Zinc in PDB 5w6e: PDE1B Complexed with Compound 3S

All present enzymatic activity of PDE1B Complexed with Compound 3S:
3.1.4.17;

The structure of PDE1B Complexed with Compound 3S, PDB code: 5w6e was solved by F.F.Vajdos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.10 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.782, 88.782, 134.806, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.6

The structure of PDE1B Complexed with Compound 3S also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the PDE1B Complexed with Compound 3S (pdb code 5w6e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the PDE1B Complexed with Compound 3S, PDB code: 5w6e:

Zinc binding site 1 out of 1 in the PDE1B Complexed with Compound 3S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PDE1B Complexed with Compound 3S within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:23.8 occ:1.00 OD1 A:ASP370 2.0 19.7 1.0 OD2 A:ASP264 2.0 20.0 1.0 NE2 A:HIS227 2.2 15.6 1.0 NE2 A:HIS263 2.2 19.1 1.0 O A:HOH1221 2.3 23.7 1.0 O A:HOH1114 2.4 17.7 1.0 CG A:ASP370 3.0 22.3 1.0 CD2 A:HIS227 3.0 21.0 1.0 CD2 A:HIS263 3.1 18.6 1.0 CG A:ASP264 3.1 21.6 1.0 CE1 A:HIS227 3.2 22.6 1.0 OD2 A:ASP370 3.3 25.8 1.0 CE1 A:HIS263 3.3 19.1 1.0 OD1 A:ASP264 3.6 18.7 1.0 MG A:MG1002 3.9 20.5 1.0 O A:HOH1171 4.0 20.1 1.0 NE2 A:HIS223 4.1 21.8 1.0 O A:HOH1295 4.2 17.8 1.0 CD2 A:HIS223 4.2 21.5 1.0 CG A:HIS227 4.2 16.6 1.0 CG A:HIS263 4.3 19.8 1.0 ND1 A:HIS227 4.3 17.0 1.0 CB A:ASP370 4.3 19.8 1.0 CB A:ASP264 4.3 18.6 1.0 ND1 A:HIS263 4.3 18.9 1.0 CG2 A:VAL231 4.8 13.6 1.0 CA A:ASP370 4.8 19.1 1.0 O A:HOH1180 4.9 19.4 1.0 O A:ASP370 4.9 21.0 1.0

J.M.Humphrey, M.Movsesian, C.W.Am Ende, S.L.Becker, T.A.Chappie, S.Jenkinson, J.L.Liras, S.Liras, C.Orozco, J.Pandit, F.F.Vajdos, F.Vandeput, E.Yang, F.S.Menniti. Discovery of Potent and Selective Periphery-Restricted Quinazoline Inhibitors of the Cyclic Nucleotide Phosphodiesterase PDE1. J. Med. Chem. V. 61 4635 2018.
ISSN: ISSN 1520-4804
PubMed: 29718668
DOI: 10.1021/ACS.JMEDCHEM.8B00374