Calcium 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
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Moa-Z-Vad-Fmk Complex, Direct Orientation (pdb code 5d61). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Moa-Z-Vad-Fmk Complex, Direct Orientation, PDB code: 5d61:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Moa-Z-Vad-Fmk Complex, Direct Orientation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Moa-Z-Vad-Fmk Complex, Direct Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca314 b:14.2 occ:1.00 O A:GLN211 2.3 14.4 1.0 OD2 A:ASP217 2.4 14.0 1.0 OD1 A:ASP214 2.4 16.5 1.0 O A:HOH428 2.4 16.0 1.0 OD2 A:ASP216 2.4 15.9 1.0 CG A:ASP216 3.3 17.6 1.0 CG A:ASP217 3.3 15.8 1.0 C A:GLN211 3.4 14.3 1.0 OD1 A:ASP216 3.5 17.3 1.0 CG A:ASP214 3.5 17.5 1.0 OD1 A:ASP217 3.7 16.8 1.0 CA A:CA315 4.0 15.2 1.0 OD2 A:ASP214 4.0 16.8 1.0 CA A:GLN211 4.1 15.0 1.0 N A:ASP214 4.3 15.2 1.0 O A:HOH540 4.3 22.8 1.0 N A:ASP217 4.5 14.1 1.0 N A:ILE212 4.5 14.0 1.0 CB A:ASP214 4.6 15.3 1.0 CB A:ASP216 4.6 14.4 1.0 CB A:ASP217 4.7 13.9 1.0 C A:ILE212 4.7 14.2 1.0 CA A:ASP214 4.8 15.3 1.0 N A:TYR213 4.9 15.0 1.0 CA A:ILE212 4.9 13.4 1.0 CB A:GLN211 4.9 15.7 1.0

Calcium binding site 2 out of 2 in the Moa-Z-Vad-Fmk Complex, Direct Orientation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Moa-Z-Vad-Fmk Complex, Direct Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca315 b:15.2 occ:1.00 O L:ALA3 2.3 23.6 1.0 OD2 A:ASP214 2.3 16.8 1.0 OD1 A:ASP216 2.4 17.3 1.0 O L:HOH102 2.4 19.9 1.0 CG A:ASP214 3.2 17.5 1.0 OD1 A:ASP214 3.3 16.5 1.0 CG A:ASP216 3.5 17.6 1.0 C L:ALA3 3.5 35.0 1.0 OD2 A:ASP216 4.0 15.9 1.0 CA A:CA314 4.0 14.2 1.0 CA L:ASP4 4.1 35.3 1.0 N L:ASP4 4.3 35.0 1.0 O A:HOH503 4.5 19.7 1.0 CA L:ALA3 4.5 36.4 1.0 CB A:ASP214 4.6 15.3 1.0 N L:ALA3 4.6 44.2 1.0 CB A:ASP216 4.7 14.4 1.0 CG2 L:VAL2 4.7 50.0 1.0 CB L:ASP4 4.7 40.8 1.0 CA A:GLN211 4.9 15.0 1.0 CB L:ALA3 4.9 39.6 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