Calcium in PDB 5d63: Moa-Z-Vad-Fmk Inhibitor Complex, Direct/Inverted Dual Orientation

The structure of Moa-Z-Vad-Fmk Inhibitor Complex, Direct/Inverted Dual Orientation, PDB code: 5d63 was solved by G.Cordara, U.Krengel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.42 / 1.65
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	121.066, 121.066, 99.950, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 18.7

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

Chlorine	(Cl)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Moa-Z-Vad-Fmk Inhibitor Complex, Direct/Inverted Dual Orientation (pdb code 5d63). 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 Inhibitor Complex, Direct/Inverted Dual Orientation, PDB code: 5d63:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Moa-Z-Vad-Fmk Inhibitor Complex, Direct/Inverted Dual 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 Inhibitor Complex, Direct/Inverted Dual Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca318 b:9.6 occ:1.00 OD1 A:ASP214 2.3 10.9 1.0 O A:GLN211 2.4 7.9 1.0 OD2 A:ASP217 2.4 10.1 1.0 O A:HOH456 2.4 10.0 1.0 OD2 A:ASP216 2.4 9.3 1.0 CG A:ASP216 3.2 9.4 1.0 CG A:ASP217 3.4 9.6 1.0 OD1 A:ASP216 3.5 10.7 1.0 C A:GLN211 3.5 8.8 1.0 CG A:ASP214 3.5 9.3 1.0 OD1 A:ASP217 3.7 10.2 1.0 CA A:CA319 3.9 9.8 1.0 OD2 A:ASP214 4.0 11.4 1.0 CA A:GLN211 4.1 9.8 1.0 O A:HOH471 4.3 13.8 1.0 N A:ASP214 4.3 9.2 1.0 N A:ASP217 4.5 8.9 1.0 N A:ILE212 4.5 9.1 1.0 CB A:ASP217 4.6 9.1 1.0 CB A:ASP216 4.6 8.6 1.0 CB A:ASP214 4.7 9.2 1.0 C A:ILE212 4.8 9.2 1.0 CA A:ILE212 4.9 9.0 1.0 CA A:ASP214 4.9 8.7 1.0 N A:TYR213 4.9 9.7 1.0 CB A:GLN211 4.9 10.1 1.0

Calcium binding site 2 out of 2 in the Moa-Z-Vad-Fmk Inhibitor Complex, Direct/Inverted Dual 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 Inhibitor Complex, Direct/Inverted Dual Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca319 b:9.8 occ:1.00 OD1 A:ASP216 2.3 10.7 1.0 OD2 A:ASP214 2.3 11.4 1.0 O L:ALA3 2.3 9.8 0.6 O L:HOH102 2.5 15.6 1.0 CG A:ASP214 3.2 9.3 1.0 OD1 A:ASP214 3.3 10.9 1.0 CG A:ASP216 3.4 9.4 1.0 C L:ALA3 3.5 16.6 0.6 CA A:CA318 3.9 9.6 1.0 OD2 A:ASP216 4.0 9.3 1.0 CA L:ASP4 4.0 17.7 0.6 N L:ASP4 4.3 17.8 0.6 O A:HOH519 4.5 13.8 1.0 CB A:ASP214 4.6 9.2 1.0 CA L:ALA3 4.6 18.3 0.6 CB A:ASP216 4.7 8.6 1.0 CB L:ASP4 4.7 19.8 0.6 CG2 L:VAL2 4.7 25.6 0.6 N L:ALA3 4.8 20.9 0.6 CA A:GLN211 4.9 9.8 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