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Sodium in PDB 5rbu: Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D01A

Enzymatic activity of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D01A

All present enzymatic activity of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D01A:
3.4.23.22;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D01A, PDB code: 5rbu 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) 49.59 / 1.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.234, 73.321, 52.509, 90.00, 109.37, 90.00
R / Rfree (%) 16.5 / 16.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D01A (pdb code 5rbu). 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 Changed State Model For Fragment F2X-Entry Library D01A, PDB code: 5rbu:

Sodium binding site 1 out of 1 in 5rbu

Go back to Sodium Binding Sites List in 5rbu
Sodium binding site 1 out of 1 in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library D01A


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 D01A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:51.6
occ:1.00
 O5 A:PG4407 2.8 44.7 1.0
O2 A:PG4407 2.9 40.8 1.0
O1 A:PG4407 3.0 49.1 1.0
O4 A:PG4407 3.2 41.9 1.0
O3 A:PG4407 3.3 40.5 1.0
C1 A:PG4407 3.6 38.8 1.0
C8 A:PG4407 3.7 46.7 1.0
C2 A:PG4407 3.8 38.8 1.0
C4 A:PG4407 3.8 38.9 1.0
C3 A:PG4407 3.8 35.4 1.0
C7 A:PG4407 4.0 43.0 1.0
C5 A:PG4407 4.1 38.5 1.0
C A:R97401 4.2 20.0 0.2
C A:R97401 4.2 20.1 0.2
C6 A:PG4407 4.3 40.8 1.0
CE2 A:PHE291 4.7 14.4 1.0
CD2 A:PHE291 4.9 14.3 1.0

Reference:

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
Page generated: Mon Aug 18 02:02:50 2025

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