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Zinc in PDB 6ye1: Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A894 (Compound 2N in Publication) in the Closed Form (Crystal Form IV)

Enzymatic activity of Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A894 (Compound 2N 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 A894 (Compound 2N 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 A894 (Compound 2N in Publication) in the Closed Form (Crystal Form IV), PDB code: 6ye1 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) 46.52 / 2.66
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 93.03, 232.12, 53.79, 90, 90, 90
R / Rfree (%) 19.3 / 26.8

Other elements in 6ye1:

The structure of Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A894 (Compound 2N in Publication) in the Closed Form (Crystal Form IV) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A894 (Compound 2N in Publication) in the Closed Form (Crystal Form IV) (pdb code 6ye1). 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 the Ampcp Derivative A894 (Compound 2N in Publication) in the Closed Form (Crystal Form IV), PDB code: 6ye1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6ye1

Go back to Zinc Binding Sites List in 6ye1
Zinc binding site 1 out of 4 in the Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A894 (Compound 2N in Publication) in the Closed Form (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 the Ampcp Derivative A894 (Compound 2N in Publication) in the Closed Form (Crystal Form IV) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:49.0
occ:1.00
 OD2 A:ASP36 1.9 46.3 1.0
NE2 A:HIS38 1.9 39.5 1.0
O5 A:OO2603 2.0 57.5 1.0
OD2 A:ASP85 2.2 46.8 1.0
CG A:ASP36 2.8 43.2 1.0
CE1 A:HIS38 2.9 39.5 1.0
CD2 A:HIS38 2.9 39.7 1.0
CB A:ASP36 3.1 37.5 1.0
CG A:ASP85 3.1 45.7 1.0
CB A:ASP85 3.3 37.8 1.0
P1 A:OO2603 3.5 57.0 1.0
ZN A:ZN602 3.6 53.6 1.0
OD1 A:ASN245 3.8 56.9 1.0
CA A:ASP36 4.0 35.2 1.0
OD1 A:ASP36 4.0 40.9 1.0
ND1 A:HIS38 4.0 40.4 1.0
CG A:HIS38 4.0 38.5 1.0
O4 A:OO2603 4.1 55.0 1.0
NE2 A:HIS220 4.1 39.8 1.0
CE1 A:HIS220 4.1 39.9 1.0
O6 A:OO2603 4.2 54.0 1.0
O A:HIS243 4.3 38.5 1.0
OD1 A:ASP85 4.3 42.7 1.0
NH1 A:ARG395 4.4 61.0 1.0
CD2 A:HIS118 4.5 49.5 1.0
C8 A:OO2603 4.6 56.4 1.0
CA A:HIS243 4.7 38.8 1.0
NH2 A:ARG395 4.8 60.3 1.0
CA A:ASP85 4.8 36.2 1.0
CG A:ASN245 4.9 65.3 1.0
NE2 A:HIS118 4.9 49.1 1.0
C A:HIS243 4.9 41.6 1.0
C A:ASP36 4.9 36.6 1.0
O A:ASP85 5.0 39.5 1.0

Zinc binding site 2 out of 4 in 6ye1

Go back to Zinc Binding Sites List in 6ye1
Zinc binding site 2 out of 4 in the Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A894 (Compound 2N in Publication) in the Closed Form (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 the Ampcp Derivative A894 (Compound 2N in Publication) in the Closed Form (Crystal Form IV) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:53.6
occ:1.00
 ND1 A:HIS243 2.0 43.3 1.0
NE2 A:HIS220 2.0 39.8 1.0
O4 A:OO2603 2.1 55.0 1.0
OD1 A:ASN117 2.2 45.7 1.0
OD2 A:ASP85 2.4 46.8 1.0
CE1 A:HIS243 2.7 42.6 1.0
CD2 A:HIS220 2.8 40.2 1.0
O5 A:OO2603 2.8 57.5 1.0
P1 A:OO2603 2.9 57.0 1.0
CG A:HIS243 3.0 41.4 1.0
CE1 A:HIS220 3.2 39.9 1.0
CG A:ASP85 3.2 45.7 1.0
CG A:ASN117 3.3 58.9 1.0
OD1 A:ASP85 3.5 42.7 1.0
CB A:HIS243 3.6 38.2 1.0
CA A:HIS243 3.6 38.8 1.0
ZN A:ZN601 3.6 49.0 1.0
C8 A:OO2603 3.7 56.4 1.0
OD2 A:ASP36 3.7 46.3 1.0
NE2 A:HIS243 3.8 42.8 1.0
ND2 A:ASN117 3.9 61.3 1.0
CD2 A:HIS243 4.0 42.6 1.0
CG A:HIS220 4.0 38.5 1.0
CD2 A:HIS118 4.1 49.5 1.0
O A:HIS243 4.2 38.5 1.0
ND1 A:HIS220 4.2 40.4 1.0
O6 A:OO2603 4.3 54.0 1.0
C A:HIS243 4.4 41.6 1.0
CB A:ASP85 4.5 37.8 1.0
NE2 A:HIS118 4.5 49.1 1.0
CB A:ASN117 4.6 37.2 1.0
N A:ASN117 4.6 40.2 1.0
N A:HIS243 4.7 40.1 1.0
CG A:ASP36 4.9 43.2 1.0

Zinc binding site 3 out of 4 in 6ye1

Go back to Zinc Binding Sites List in 6ye1
Zinc binding site 3 out of 4 in the Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A894 (Compound 2N in Publication) in the Closed Form (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 the Ampcp Derivative A894 (Compound 2N in Publication) in the Closed Form (Crystal Form IV) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:55.9
occ:1.00
 OD2 B:ASP36 1.9 46.5 1.0
O5 B:OO2603 2.2 57.3 1.0
NE2 B:HIS38 2.2 37.6 1.0
OD2 B:ASP85 2.5 52.5 1.0
CG B:ASP36 2.9 43.8 1.0
CD2 B:HIS38 3.1 38.5 1.0
CB B:ASP36 3.2 39.1 1.0
CE1 B:HIS38 3.2 37.4 1.0
P1 B:OO2603 3.3 52.9 1.0
ZN B:ZN602 3.4 54.5 1.0
OD1 B:ASN245 3.5 36.1 1.0
CG B:ASP85 3.5 51.3 1.0
O4 B:OO2603 3.6 53.8 1.0
CB B:ASP85 3.7 40.9 1.0
C8 B:OO2603 4.0 55.6 1.0
OD1 B:ASP36 4.0 44.5 1.0
O B:HIS243 4.0 49.4 1.0
CA B:ASP36 4.2 37.6 1.0
CG B:HIS38 4.2 38.3 1.0
NE2 B:HIS220 4.3 45.7 1.0
ND1 B:HIS38 4.3 39.0 1.0
NH1 B:ARG395 4.3 35.0 1.0
CE1 B:HIS220 4.3 45.3 1.0
CG B:ASN245 4.5 52.4 1.0
CA B:HIS243 4.5 41.3 1.0
O6 B:OO2603 4.6 48.0 1.0
OD1 B:ASP85 4.7 52.6 1.0
CD2 B:HIS118 4.7 51.8 1.0
C B:HIS243 4.7 48.5 1.0
NH2 B:ARG395 4.7 38.4 1.0
ND2 B:ASN245 4.8 49.6 1.0
NE2 B:HIS118 4.9 51.5 1.0
CZ B:ARG395 5.0 53.8 1.0

Zinc binding site 4 out of 4 in 6ye1

Go back to Zinc Binding Sites List in 6ye1
Zinc binding site 4 out of 4 in the Human Ecto-5'-Nucleotidase (CD73) in Complex with the Ampcp Derivative A894 (Compound 2N in Publication) in the Closed Form (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 the Ampcp Derivative A894 (Compound 2N in Publication) in the Closed Form (Crystal Form IV) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:54.5
occ:1.00
 O4 B:OO2603 1.9 53.8 1.0
NE2 B:HIS220 2.0 45.7 1.0
OD2 B:ASP85 2.1 52.5 1.0
ND1 B:HIS243 2.3 43.2 1.0
OD1 B:ASN117 2.4 56.0 1.0
CD2 B:HIS220 2.9 46.5 1.0
CG B:ASP85 3.0 51.3 1.0
CE1 B:HIS220 3.0 45.3 1.0
CE1 B:HIS243 3.0 41.8 1.0
P1 B:OO2603 3.1 52.9 1.0
CG B:HIS243 3.3 42.7 1.0
OD1 B:ASP85 3.4 52.6 1.0
ZN B:ZN601 3.4 55.9 1.0
O5 B:OO2603 3.4 57.3 1.0
OD2 B:ASP36 3.4 46.5 1.0
CG B:ASN117 3.5 66.9 1.0
CA B:HIS243 3.6 41.3 1.0
CB B:HIS243 3.7 40.6 1.0
CD2 B:HIS118 4.0 51.8 1.0
ND2 B:ASN117 4.0 58.9 1.0
CG B:HIS220 4.0 44.4 1.0
O B:HIS243 4.1 49.4 1.0
NE2 B:HIS243 4.1 42.4 1.0
ND1 B:HIS220 4.1 45.9 1.0
O6 B:OO2603 4.2 48.0 1.0
CB B:ASP85 4.2 40.9 1.0
CD2 B:HIS243 4.2 42.8 1.0
C8 B:OO2603 4.2 55.6 1.0
C B:HIS243 4.3 48.5 1.0
NE2 B:HIS118 4.5 51.5 1.0
N B:HIS243 4.6 42.2 1.0
CG B:ASP36 4.6 43.8 1.0
N B:ASN117 4.7 44.8 1.0
CB B:ASN117 4.7 45.5 1.0
NE2 B:HIS38 4.8 37.6 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: Tue Oct 29 11:28:17 2024

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