Calcium in PDB 5d62: Moa-Z-Vad-Fmk Complex, Inverted Orientation

The structure of Moa-Z-Vad-Fmk Complex, Inverted Orientation, PDB code: 5d62 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)	46.41 / 1.70
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	120.998, 120.998, 99.957, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 19.8

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

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Moa-Z-Vad-Fmk Complex, Inverted Orientation (pdb code 5d62). 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, Inverted Orientation, PDB code: 5d62:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Moa-Z-Vad-Fmk Complex, Inverted 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, Inverted Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca317 b:12.2 occ:1.00 OD1 A:ASP214 2.3 15.6 1.0 O A:HOH427 2.3 13.4 1.0 OD2 A:ASP217 2.4 11.8 1.0 O A:GLN211 2.4 12.2 1.0 OD2 A:ASP216 2.5 12.6 1.0 CG A:ASP216 3.3 13.4 1.0 CG A:ASP217 3.4 12.3 1.0 OD1 A:ASP216 3.5 14.4 1.0 C A:GLN211 3.5 12.6 1.0 CG A:ASP214 3.5 13.0 1.0 OD1 A:ASP217 3.7 13.4 1.0 CA A:CA318 4.0 13.5 1.0 OD2 A:ASP214 4.1 14.0 1.0 CA A:GLN211 4.1 12.5 1.0 O A:HOH482 4.2 19.1 1.0 N A:ASP214 4.3 14.2 1.0 N A:ASP217 4.5 12.0 1.0 N A:ILE212 4.6 12.2 1.0 CB A:ASP214 4.6 14.4 1.0 CB A:ASP216 4.7 12.1 1.0 CB A:ASP217 4.7 11.1 1.0 C A:ILE212 4.7 13.8 1.0 CA A:ASP214 4.9 13.5 1.0 N A:TYR213 4.9 12.8 1.0 CA A:ILE212 4.9 12.0 1.0 CB A:GLN211 4.9 13.5 1.0

Calcium binding site 2 out of 2 in the Moa-Z-Vad-Fmk Complex, Inverted 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, Inverted Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca318 b:13.5 occ:1.00 OD2 A:ASP214 2.3 14.0 1.0 OD1 A:ASP216 2.3 14.4 1.0 O A:HOH600 2.5 16.9 1.0 CG A:ASP214 3.1 13.0 1.0 OD1 A:ASP214 3.3 15.6 1.0 CG A:ASP216 3.4 13.4 1.0 OD2 A:ASP216 3.9 12.6 1.0 CA A:CA317 4.0 12.2 1.0 O A:HOH474 4.5 16.4 1.0 CB A:ASP214 4.5 14.4 1.0 CB A:ASP216 4.7 12.1 1.0 CA A:GLN211 4.8 12.5 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