Sodium in PDB 5rdk: Pandda Analysis Group Deposition -- Endothiapepsin Ground State Model 44

All present enzymatic activity of Pandda Analysis Group Deposition -- Endothiapepsin Ground State Model 44:
3.4.23.22;

The structure of Pandda Analysis Group Deposition -- Endothiapepsin Ground State Model 44, PDB code: 5rdk was solved by M.S.Weiss, J.Wollenhaupt, A.Metz, T.Barthel, G.M.A.Lima, A.Heine, U.Mueller, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.67 / 1.03
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.146, 73.068, 52.310, 90.00, 109.22, 90.00
R / Rfree (%)	15.7 / 15.7

The binding sites of Sodium atom in the Pandda Analysis Group Deposition -- Endothiapepsin Ground State Model 44 (pdb code 5rdk). 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 Pandda Analysis Group Deposition -- Endothiapepsin Ground State Model 44, PDB code: 5rdk:

Sodium binding site 1 out of 1 in the Pandda Analysis Group Deposition -- Endothiapepsin Ground State Model 44


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pandda Analysis Group Deposition -- Endothiapepsin Ground State Model 44 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:53.4 occ:1.00 O5 A:PG4407 2.8 47.7 1.0 O4 A:PG4407 3.0 43.3 1.0 O2 A:PG4407 3.0 40.8 1.0 O1 A:PG4407 3.2 49.2 1.0 O3 A:PG4407 3.3 38.7 1.0 C8 A:PG4407 3.6 48.7 1.0 C1 A:PG4407 3.7 41.7 1.0 C4 A:PG4407 3.7 35.3 1.0 C5 A:PG4407 3.9 36.9 1.0 C7 A:PG4407 3.9 43.0 1.0 C3 A:PG4407 3.9 32.2 1.0 C2 A:PG4407 3.9 38.5 1.0 C6 A:PG4407 4.0 38.5 1.0 CE2 A:PHE291 4.9 14.3 1.0

J.Wollenhaupt, A.Metz, T.Barthel, G.M.A.Lima, A.Heine, U.Mueller, G.Klebe, M.S.Weiss. F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries For Crystallographic Fragment Screening. Structure 2020.
ISSN: ISSN 0969-2126
PubMed: 32413289
DOI: 10.1016/J.STR.2020.04.019