Sodium in PDB 5rbr: Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library C04A

All present enzymatic activity of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library C04A:
3.4.23.22;

The structure of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library C04A, PDB code: 5rbr 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)	42.79 / 0.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.285, 72.924, 52.486, 90.00, 109.25, 90.00
R / Rfree (%)	15.5 / 15.5

The binding sites of Sodium atom in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library C04A (pdb code 5rbr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library C04A, PDB code: 5rbr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library C04A


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 Changed State Model For Fragment F2X-Entry Library C04A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:44.7 occ:0.32 NA A:NA410 0.0 44.7 0.3 NA A:NA410 0.5 43.8 0.3 C2 A:R8S401 1.5 11.2 0.2 C2 A:R8S401 1.5 11.2 0.2 C3 A:R8S401 2.0 11.4 0.2 C3 A:R8S401 2.0 11.4 0.2 C1 A:R8S401 2.3 10.5 0.2 C1 A:R8S401 2.3 10.7 0.2 O5 A:PG4409 2.8 41.7 0.3 O5 A:PG4409 2.9 40.9 0.3 O A:R8S401 3.0 11.1 0.2 O A:R8S401 3.0 11.0 0.2 N A:R8S401 3.0 11.1 0.2 N A:R8S401 3.0 11.0 0.2 O4 A:PG4409 3.0 38.8 0.3 O4 A:PG4409 3.1 39.5 0.3 N1 A:R8S401 3.2 10.9 0.2 N1 A:R8S401 3.2 10.8 0.2 O2 A:PG4409 3.2 38.0 0.3 O2 A:PG4409 3.2 38.7 0.3 O1 A:PG4409 3.4 40.9 0.3 O1 A:PG4409 3.4 40.1 0.3 C4 A:R8S401 3.4 11.5 0.2 C4 A:R8S401 3.4 11.5 0.2 C8 A:PG4409 3.5 41.5 0.3 C8 A:PG4409 3.5 42.2 0.3 O3 A:PG4409 3.5 38.0 0.3 O3 A:PG4409 3.5 39.0 0.3 C4 A:PG4409 3.6 38.8 0.3 C4 A:PG4409 3.6 38.0 0.3 C3 A:PG4409 3.8 37.8 0.3 C3 A:PG4409 3.8 37.0 0.3 C7 A:PG4409 3.9 40.2 0.3 C7 A:PG4409 3.9 40.9 0.3 C1 A:PG4409 3.9 37.0 0.3 C1 A:PG4409 3.9 37.8 0.3 C5 A:PG4409 4.1 37.1 0.3 C5 A:PG4409 4.1 38.0 0.3 C2 A:PG4409 4.1 37.1 0.3 C2 A:PG4409 4.1 37.8 0.3 C6 A:PG4409 4.1 37.5 0.3 C6 A:PG4409 4.2 38.3 0.3 C A:R8S401 4.2 11.4 0.2 C A:R8S401 4.2 11.5 0.2 N2 A:R8S401 4.7 11.2 0.2 N2 A:R8S401 4.7 11.1 0.2 O A:HOH544 4.7 17.9 0.2 O A:HOH544 4.7 14.8 0.2 CE2 A:PHE291 4.8 9.3 0.2 CE2 A:PHE291 4.8 9.4 0.2 CZ A:PHE291 4.8 9.4 0.2 CZ A:PHE291 4.9 9.5 0.2 CE2 A:PHE291 4.9 11.1 0.3 CE2 A:PHE291 4.9 11.0 0.3

Sodium binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library C04A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library C04A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:43.8 occ:0.31 NA A:NA410 0.0 43.8 0.3 NA A:NA410 0.5 44.7 0.3 C2 A:R8S401 1.1 11.2 0.2 C2 A:R8S401 1.1 11.2 0.2 C3 A:R8S401 1.9 11.4 0.2 C3 A:R8S401 1.9 11.4 0.2 C1 A:R8S401 2.2 10.5 0.2 C1 A:R8S401 2.2 10.7 0.2 O5 A:PG4409 2.6 41.7 0.3 O5 A:PG4409 2.6 40.9 0.3 O A:R8S401 2.9 11.1 0.2 O A:R8S401 2.9 11.0 0.2 N A:R8S401 3.0 11.1 0.2 N A:R8S401 3.0 11.0 0.2 O1 A:PG4409 3.1 40.9 0.3 O1 A:PG4409 3.1 40.1 0.3 O4 A:PG4409 3.1 38.8 0.3 N1 A:R8S401 3.2 10.9 0.2 N1 A:R8S401 3.2 10.8 0.2 O4 A:PG4409 3.2 39.5 0.3 O2 A:PG4409 3.2 38.0 0.3 O2 A:PG4409 3.3 38.7 0.3 C4 A:R8S401 3.4 11.5 0.2 C8 A:PG4409 3.4 41.5 0.3 C4 A:R8S401 3.4 11.5 0.2 C8 A:PG4409 3.4 42.2 0.3 O3 A:PG4409 3.6 38.0 0.3 O3 A:PG4409 3.6 39.0 0.3 C4 A:PG4409 3.8 38.8 0.3 C4 A:PG4409 3.8 38.0 0.3 C1 A:PG4409 3.8 37.0 0.3 C1 A:PG4409 3.8 37.8 0.3 C7 A:PG4409 3.8 40.2 0.3 C3 A:PG4409 3.8 37.8 0.3 C3 A:PG4409 3.9 37.0 0.3 C7 A:PG4409 3.9 40.9 0.3 C2 A:PG4409 4.0 37.1 0.3 C2 A:PG4409 4.0 37.8 0.3 C A:R8S401 4.2 11.4 0.2 C A:R8S401 4.2 11.5 0.2 C6 A:PG4409 4.2 37.5 0.3 C5 A:PG4409 4.2 37.1 0.3 C5 A:PG4409 4.2 38.0 0.3 C6 A:PG4409 4.2 38.3 0.3 CE2 A:PHE291 4.3 9.3 0.2 CE2 A:PHE291 4.3 9.4 0.2 CZ A:PHE291 4.4 9.4 0.2 CZ A:PHE291 4.4 9.5 0.2 CE2 A:PHE291 4.5 11.1 0.3 CE2 A:PHE291 4.5 11.0 0.3 CD2 A:PHE291 4.6 8.8 0.2 CD2 A:PHE291 4.6 10.4 0.3 CD2 A:PHE291 4.6 10.3 0.3 CD2 A:PHE291 4.7 8.8 0.2 CE1 A:PHE291 4.7 9.3 0.2 CE1 A:PHE291 4.7 9.4 0.2 O A:HOH544 4.7 17.9 0.2 O A:HOH544 4.7 14.8 0.2 N2 A:R8S401 4.7 11.2 0.2 N2 A:R8S401 4.7 11.1 0.2 CZ A:PHE291 4.9 12.0 0.3 CZ A:PHE291 4.9 11.9 0.3 CG A:PHE291 4.9 8.4 0.2 CG A:PHE291 4.9 8.4 0.2 CD1 A:PHE291 4.9 9.2 0.2 CD1 A:PHE291 4.9 9.1 0.2

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