Magnesium in PDB 5cr7: Human Cytosolic 5'-Nucleotidase II in Complex with N-(9H-Purin-6-Yl)- 3-(3-Pyrrol-1-Ylphenyl)Benzamide

All present enzymatic activity of Human Cytosolic 5'-Nucleotidase II in Complex with N-(9H-Purin-6-Yl)- 3-(3-Pyrrol-1-Ylphenyl)Benzamide:
3.1.3.5;

The structure of Human Cytosolic 5'-Nucleotidase II in Complex with N-(9H-Purin-6-Yl)- 3-(3-Pyrrol-1-Ylphenyl)Benzamide, PDB code: 5cr7 was solved by N.Aghajari, P.Preeti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.37 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.650, 123.880, 90.580, 90.00, 115.49, 90.00
R / Rfree (%)	22 / 26.5

The binding sites of Magnesium atom in the Human Cytosolic 5'-Nucleotidase II in Complex with N-(9H-Purin-6-Yl)- 3-(3-Pyrrol-1-Ylphenyl)Benzamide (pdb code 5cr7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Cytosolic 5'-Nucleotidase II in Complex with N-(9H-Purin-6-Yl)- 3-(3-Pyrrol-1-Ylphenyl)Benzamide, PDB code: 5cr7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Cytosolic 5'-Nucleotidase II in Complex with N-(9H-Purin-6-Yl)- 3-(3-Pyrrol-1-Ylphenyl)Benzamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Cytosolic 5'-Nucleotidase II in Complex with N-(9H-Purin-6-Yl)- 3-(3-Pyrrol-1-Ylphenyl)Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg610 b:3.8 occ:1.00 OD2 A:ASP52 2.0 8.8 1.0 O A:HOH739 2.1 25.0 1.0 O3 A:PO4608 2.2 13.4 1.0 O A:ASP54 2.3 14.2 1.0 OD1 A:ASP351 2.3 16.2 1.0 CG A:ASP52 3.0 17.6 1.0 CG A:ASP351 3.2 12.8 1.0 OD2 A:ASP351 3.3 9.3 1.0 OD1 A:ASP52 3.4 23.7 1.0 C A:ASP54 3.4 13.9 1.0 P A:PO4608 3.7 24.0 1.0 O A:HOH709 4.0 31.2 1.0 CB A:ASP54 4.1 15.8 1.0 CA A:ASP54 4.1 11.2 1.0 O2 A:PO4608 4.1 12.4 1.0 N A:ASP54 4.2 12.2 1.0 CB A:ASP52 4.3 17.4 1.0 O1 A:PO4608 4.3 14.9 1.0 OG1 A:THR56 4.3 20.9 1.0 N A:TYR55 4.5 18.1 1.0 CB A:ASP351 4.6 15.8 1.0 CB A:TYR55 4.6 12.8 1.0 O4 A:PO4608 4.7 17.9 1.0 C A:MET53 4.9 10.2 1.0 O A:HOH727 4.9 15.0 1.0 N A:ASP351 4.9 19.4 1.0 CA A:TYR55 5.0 24.7 1.0

Magnesium binding site 2 out of 2 in the Human Cytosolic 5'-Nucleotidase II in Complex with N-(9H-Purin-6-Yl)- 3-(3-Pyrrol-1-Ylphenyl)Benzamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Cytosolic 5'-Nucleotidase II in Complex with N-(9H-Purin-6-Yl)- 3-(3-Pyrrol-1-Ylphenyl)Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg609 b:6.3 occ:1.00 OD1 B:ASP351 2.1 15.1 1.0 OD2 B:ASP52 2.1 9.8 1.0 O1 B:PO4606 2.4 9.4 1.0 O B:ASP54 2.5 13.8 1.0 CG B:ASP52 3.0 20.1 1.0 CG B:ASP351 3.2 13.6 1.0 OD1 B:ASP52 3.2 23.3 1.0 C B:ASP54 3.6 14.8 1.0 O B:HOH742 3.6 32.9 1.0 OD2 B:ASP351 3.7 13.8 1.0 P B:PO4606 3.8 21.5 1.0 CB B:ASP54 4.1 12.1 1.0 CA B:ASP54 4.2 14.6 1.0 O2 B:PO4606 4.3 19.3 1.0 N B:ASP54 4.3 10.8 1.0 CB B:ASP52 4.4 22.9 1.0 O4 B:PO4606 4.5 11.5 1.0 CB B:ASP351 4.5 13.8 1.0 OG1 B:THR56 4.7 25.2 1.0 N B:TYR55 4.7 12.0 1.0 CB B:TYR55 4.7 11.9 1.0 O3 B:PO4606 4.8 18.9 1.0 N B:ASP351 4.9 17.8 1.0

Z.Marton, R.Guillon, I.Krimm, R.Rahimova, D.Egron, L.P.Jordheim, N.Aghajari, C.Dumontet, C.Perigaud, C.Lionne, S.Peyrottes, L.Chaloin. Identification of Noncompetitive Inhibitors of Cytosolic 5'-Nucleotidase II Using A Fragment-Based Approach. J.Med.Chem. V. 58 9680 2015.
ISSN: ISSN 0022-2623
PubMed: 26599519
DOI: 10.1021/ACS.JMEDCHEM.5B01616