A:ARG273 4.7 105.1 1.0
NZ A:LYS208 4.8 76.1 1.0
CD A:LYS208 4.8 75.6 1.0
N A:LYS214 4.8 77.1 1.0
CB A:ASP237 4.8 79.4 1.0
NH1 A:ARG273 4.8 86.2 1.0
CA A:ASN299 4.8 80.2 1.0
H A:ILE215 4.9 93.1 1.0
C A:GLY235 5.0 87.6 1.0
HB2 A:ASP237 5.0 96.9 1.0

Reference:

M.Scortichini, R.M.Idris, S.Moschutz, A.Keim, V.Salmaso, C.Dobelmann, P.Oliva, K.Losenkova, H.Irjala, S.Vaittinen, J.Sandholm, G.G.Yegutkin, N.Strater, A.Junker, C.E.Muller, K.A.Jacobson. Structure-Activity Relationship of 3-Methylcytidine-5'-Alpha , Beta-Methylenediphosphates As CD73 Inhibitors. J.Med.Chem. V. 65 2409 2022.
ISSN: ISSN 0022-2623
PubMed: 35080883
DOI: 10.1021/ACS.JMEDCHEM.1C01852
Page generated: Thu Jul 10 00:34:52 2025

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