Sodium in PDB 6tvg: Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp in the Open State

Enzymatic activity of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp in the Open State

All present enzymatic activity of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp in the Open State:
3.1.3.5;

Protein crystallography data

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp in the Open State, PDB code: 6tvg 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) 47.19 / 1.48
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.259, 131.268, 66.213, 90.00, 90.00, 90.00
R / Rfree (%) 12.8 / 16.7

Other elements in 6tvg:

The structure of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp in the Open State also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp in the Open State (pdb code 6tvg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp in the Open State, PDB code: 6tvg:

Sodium binding site 1 out of 1 in 6tvg

Go back to Sodium Binding Sites List in 6tvg
Sodium binding site 1 out of 1 in the Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp in the Open State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human CD73 (Ecto 5'-Nucleotidase) in Complex with Ampcp in the Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:14.5
occ:1.00
 H A:GLU224 2.5 12.4 1.0
O A:HOH962 3.0 30.8 1.0
O A:HOH923 3.1 18.0 1.0
HG2 A:GLU224 3.1 16.2 1.0
HB2 A:GLU224 3.1 13.8 1.0
O A:HOH751 3.1 11.4 1.0
HA3 A:GLY222 3.2 11.9 1.0
HB3 A:SER244 3.2 11.7 1.0
H A:PHE223 3.3 11.8 1.0
N A:GLU224 3.3 10.3 1.0
N A:PHE223 3.5 9.8 1.0
CB A:GLU224 3.7 11.5 1.0
HB3 A:PHE223 3.8 12.4 1.0
CG A:GLU224 3.8 13.5 1.0
C A:GLY222 3.8 9.6 1.0
CA A:GLY222 3.9 9.9 1.0
CB A:SER244 4.0 9.8 1.0
HG3 A:GLU224 4.0 16.2 1.0
HB2 A:SER244 4.1 11.7 1.0
HA2 A:GLY222 4.1 11.9 1.0
CA A:GLU224 4.1 11.1 1.0
OG A:SER244 4.2 9.4 1.0
H A:MET225 4.2 11.3 1.0
C A:PHE223 4.3 9.7 1.0
CA A:PHE223 4.3 9.8 1.0
CB A:PHE223 4.5 10.4 1.0
O A:GLY222 4.6 9.9 1.0
HB3 A:GLU224 4.6 13.8 1.0
O A:HOH815 4.8 23.2 1.0
HB2 A:PHE223 4.8 12.4 1.0
HA A:GLU224 4.8 13.3 1.0
O A:SER221 4.9 9.5 1.0
N A:MET225 4.9 9.4 1.0
HG A:SER244 5.0 11.3 1.0

Reference:

S.Bhattarai, J.Pippel, E.R.Scaletti, R.Idris, M.Freundlieb, G.Rolshoven, C.Renn, S.Y.Lee, A.Abdelrahman, H.Zimmermann, A.El-Tayeb, C.E.Muller, N.Strater. 2-Substituted Alpha , Beta Methylene-Adp Derivatives: Potent Competitive Ecto-5'-Nucleotidase (CD73) Inhibitors with Variable Binding Modes. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32045236
DOI: 10.1021/ACS.JMEDCHEM.9B01611
Page generated: Tue Dec 15 14:27:38 2020

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