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Zinc in PDB 7qga: 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: 7qga 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) 21.89 / 1.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.042, 130.046, 66.004, 90, 90, 90
R / Rfree (%) 16.5 / 18.4

Other elements in 7qga:

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:

Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 7qga). 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 CD73 (Ecto 5'-Nucleotidase) in Complex with MRS4598 (A 3-Methyl- Cmpcp Derivative, Compound 16 in Paper) in the Open State, PDB code: 7qga:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7qga

Go back to Zinc Binding Sites List in 7qga
Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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:Zn601

b:8.6
occ:1.00
 NE2 A:HIS220 2.0 6.5 1.0
O A:HOH791 2.1 6.8 1.0
OD1 A:ASN117 2.1 7.8 1.0
ND1 A:HIS243 2.1 8.5 1.0
OD2 A:ASP85 2.2 6.8 1.0
CE1 A:HIS243 3.0 9.3 1.0
CE1 A:HIS220 3.0 7.7 1.0
CD2 A:HIS220 3.0 6.5 1.0
CG A:ASP85 3.1 6.9 1.0
CG A:HIS243 3.2 8.1 1.0
CG A:ASN117 3.2 8.2 1.0
O A:HOH765 3.2 9.1 1.0
ZN A:ZN602 3.2 8.2 1.0
OD1 A:ASP85 3.5 6.5 1.0
CA A:HIS243 3.6 5.6 1.0
CB A:HIS243 3.6 6.7 1.0
OD1 A:ASP36 3.6 6.7 1.0
ND2 A:ASN117 3.7 8.9 1.0
O A:HIS243 4.1 7.1 1.0
CG A:HIS220 4.2 5.9 1.0
ND1 A:HIS220 4.2 6.7 1.0
NE2 A:HIS243 4.2 9.7 1.0
CB A:ASP85 4.2 6.2 1.0
CD2 A:HIS243 4.3 9.0 1.0
CD2 A:HIS118 4.3 6.8 1.0
C A:HIS243 4.4 6.2 1.0
N A:ASN117 4.4 6.1 1.0
CB A:ASN117 4.5 5.9 1.0
N A:HIS243 4.5 5.5 1.0
CG A:ASP36 4.8 6.8 1.0
O A:HOH729 4.8 7.5 1.0
NE2 A:HIS38 4.9 6.8 1.0
N A:HIS118 5.0 5.5 1.0
CA A:ASN117 5.0 5.8 1.0

Zinc binding site 2 out of 2 in 7qga

Go back to Zinc Binding Sites List in 7qga
Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn binding site number 2 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:Zn602

b:8.2
occ:1.00
 O A:HOH791 2.0 6.8 1.0
OD1 A:ASP36 2.0 6.7 1.0
NE2 A:HIS38 2.1 6.8 1.0
O A:HOH729 2.1 7.5 1.0
OD2 A:ASP85 2.2 6.8 1.0
CD2 A:HIS38 3.0 6.3 1.0
CE1 A:HIS38 3.1 7.1 1.0
CG A:ASP36 3.1 6.8 1.0
CG A:ASP85 3.2 6.9 1.0
ZN A:ZN601 3.2 8.6 1.0
CB A:ASP85 3.4 6.2 1.0
CB A:ASP36 3.6 6.5 1.0
O A:HOH765 4.1 9.1 1.0
OD1 A:ASN245 4.1 9.5 1.0
OD2 A:ASP36 4.2 7.1 1.0
CG A:HIS38 4.2 5.9 1.0
ND1 A:HIS38 4.2 6.5 1.0
O A:HIS243 4.2 7.1 1.0
O A:HOH822 4.2 11.6 1.0
CA A:ASP36 4.2 5.1 1.0
NE2 A:HIS220 4.3 6.5 1.0
CE1 A:HIS220 4.3 7.7 1.0
CD2 A:HIS118 4.3 6.8 1.0
O A:HOH1252 4.3 10.6 1.0
OD1 A:ASP85 4.4 6.5 1.0
CA A:HIS243 4.5 5.6 1.0
CB A:SER520 4.7 9.6 1.0
ND1 A:HIS243 4.7 8.5 1.0
C A:HIS243 4.8 6.2 1.0
NE2 A:HIS118 4.9 7.4 1.0
OD1 A:ASN117 4.9 7.8 1.0
CA A:ASP85 4.9 6.1 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: Wed Oct 30 09:52:55 2024

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