Sodium in PDB 5d61: Moa-Z-Vad-Fmk Complex, Direct Orientation

The structure of Moa-Z-Vad-Fmk Complex, Direct Orientation, PDB code: 5d61 was solved by G.Cordara, A.Van Eerde, E.M.Grahn, I.J.Goldstein, U.Krengel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.30 / 1.60
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	120.607, 120.607, 100.129, 90.00, 90.00, 120.00
R / Rfree (%)	16.1 / 18.6

The structure of Moa-Z-Vad-Fmk Complex, Direct Orientation also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	2 atoms

The binding sites of Sodium atom in the Moa-Z-Vad-Fmk Complex, Direct Orientation (pdb code 5d61). 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 Moa-Z-Vad-Fmk Complex, Direct Orientation, PDB code: 5d61:

Sodium binding site 1 out of 1 in the Moa-Z-Vad-Fmk Complex, Direct Orientation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Moa-Z-Vad-Fmk Complex, Direct Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na317 b:35.2 occ:1.00 O A:HOH562 2.0 31.2 1.0 O A:HOH545 2.1 30.5 1.0 O A:GLN276 2.2 21.2 1.0 O A:HOH648 2.3 40.5 1.0 C A:GLN276 3.4 18.9 1.0 O A:HOH567 3.5 41.4 1.0 O A:PRO204 3.9 23.0 1.0 O A:HOH522 4.0 28.2 1.0 CA A:GLN276 4.3 16.5 1.0 O A:SER206 4.3 23.6 1.0 N A:ASN277 4.4 16.5 1.0 CA A:ASN277 4.4 19.2 1.0 CB A:GLN276 4.7 18.5 1.0 CB A:ASN277 4.7 18.9 1.0 C A:PRO204 4.8 20.1 1.0 O A:HOH575 4.9 31.2 1.0 O A:LEU203 5.0 20.7 1.0

G.Cordara, A.Van Eerde, E.M.Grahn, H.C.Winter, I.J.Goldstein, U.Krengel. An Unusual Member of the Papain Superfamily: Mapping the Catalytic Cleft of the Marasmius Oreades Agglutinin (Moa) with A Caspase Inhibitor. Plos One V. 11 49407 2016.
ISSN: ESSN 1932-6203
PubMed: 26901797
DOI: 10.1371/JOURNAL.PONE.0149407