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Sodium in PDB 5rca: Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library G08B

Enzymatic activity of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library G08B

All present enzymatic activity of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library G08B:
3.4.23.22;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library G08B, PDB code: 5rca 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) 42.66 / 1.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.131, 72.994, 52.411, 90.00, 109.18, 90.00
R / Rfree (%) 15.7 / 15.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library G08B (pdb code 5rca). 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 G08B, PDB code: 5rca:

Sodium binding site 1 out of 1 in 5rca

Go back to Sodium Binding Sites List in 5rca
Sodium binding site 1 out of 1 in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library G08B


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 G08B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:63.7
occ:1.00
 O5 A:PG4409 2.6 53.3 1.0
O1 A:PG4409 3.1 51.2 1.0
O2 A:PG4409 3.1 44.7 1.0
O4 A:PG4409 3.3 48.4 1.0
O3 A:PG4409 3.4 45.9 1.0
C8 A:PG4409 3.5 54.0 1.0
C4 A:PG4409 3.8 41.7 1.0
C7 A:PG4409 3.9 49.0 1.0
C3 A:PG4409 3.9 38.6 1.0
C1 A:PG4409 4.0 44.6 1.0
C2 A:PG4409 4.1 40.5 1.0
C5 A:PG4409 4.1 43.2 1.0
C6 A:PG4409 4.2 47.2 1.0
CE2 A:PHE291 4.8 14.1 1.0
CD2 A:PHE291 5.0 13.9 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: Tue Dec 15 11:31:44 2020

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