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Sodium in PDB 5rcd: Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library H03A

Enzymatic activity of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library H03A

All present enzymatic activity of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library H03A:
3.4.23.22;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library H03A, PDB code: 5rcd 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) 42.80 / 1.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.353, 73.099, 52.727, 90.00, 109.45, 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 H03A (pdb code 5rcd). 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 H03A, PDB code: 5rcd:

Sodium binding site 1 out of 1 in 5rcd

Go back to Sodium Binding Sites List in 5rcd
Sodium binding site 1 out of 1 in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library H03A


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 H03A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:57.3
occ:1.00
 O2 A:PG4410 2.8 47.5 1.0
O1 A:PG4410 3.2 50.4 1.0
O4 A:PG4410 3.2 56.3 1.0
C8 A:PG4410 3.5 58.4 1.0
C7 A:PG4410 3.5 54.8 1.0
O5 A:PG4410 3.5 55.4 1.0
C5 A:PG4410 3.6 51.7 1.0
C3 A:PG4410 3.7 45.7 1.0
C4 A:PG4410 3.7 49.6 1.0
C6 A:PG4410 3.8 50.7 1.0
C2 A:PG4410 3.9 42.2 1.0
C1 A:PG4410 3.9 45.8 1.0
O3 A:PG4410 3.9 51.8 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 Oct 7 23:52:26 2024

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