Calcium in PDB 3wht: Crystal Structure of Ergic-53/MCFD2, Calcium-Free Form

The structure of Crystal Structure of Ergic-53/MCFD2, Calcium-Free Form, PDB code: 3wht was solved by T.Satoh, K.Suzuki, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.990, 59.760, 55.070, 90.00, 104.90, 90.00
R / Rfree (%)	17.5 / 20.2

The structure of Crystal Structure of Ergic-53/MCFD2, Calcium-Free Form also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Ergic-53/MCFD2, Calcium-Free Form (pdb code 3wht). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Ergic-53/MCFD2, Calcium-Free Form, PDB code: 3wht:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Ergic-53/MCFD2, Calcium-Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Ergic-53/MCFD2, Calcium-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:11.3 occ:1.00 O B:LEU87 2.3 13.1 1.0 OD1 B:ASP81 2.3 11.3 1.0 OD1 B:ASP83 2.4 13.7 1.0 OD1 B:ASN85 2.4 13.5 1.0 OE2 B:GLU92 2.4 11.8 1.0 O B:HOH602 2.5 11.4 1.0 OE1 B:GLU92 2.5 10.9 1.0 CD B:GLU92 2.8 11.7 1.0 CG B:ASP83 3.3 15.0 1.0 CG B:ASN85 3.4 13.3 1.0 CG B:ASP81 3.4 12.3 1.0 C B:LEU87 3.5 14.1 1.0 OD2 B:ASP83 3.7 16.2 1.0 ND2 B:ASN85 3.9 14.4 1.0 CA B:ASP81 4.1 11.6 1.0 N B:LEU87 4.2 13.4 1.0 CB B:ASP81 4.2 11.9 1.0 N B:ASN85 4.3 12.9 1.0 CG B:GLU92 4.3 10.9 1.0 OD2 B:ASP81 4.3 13.4 1.0 CA B:LEU87 4.4 14.5 1.0 N B:LEU88 4.4 12.8 1.0 CA B:LEU88 4.4 13.3 1.0 C B:ASP81 4.4 12.8 1.0 N B:ASP83 4.4 13.1 1.0 OD2 B:ASP89 4.5 14.1 1.0 N B:GLY84 4.6 13.0 1.0 CB B:ASN85 4.6 13.6 1.0 N B:TYR82 4.6 12.5 1.0 CB B:ASP83 4.6 14.7 1.0 CB B:LEU87 4.7 16.1 1.0 O B:HOH604 4.8 12.4 1.0 CA B:ASN85 4.8 13.3 1.0 N B:ASP89 4.8 12.2 1.0 CA B:ASP83 4.9 14.3 1.0 N B:ASN86 4.9 14.8 1.0 CD2 B:LEU88 5.0 15.7 1.0 C B:ASP83 5.0 14.9 1.0 O B:ASP81 5.0 12.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Ergic-53/MCFD2, Calcium-Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Ergic-53/MCFD2, Calcium-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:20.1 occ:1.00 OD1 B:ASP129 2.3 20.8 1.0 O B:HOH622 2.3 23.6 1.0 O B:TYR135 2.4 15.3 1.0 OD1 B:ASN131 2.4 24.4 1.0 OD1 B:ASP133 2.4 20.4 1.0 O B:HOH659 2.7 26.1 1.0 O B:HOH606 2.7 26.7 1.0 CG B:ASP133 3.3 19.9 1.0 CG B:ASN131 3.4 25.9 1.0 CG B:ASP129 3.5 19.8 1.0 C B:TYR135 3.5 16.1 1.0 OD2 B:ASP133 3.7 21.2 1.0 ND2 B:ASN131 4.0 27.1 1.0 OE1 B:GLU140 4.0 23.7 1.0 OD2 B:ASP129 4.2 20.3 1.0 N B:TYR135 4.2 13.6 1.0 OE2 B:GLU140 4.2 28.4 1.0 N B:ASP133 4.3 18.5 1.0 CA B:TYR135 4.3 13.9 1.0 N B:ASN131 4.3 23.7 1.0 CA B:ASP129 4.4 22.2 1.0 CB B:TYR135 4.4 15.0 1.0 CB B:ASP129 4.4 21.9 1.0 CB B:ASP133 4.5 18.9 1.0 N B:ILE136 4.5 16.4 1.0 CD B:GLU140 4.6 24.8 1.0 N B:LYS130 4.6 25.1 1.0 CB B:ASN131 4.6 24.3 1.0 O B:HOH620 4.6 32.2 1.0 C B:ASP129 4.6 23.7 1.0 CA B:ILE136 4.6 17.4 1.0 N B:ASN132 4.6 21.8 1.0 CA B:ASN131 4.8 23.5 1.0 CA B:ASP133 4.8 17.9 1.0 C B:ASN131 4.8 23.1 1.0 N B:GLY134 4.9 15.2 1.0

T.Satoh, K.Suzuki, T.Yamaguchi, K.Kato. Structural Basis For Disparate Sugar-Binding Specificities in the Homologous Cargo Receptors Ergic-53 and VIP36 Plos One V. 9 87963 2014.
ISSN: ESSN 1932-6203
PubMed: 24498414
DOI: 10.1371/JOURNAL.PONE.0087963