Zinc in PDB 6xue: Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV

Enzymatic activity of Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV

All present enzymatic activity of Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV:
3.1.3.5;

Protein crystallography data

The structure of Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV, PDB code: 6xue was solved by N.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.30 / 1.94
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.019, 232.175, 54.830, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22.4

Other elements in 6xue:

The structure of Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV (pdb code 6xue). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV, PDB code: 6xue:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6xue

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Zinc binding site 1 out of 4 in the Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:45.1
occ:0.58
 O4 A:PO4605 1.9 26.6 0.6
OD1 A:ASP36 2.0 44.1 1.0
NE2 A:HIS38 2.3 47.8 1.0
OD2 A:ASP85 2.4 49.0 1.0
P A:PO4605 3.1 24.5 0.6
CG A:ASP36 3.1 41.8 1.0
CE1 A:HIS38 3.2 47.1 1.0
ZN A:ZN602 3.3 46.0 1.0
CG A:ASP85 3.3 41.4 1.0
O1 A:PO4605 3.4 20.1 0.6
CD2 A:HIS38 3.4 47.7 1.0
CB A:ASP85 3.6 39.3 1.0
CB A:ASP36 3.7 37.0 1.0
O2 A:PO4605 3.9 23.1 0.6
OD2 A:ASP36 4.1 44.3 1.0
OD1 A:ASN245 4.2 57.2 1.0
O3 A:PO4605 4.2 27.2 0.6
NE2 A:HIS220 4.2 42.6 1.0
CD2 A:HIS118 4.2 43.2 1.0
CE1 A:HIS220 4.3 42.3 1.0
ND1 A:HIS38 4.4 47.2 1.0
CA A:ASP36 4.4 35.7 1.0
O A:HIS243 4.4 44.0 1.0
OD1 A:ASP85 4.5 39.2 1.0
CG A:HIS38 4.5 45.4 1.0
NH1 A:ARG395 4.5 43.6 1.0
CA A:HIS243 4.6 38.1 1.0
NE2 A:HIS118 4.7 43.5 1.0
ND1 A:HIS243 4.8 42.1 1.0
C A:HIS243 4.9 43.6 1.0

Zinc binding site 2 out of 4 in 6xue

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Zinc binding site 2 out of 4 in the Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:46.0
occ:1.00
 O1 A:PO4605 2.1 20.1 0.6
OD1 A:ASN117 2.2 44.9 1.0
ND1 A:HIS243 2.2 42.1 1.0
NE2 A:HIS220 2.2 42.6 1.0
OD2 A:ASP85 2.2 49.0 1.0
CE1 A:HIS243 3.0 41.1 1.0
CD2 A:HIS220 3.1 43.1 1.0
CG A:ASN117 3.1 49.3 1.0
CG A:ASP85 3.2 41.4 1.0
CE1 A:HIS220 3.3 42.3 1.0
ZN A:ZN601 3.3 45.1 0.6
CG A:HIS243 3.3 40.7 1.0
P A:PO4605 3.3 24.5 0.6
ND2 A:ASN117 3.5 37.3 1.0
OD1 A:ASP85 3.7 39.2 1.0
O4 A:PO4605 3.7 26.6 0.6
CB A:HIS243 3.8 38.2 1.0
CA A:HIS243 3.8 38.1 1.0
O2 A:PO4605 3.9 23.1 0.6
OD1 A:ASP36 4.0 44.1 1.0
NE2 A:HIS243 4.2 41.1 1.0
CG A:HIS220 4.3 41.0 1.0
CD2 A:HIS118 4.3 43.2 1.0
H12 A:O1H603 4.3 27.6 0.9
O A:HIS243 4.4 44.0 1.0
CD2 A:HIS243 4.4 42.0 1.0
ND1 A:HIS220 4.4 41.8 1.0
CB A:ASP85 4.4 39.3 1.0
CB A:ASN117 4.5 38.0 1.0
O3 A:PO4605 4.6 27.2 0.6
N A:ASN117 4.6 37.8 1.0
C A:HIS243 4.6 43.6 1.0
N A:HIS243 4.8 39.4 1.0
NE2 A:HIS118 5.0 43.5 1.0

Zinc binding site 3 out of 4 in 6xue

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Zinc binding site 3 out of 4 in the Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:43.0
occ:0.48
 O4 B:PO4605 1.9 31.2 0.6
OD2 B:ASP36 1.9 48.3 1.0
NE2 B:HIS38 2.3 45.8 1.0
OD2 B:ASP85 2.3 44.8 1.0
CG B:ASP36 3.0 44.6 1.0
P B:PO4605 3.1 28.4 0.6
CE1 B:HIS38 3.2 45.4 1.0
ZN B:ZN602 3.3 46.7 1.0
CG B:ASP85 3.3 42.4 1.0
O1 B:PO4605 3.3 24.1 0.6
CD2 B:HIS38 3.4 46.5 1.0
CB B:ASP85 3.5 40.4 1.0
CB B:ASP36 3.7 40.3 1.0
O2 B:PO4605 4.0 24.5 0.6
O B:HOH802 4.0 48.7 1.0
OD1 B:ASP36 4.1 45.1 1.0
OD1 B:ASN245 4.1 57.8 1.0
CE1 B:HIS220 4.2 43.0 1.0
NE2 B:HIS220 4.2 43.4 1.0
O3 B:PO4605 4.2 30.2 0.6
CD2 B:HIS118 4.3 44.4 1.0
O B:HIS243 4.4 44.2 1.0
ND1 B:HIS38 4.4 46.1 1.0
CA B:ASP36 4.4 39.5 1.0
OD1 B:ASP85 4.5 42.6 1.0
CG B:HIS38 4.5 44.8 1.0
CA B:HIS243 4.5 39.2 1.0
NH1 B:ARG395 4.6 47.0 1.0
NE2 B:HIS118 4.8 44.8 1.0
ND1 B:HIS243 4.8 43.6 1.0
C B:HIS243 4.9 44.8 1.0

Zinc binding site 4 out of 4 in 6xue

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Zinc binding site 4 out of 4 in the Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Ecto-5'-Nucleotidase (CD73) in Complex with A2396 (Compound 74 in Publication) in the Closed Form in Crystal Form IV within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:46.7
occ:1.00
 NE2 B:HIS220 2.2 43.4 1.0
O1 B:PO4605 2.2 24.1 0.6
ND1 B:HIS243 2.2 43.6 1.0
OD1 B:ASN117 2.2 42.7 1.0
OD2 B:ASP85 2.2 44.8 1.0
CE1 B:HIS243 3.0 43.2 1.0
CD2 B:HIS220 3.1 43.9 1.0
CG B:ASP85 3.1 42.4 1.0
CE1 B:HIS220 3.2 43.0 1.0
CG B:ASN117 3.2 54.0 1.0
ZN B:ZN601 3.3 43.0 0.5
P B:PO4605 3.4 28.4 0.6
CG B:HIS243 3.4 42.3 1.0
ND2 B:ASN117 3.5 45.5 1.0
OD1 B:ASP85 3.5 42.6 1.0
O4 B:PO4605 3.7 31.2 0.6
CA B:HIS243 3.8 39.2 1.0
CB B:HIS243 3.8 39.5 1.0
O2 B:PO4605 4.0 24.5 0.6
OD2 B:ASP36 4.0 48.3 1.0
NE2 B:HIS243 4.2 43.4 1.0
CD2 B:HIS118 4.3 44.4 1.0
CG B:HIS220 4.3 42.5 1.0
H12 B:O1H603 4.3 30.8 0.9
ND1 B:HIS220 4.3 42.8 1.0
CB B:ASP85 4.3 40.4 1.0
O B:HIS243 4.4 44.2 1.0
CD2 B:HIS243 4.4 43.6 1.0
N B:ASN117 4.5 40.1 1.0
CB B:ASN117 4.6 38.7 1.0
O3 B:PO4605 4.6 30.2 0.6
C B:HIS243 4.7 44.8 1.0
N B:HIS243 4.8 39.9 1.0
NE2 B:HIS118 5.0 44.8 1.0

Reference:

J.W.Beatty, E.A.Lindsey, R.Thomas-Tran, L.Debien, D.Mandal, J.L.Jeffrey, A.T.Tran, J.Fournier, S.D.Jacob, X.Yan, S.L.Drew, E.Ginn, A.Chen, A.T.Pham, S.Zhao, L.Jin, S.W.Young, N.P.Walker, M.R.Leleti, S.Moschutz, N.Strater, J.P.Powers, K.V.Lawson. Discovery of Potent and Selective Non-Nucleotide Small Molecule Inhibitors of CD73. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32212732
DOI: 10.1021/ACS.JMEDCHEM.9B01713
Page generated: Wed Dec 16 13:12:07 2020

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