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Zinc in PDB 6z9d: Human Ecto-5'-Nucleotidase (CD73) in Complex with Aopcp Derivative AB680 (Compound 55 in Publication) in the Closed Form (Crystal Form III)

Enzymatic activity of Human Ecto-5'-Nucleotidase (CD73) in Complex with Aopcp Derivative AB680 (Compound 55 in Publication) in the Closed Form (Crystal Form III)

All present enzymatic activity of Human Ecto-5'-Nucleotidase (CD73) in Complex with Aopcp Derivative AB680 (Compound 55 in Publication) in the Closed Form (Crystal Form III):
3.1.3.5;

Protein crystallography data

The structure of Human Ecto-5'-Nucleotidase (CD73) in Complex with Aopcp Derivative AB680 (Compound 55 in Publication) in the Closed Form (Crystal Form III), PDB code: 6z9d was solved by N.Strater, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.13 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 53.226, 94.254, 235.428, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 25.4

Other elements in 6z9d:

The structure of Human Ecto-5'-Nucleotidase (CD73) in Complex with Aopcp Derivative AB680 (Compound 55 in Publication) in the Closed Form (Crystal Form III) also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Calcium (Ca) 1 atom
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Ecto-5'-Nucleotidase (CD73) in Complex with Aopcp Derivative AB680 (Compound 55 in Publication) in the Closed Form (Crystal Form III) (pdb code 6z9d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Ecto-5'-Nucleotidase (CD73) in Complex with Aopcp Derivative AB680 (Compound 55 in Publication) in the Closed Form (Crystal Form III), PDB code: 6z9d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6z9d

Go back to Zinc Binding Sites List in 6z9d
Zinc binding site 1 out of 2 in the Human Ecto-5'-Nucleotidase (CD73) in Complex with Aopcp Derivative AB680 (Compound 55 in Publication) in the Closed Form (Crystal Form III)


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 Aopcp Derivative AB680 (Compound 55 in Publication) in the Closed Form (Crystal Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:58.5
occ:1.00
 NE2 A:HIS38 2.1 44.8 1.0
O3 A:QDH604 2.1 41.8 1.0
OD1 A:ASP36 2.1 41.3 1.0
OD2 A:ASP85 2.4 33.7 1.0
O A:HOH707 2.4 41.8 1.0
O A:HOH710 2.5 50.8 1.0
CE1 A:HIS38 3.1 44.4 1.0
CD2 A:HIS38 3.1 44.6 1.0
CG A:ASP36 3.2 37.9 1.0
CG A:ASP85 3.2 40.9 1.0
P1 A:QDH604 3.3 43.1 1.0
O4 A:QDH604 3.3 44.5 1.0
CB A:ASP85 3.4 35.6 1.0
ZN A:ZN602 3.5 42.5 1.0
CB A:ASP36 3.8 31.6 1.0
C4 A:QDH604 3.9 40.0 1.0
CD2 A:HIS118 4.0 45.3 1.0
OD2 A:ASP36 4.2 36.7 1.0
ND1 A:HIS38 4.2 44.6 1.0
CG A:HIS38 4.2 42.4 1.0
CE1 A:HIS220 4.2 39.5 1.0
NE2 A:HIS220 4.3 40.2 1.0
OD1 A:ASN245 4.3 45.0 1.0
CA A:ASP36 4.3 31.3 1.0
NH1 A:ARG395 4.4 38.7 1.0
O5 A:QDH604 4.4 49.0 1.0
OD1 A:ASP85 4.4 38.9 1.0
NE2 A:HIS118 4.5 45.0 1.0
O6 A:QDH604 4.5 37.0 1.0
O A:HIS243 4.7 41.3 1.0
CA A:HIS243 4.8 34.1 1.0
CA A:ASP85 4.9 35.4 1.0
P A:QDH604 5.0 40.6 1.0

Zinc binding site 2 out of 2 in 6z9d

Go back to Zinc Binding Sites List in 6z9d
Zinc binding site 2 out of 2 in the Human Ecto-5'-Nucleotidase (CD73) in Complex with Aopcp Derivative AB680 (Compound 55 in Publication) in the Closed Form (Crystal Form III)


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 Aopcp Derivative AB680 (Compound 55 in Publication) in the Closed Form (Crystal Form III) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:42.5
occ:1.00
 O4 A:QDH604 2.0 44.5 1.0
O A:HOH707 2.0 41.8 1.0
NE2 A:HIS220 2.0 40.2 1.0
ND1 A:HIS243 2.2 38.3 1.0
OD1 A:ASN117 2.2 38.1 1.0
OD2 A:ASP85 2.3 33.7 1.0
CD2 A:HIS220 2.9 40.4 1.0
CE1 A:HIS243 3.0 39.2 1.0
CE1 A:HIS220 3.1 39.5 1.0
CG A:ASN117 3.2 46.5 1.0
CG A:ASP85 3.2 40.9 1.0
CG A:HIS243 3.3 37.1 1.0
P1 A:QDH604 3.3 43.1 1.0
ZN A:ZN601 3.5 58.5 1.0
ND2 A:ASN117 3.5 36.7 1.0
OD1 A:ASP85 3.7 38.9 1.0
O3 A:QDH604 3.7 41.8 1.0
CB A:HIS243 3.7 33.6 1.0
CA A:HIS243 3.8 34.1 1.0
C4 A:QDH604 3.9 40.0 1.0
OD1 A:ASP36 4.1 41.3 1.0
CG A:HIS220 4.1 38.4 1.0
ND1 A:HIS220 4.2 39.2 1.0
NE2 A:HIS243 4.2 39.2 1.0
CD2 A:HIS118 4.3 45.3 1.0
O A:HIS243 4.3 41.3 1.0
CD2 A:HIS243 4.4 39.0 1.0
O5 A:QDH604 4.4 49.0 1.0
CB A:ASP85 4.4 35.6 1.0
N A:ASN117 4.5 34.1 1.0
CB A:ASN117 4.5 32.4 1.0
C A:HIS243 4.6 40.5 1.0
N A:HIS243 4.7 33.1 1.0
NE2 A:HIS118 4.8 45.0 1.0
CA A:ASN117 5.0 34.9 1.0

Reference:

K.V.Lawson, J.Kalisiak, E.A.Lindsey, E.T.Newcomb, M.R.Leleti, L.Debien, B.R.Rosen, D.H.Miles, E.U.Sharif, J.L.Jeffrey, J.B.L.Tan, A.Chen, S.Zhao, G.Xu, L.Fu, L.Jin, T.W.Park, W.Berry, S.Moschutz, E.Scaletti, N.Strater, N.P.Walker, S.W.Young, M.J.Walters, U.Schindler, J.P.Powers. Discovery of AB680: A Potent and Selective Inhibitor of CD73. J.Med.Chem. V. 63 11448 2020.
ISSN: ISSN 0022-2623
PubMed: 32614585
DOI: 10.1021/ACS.JMEDCHEM.0C00525
Page generated: Tue Oct 29 15:33:09 2024

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