Zinc in PDB 7jv8: Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35

Enzymatic activity of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35

All present enzymatic activity of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35:
3.1.3.5;

Protein crystallography data

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35, PDB code: 7jv8 was solved by P.Gibbons, X.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 126.17 / 2.46
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.876, 102.354, 129.609, 90.00, 103.22, 90.00
R / Rfree (%) 22 / 27.9

Other elements in 7jv8:

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 also contains other interesting chemical elements:

Calcium (Ca) 4 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 (pdb code 7jv8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35, PDB code: 7jv8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7jv8

Go back to Zinc Binding Sites List in 7jv8
Zinc binding site 1 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:34.6
occ:1.00
 OD2 A:ASP36 2.0 29.3 1.0
OD2 A:ASP85 2.1 33.5 1.0
O A:HOH720 2.1 22.4 1.0
NE2 A:HIS38 2.2 34.0 1.0
O1 A:VPD604 2.2 30.2 1.0
O4 A:VPD604 2.9 23.0 1.0
CG A:ASP85 3.0 26.1 1.0
P2 A:VPD604 3.1 28.6 1.0
CE1 A:HIS38 3.1 29.1 1.0
CG A:ASP36 3.1 30.1 1.0
CD2 A:HIS38 3.2 28.3 1.0
CB A:ASP85 3.2 26.8 1.0
ZN A:ZN602 3.5 25.6 1.0
CB A:ASP36 3.6 30.1 1.0
O7 A:VPD604 3.8 34.5 1.0
ND2 A:ASN245 4.1 28.8 1.0
OD1 A:ASP85 4.1 25.0 1.0
O3 A:VPD604 4.2 24.4 1.0
NH2 A:ARG395 4.2 26.2 1.0
C6 A:VPD604 4.2 28.7 1.0
OD1 A:ASP36 4.2 26.8 1.0
CE1 A:HIS220 4.2 29.2 1.0
ND1 A:HIS38 4.2 23.4 1.0
CA A:ASP36 4.3 28.6 1.0
CG A:HIS38 4.3 25.4 1.0
C5 A:VPD604 4.3 25.7 1.0
NE2 A:HIS220 4.4 25.7 1.0
CD2 A:HIS118 4.4 20.0 1.0
O A:HIS243 4.6 30.0 1.0
CA A:HIS243 4.7 24.5 1.0
CA A:ASP85 4.7 25.1 1.0
NE2 A:HIS118 4.8 23.9 1.0

Zinc binding site 2 out of 8 in 7jv8

Go back to Zinc Binding Sites List in 7jv8
Zinc binding site 2 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:25.6
occ:1.00
 OD1 A:ASN117 2.0 30.2 1.0
OD2 A:ASP85 2.1 33.5 1.0
NE2 A:HIS220 2.1 25.7 1.0
ND1 A:HIS243 2.1 20.8 1.0
O1 A:VPD604 2.2 30.2 1.0
O3 A:VPD604 2.6 24.4 1.0
P2 A:VPD604 2.9 28.6 1.0
CG A:ASP85 2.9 26.1 1.0
CE1 A:HIS243 2.9 25.7 1.0
CE1 A:HIS220 3.1 29.2 1.0
CD2 A:HIS220 3.1 24.1 1.0
CG A:ASN117 3.1 29.3 1.0
CG A:HIS243 3.2 24.8 1.0
OD1 A:ASP85 3.2 25.0 1.0
ZN A:ZN601 3.5 34.6 1.0
ND2 A:ASN117 3.6 26.4 1.0
CB A:HIS243 3.7 23.5 1.0
CA A:HIS243 3.8 24.5 1.0
O4 A:VPD604 4.0 23.0 1.0
OD2 A:ASP36 4.0 29.3 1.0
NE2 A:HIS243 4.1 23.9 1.0
ND1 A:HIS220 4.2 28.9 1.0
CD2 A:HIS118 4.2 20.0 1.0
CG A:HIS220 4.2 27.2 1.0
CD2 A:HIS243 4.2 25.4 1.0
C8 A:VPD604 4.3 26.7 1.0
CB A:ASP85 4.3 26.8 1.0
C5 A:VPD604 4.3 25.7 1.0
CB A:ASN117 4.4 26.9 1.0
O A:HIS243 4.5 30.0 1.0
N A:ASN117 4.5 30.1 1.0
C A:HIS243 4.7 24.6 1.0
N A:HIS243 4.7 28.5 1.0
NE2 A:HIS118 4.8 23.9 1.0

Zinc binding site 3 out of 8 in 7jv8

Go back to Zinc Binding Sites List in 7jv8
Zinc binding site 3 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:47.4
occ:1.00
 OD2 B:ASP36 2.0 38.6 1.0
OD2 B:ASP85 2.1 46.7 1.0
NE2 B:HIS38 2.1 42.8 1.0
O B:HOH711 2.2 60.0 1.0
O1 B:VPD604 2.2 45.4 1.0
O4 B:VPD604 2.7 37.5 1.0
CG B:ASP85 3.0 34.3 1.0
P2 B:VPD604 3.0 39.6 1.0
CG B:ASP36 3.1 37.9 1.0
CE1 B:HIS38 3.1 35.6 1.0
CD2 B:HIS38 3.1 38.4 1.0
CB B:ASP85 3.2 31.9 1.0
ZN B:ZN602 3.5 41.8 1.0
CB B:ASP36 3.5 36.9 1.0
O7 B:VPD604 4.0 38.4 1.0
ND2 B:ASN245 4.0 75.6 1.0
O3 B:VPD604 4.1 34.5 1.0
OD1 B:ASP85 4.1 26.8 1.0
OD1 B:ASP36 4.2 30.0 1.0
C6 B:VPD604 4.2 36.1 1.0
ND1 B:HIS38 4.2 38.0 1.0
CA B:ASP36 4.2 33.4 1.0
CG B:HIS38 4.3 35.5 1.0
CE1 B:HIS220 4.3 31.3 1.0
NH2 B:ARG395 4.3 49.5 1.0
C5 B:VPD604 4.4 43.3 1.0
CD2 B:HIS118 4.4 40.5 1.0
NE2 B:HIS220 4.4 30.5 1.0
O B:HIS243 4.6 61.2 1.0
CA B:HIS243 4.7 51.8 1.0
CA B:ASP85 4.8 30.9 1.0
NE2 B:HIS118 4.9 46.8 1.0

Zinc binding site 4 out of 8 in 7jv8

Go back to Zinc Binding Sites List in 7jv8
Zinc binding site 4 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:41.8
occ:1.00
 OD1 B:ASN117 2.0 32.8 1.0
OD2 B:ASP85 2.1 46.7 1.0
NE2 B:HIS220 2.1 30.5 1.0
ND1 B:HIS243 2.1 49.6 1.0
O1 B:VPD604 2.2 45.4 1.0
O3 B:VPD604 2.6 34.5 1.0
CG B:ASP85 2.9 34.3 1.0
CE1 B:HIS243 2.9 45.8 1.0
P2 B:VPD604 3.0 39.6 1.0
CE1 B:HIS220 3.1 31.3 1.0
CD2 B:HIS220 3.1 32.5 1.0
CG B:ASN117 3.1 38.5 1.0
OD1 B:ASP85 3.2 26.8 1.0
CG B:HIS243 3.2 45.6 1.0
ZN B:ZN601 3.5 47.4 1.0
ND2 B:ASN117 3.6 35.3 1.0
CB B:HIS243 3.7 44.6 1.0
CA B:HIS243 3.7 51.8 1.0
OD2 B:ASP36 3.9 38.6 1.0
O4 B:VPD604 3.9 37.5 1.0
NE2 B:HIS243 4.1 45.2 1.0
CD2 B:HIS118 4.1 40.5 1.0
ND1 B:HIS220 4.2 28.2 1.0
CG B:HIS220 4.2 35.4 1.0
CD2 B:HIS243 4.2 43.4 1.0
CB B:ASP85 4.3 31.9 1.0
C8 B:VPD604 4.4 47.1 1.0
C5 B:VPD604 4.4 43.3 1.0
CB B:ASN117 4.4 32.4 1.0
O B:HIS243 4.5 61.2 1.0
N B:ASN117 4.6 38.0 1.0
C B:HIS243 4.6 56.1 1.0
N B:HIS243 4.7 43.7 1.0
NE2 B:HIS118 4.8 46.8 1.0

Zinc binding site 5 out of 8 in 7jv8

Go back to Zinc Binding Sites List in 7jv8
Zinc binding site 5 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:52.8
occ:1.00
 OD2 C:ASP36 2.0 57.2 1.0
OD2 C:ASP85 2.0 43.7 1.0
NE2 C:HIS38 2.2 52.7 1.0
O C:HOH723 2.2 35.9 1.0
O1 C:VPD604 2.2 39.3 1.0
CG C:ASP85 2.9 34.9 1.0
O4 C:VPD604 3.0 31.6 1.0
CG C:ASP36 3.1 45.8 1.0
P2 C:VPD604 3.1 42.3 1.0
CE1 C:HIS38 3.1 56.6 1.0
CB C:ASP85 3.2 38.7 1.0
CD2 C:HIS38 3.2 43.9 1.0
ZN C:ZN602 3.4 38.2 1.0
CB C:ASP36 3.6 44.6 1.0
OD1 C:ASP85 4.1 28.5 1.0
O7 C:VPD604 4.1 46.6 1.0
O3 C:VPD604 4.1 28.3 1.0
OD1 C:ASP36 4.2 59.3 1.0
OD1 C:ASN245 4.2 53.5 1.0
NH2 C:ARG395 4.2 67.9 1.0
CE1 C:HIS220 4.2 43.1 1.0
ND1 C:HIS38 4.3 45.7 1.0
CA C:ASP36 4.3 47.6 1.0
C6 C:VPD604 4.3 47.7 1.0
CD2 C:HIS118 4.3 55.4 1.0
NE2 C:HIS220 4.3 50.1 1.0
CG C:HIS38 4.3 42.7 1.0
C5 C:VPD604 4.5 43.6 1.0
O C:HIS243 4.6 62.0 1.0
CA C:HIS243 4.7 48.4 1.0
CA C:ASP85 4.7 39.1 1.0
NE2 C:HIS118 4.8 55.4 1.0

Zinc binding site 6 out of 8 in 7jv8

Go back to Zinc Binding Sites List in 7jv8
Zinc binding site 6 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:38.2
occ:1.00
 OD1 C:ASN117 2.0 36.9 1.0
OD2 C:ASP85 2.0 43.7 1.0
NE2 C:HIS220 2.1 50.1 1.0
ND1 C:HIS243 2.1 56.0 1.0
O1 C:VPD604 2.2 39.3 1.0
O3 C:VPD604 2.6 28.3 1.0
CG C:ASP85 2.9 34.9 1.0
CE1 C:HIS243 3.0 55.9 1.0
P2 C:VPD604 3.0 42.3 1.0
CE1 C:HIS220 3.1 43.1 1.0
CD2 C:HIS220 3.1 52.5 1.0
CG C:ASN117 3.1 38.0 1.0
OD1 C:ASP85 3.2 28.5 1.0
CG C:HIS243 3.2 56.7 1.0
ZN C:ZN601 3.4 52.8 1.0
ND2 C:ASN117 3.6 37.8 1.0
CB C:HIS243 3.7 57.9 1.0
CA C:HIS243 3.8 48.4 1.0
OD2 C:ASP36 4.0 57.2 1.0
O4 C:VPD604 4.1 31.6 1.0
NE2 C:HIS243 4.1 61.5 1.0
CD2 C:HIS118 4.1 55.4 1.0
ND1 C:HIS220 4.2 46.1 1.0
CG C:HIS220 4.2 45.8 1.0
CD2 C:HIS243 4.2 59.6 1.0
CB C:ASP85 4.3 38.7 1.0
C5 C:VPD604 4.4 43.6 1.0
CB C:ASN117 4.4 35.4 1.0
C8 C:VPD604 4.5 44.3 1.0
O C:HIS243 4.5 62.0 1.0
N C:ASN117 4.6 41.2 1.0
C C:HIS243 4.7 52.5 1.0
N C:HIS243 4.7 48.5 1.0
NE2 C:HIS118 4.8 55.4 1.0

Zinc binding site 7 out of 8 in 7jv8

Go back to Zinc Binding Sites List in 7jv8
Zinc binding site 7 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:36.1
occ:1.00
 OD2 D:ASP36 2.0 23.4 1.0
OD2 D:ASP85 2.1 31.2 1.0
NE2 D:HIS38 2.1 34.2 1.0
O1 D:VPD604 2.2 29.9 1.0
O D:HOH708 2.3 34.2 1.0
CG D:ASP85 3.0 28.7 1.0
CE1 D:HIS38 3.1 36.0 1.0
CG D:ASP36 3.1 20.9 1.0
O4 D:VPD604 3.1 27.4 1.0
CD2 D:HIS38 3.1 36.4 1.0
P2 D:VPD604 3.2 28.7 1.0
CB D:ASP85 3.2 28.8 1.0
ZN D:ZN602 3.5 29.4 1.0
CB D:ASP36 3.5 24.4 1.0
O7 D:VPD604 3.8 24.2 1.0
ND2 D:ASN245 4.1 36.5 1.0
OD1 D:ASP85 4.1 27.2 1.0
C6 D:VPD604 4.2 21.5 1.0
OD1 D:ASP36 4.2 22.6 1.0
ND1 D:HIS38 4.2 37.7 1.0
NH2 D:ARG395 4.2 33.0 1.0
CA D:ASP36 4.2 22.6 1.0
CG D:HIS38 4.2 35.6 1.0
O3 D:VPD604 4.3 29.9 1.0
CE1 D:HIS220 4.3 24.5 1.0
CD2 D:HIS118 4.3 27.4 1.0
NE2 D:HIS220 4.4 25.1 1.0
C5 D:VPD604 4.4 24.6 1.0
O D:HIS243 4.7 30.8 1.0
CA D:HIS243 4.7 28.3 1.0
CA D:ASP85 4.7 26.5 1.0
NE2 D:HIS118 4.8 32.9 1.0

Zinc binding site 8 out of 8 in 7jv8

Go back to Zinc Binding Sites List in 7jv8
Zinc binding site 8 out of 8 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Compound 35 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:29.4
occ:1.00
 OD1 D:ASN117 2.0 35.9 1.0
OD2 D:ASP85 2.1 31.2 1.0
NE2 D:HIS220 2.1 25.1 1.0
ND1 D:HIS243 2.2 30.0 1.0
O1 D:VPD604 2.2 29.9 1.0
O3 D:VPD604 2.6 29.9 1.0
P2 D:VPD604 2.9 28.7 1.0
CG D:ASP85 2.9 28.7 1.0
CE1 D:HIS243 3.0 35.6 1.0
CE1 D:HIS220 3.1 24.5 1.0
CD2 D:HIS220 3.1 28.4 1.0
CG D:ASN117 3.1 35.2 1.0
OD1 D:ASP85 3.2 27.2 1.0
CG D:HIS243 3.3 27.8 1.0
ZN D:ZN601 3.5 36.1 1.0
ND2 D:ASN117 3.6 32.6 1.0
CB D:HIS243 3.7 27.3 1.0
CA D:HIS243 3.8 28.3 1.0
OD2 D:ASP36 3.9 23.4 1.0
O4 D:VPD604 4.0 27.4 1.0
CD2 D:HIS118 4.1 27.4 1.0
NE2 D:HIS243 4.2 23.5 1.0
ND1 D:HIS220 4.2 30.1 1.0
CG D:HIS220 4.2 31.1 1.0
CB D:ASP85 4.3 28.8 1.0
C8 D:VPD604 4.3 24.6 1.0
CD2 D:HIS243 4.3 27.7 1.0
C5 D:VPD604 4.3 24.6 1.0
CB D:ASN117 4.4 30.7 1.0
O D:HIS243 4.5 30.8 1.0
N D:ASN117 4.6 31.2 1.0
C D:HIS243 4.6 29.1 1.0
N D:HIS243 4.7 26.3 1.0
NE2 D:HIS118 4.8 32.9 1.0

Reference:

X.Du, J.Moore, B.R.Blank, J.Eksterowicz, D.Sutimantanapi, N.Yuen, T.Metzger, B.Chan, T.Huang, X.Chen, Y.Chen, F.Duong, W.Kong, J.H.Chang, J.Sun, T.Zavorotinskaya, Q.Ye, M.R.Junttila, C.Ndubaku, L.S.Friedman, V.R.Fantin, D.Sun. Orally Bioavailable Small-Molecule CD73 Inhibitor (Op-5244) Reverses Immunosuppression Through Blockade of Adenosine Production. J.Med.Chem. V. 63 10433 2020.
ISSN: ISSN 0022-2623
PubMed: 32865411
DOI: 10.1021/ACS.JMEDCHEM.0C01086
Page generated: Tue Oct 29 21:06:15 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy