Calcium in PDB 3wnx: Crystal Structure of Ergic-53/MCFD2, Calcium/MAN3-Bound Form

The structure of Crystal Structure of Ergic-53/MCFD2, Calcium/MAN3-Bound Form, PDB code: 3wnx was solved by T.Satoh, K.Suzuki, T.Yamaguchi, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.257, 58.212, 55.435, 90.00, 109.32, 90.00
R / Rfree (%)	20.3 / 28.7

The binding sites of Calcium atom in the Crystal Structure of Ergic-53/MCFD2, Calcium/MAN3-Bound Form (pdb code 3wnx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Ergic-53/MCFD2, Calcium/MAN3-Bound Form, PDB code: 3wnx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Calcium/MAN3-Bound 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/MAN3-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:81.5 occ:1.00 OD1 A:ASN156 2.1 0.4 1.0 OD2 A:ASP152 2.3 95.5 1.0 OD1 A:ASP152 2.3 83.0 1.0 CG A:ASP152 2.6 92.1 1.0 O A:PHE154 2.7 72.9 1.0 CG A:ASN156 2.9 0.6 1.0 OD1 A:ASP181 3.2 77.3 1.0 CB A:ASN156 3.6 0.7 1.0 ND2 A:ASN156 3.8 0.4 1.0 C A:PHE154 3.8 92.6 1.0 CG A:ASP181 4.1 88.6 1.0 N A:ASN156 4.1 0.0 1.0 CB A:ASP152 4.1 87.8 1.0 O A:HIS178 4.2 97.4 1.0 ND2 A:ASN162 4.3 78.9 1.0 OH A:TYR176 4.3 88.4 1.0 CA A:PHE154 4.4 89.8 1.0 CB A:PHE154 4.5 86.7 1.0 CA A:ASN156 4.5 0.7 1.0 CA A:ASP181 4.5 0.2 1.0 N A:PHE154 4.5 88.1 1.0 CB A:ASP181 4.7 93.5 1.0 O A:ASP121 4.8 75.3 1.0 NE2 A:HIS178 4.8 0.8 1.0 CZ A:PHE138 4.9 96.3 1.0 CA A:ASP152 4.9 81.8 1.0 OD2 A:ASP181 4.9 81.6 1.0 N A:ASP181 4.9 0.3 1.0 N A:ASP155 4.9 97.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Calcium/MAN3-Bound 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/MAN3-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:91.2 occ:1.00 OD2 A:ASP181 1.9 81.6 1.0 OD1 A:ASN161 2.2 76.5 1.0 OD1 A:ASP155 2.5 93.0 1.0 OD1 A:ASP157 2.6 0.7 1.0 CG A:ASP181 3.0 88.6 1.0 CG A:ASN161 3.1 77.2 1.0 OD1 A:ASN162 3.1 83.4 1.0 ND2 A:ASN161 3.3 76.0 1.0 OD1 A:ASP181 3.4 77.3 1.0 CA A:ASP155 3.4 1.0 1.0 CG A:ASP157 3.5 0.1 1.0 CG A:ASN162 3.5 80.0 1.0 N A:ASN156 3.5 0.0 1.0 C A:ASP155 3.6 0.9 1.0 CG A:ASP155 3.6 99.7 1.0 N A:ASP157 3.8 0.9 1.0 ND2 A:ASN162 3.8 78.9 1.0 OD2 A:ASP157 3.9 95.5 1.0 CB A:ASP155 4.1 0.8 1.0 O A:ASP155 4.3 93.9 1.0 CB A:ASP181 4.3 93.5 1.0 N A:LYS159 4.3 96.5 1.0 CB A:LYS159 4.4 0.0 1.0 CB A:ASN162 4.4 83.2 1.0 CB A:ASN161 4.5 77.5 1.0 CA A:ASP157 4.5 0.8 1.0 CA A:ASN156 4.6 0.7 1.0 CB A:ASP157 4.6 0.1 1.0 N A:ASN161 4.6 79.2 1.0 O A:PHE154 4.6 72.9 1.0 OD2 A:ASP155 4.6 93.5 1.0 N A:ASP155 4.6 97.4 1.0 N A:GLY158 4.6 0.5 1.0 C A:ASN156 4.7 0.5 1.0 C A:ASP157 4.7 0.7 1.0 N A:ASN162 4.7 85.6 1.0 C A:ASN161 4.8 88.4 1.0 CA A:LYS159 4.9 0.8 1.0 CA A:ASN161 4.9 79.5 1.0 CG A:LYS159 5.0 0.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Calcium/MAN3-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Ergic-53/MCFD2, Calcium/MAN3-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:66.0 occ:1.00 OD1 B:ASN85 2.1 70.9 1.0 O B:LEU87 2.2 54.0 1.0 OD1 B:ASP83 2.3 74.2 1.0 OE1 B:GLU92 2.4 50.6 1.0 OD1 B:ASP81 2.4 62.6 1.0 OE2 B:GLU92 2.5 58.1 1.0 CD B:GLU92 2.8 55.4 1.0 CG B:ASN85 2.9 68.0 1.0 CG B:ASP83 3.0 71.5 1.0 OD2 B:ASP83 3.1 64.5 1.0 ND2 B:ASN85 3.2 64.5 1.0 C B:LEU87 3.4 59.3 1.0 CG B:ASP81 3.7 62.3 1.0 CG B:GLU92 4.2 53.6 1.0 N B:ASN85 4.3 60.3 1.0 CB B:ASN85 4.3 64.3 1.0 N B:LEU88 4.3 58.8 1.0 CA B:ASP81 4.3 60.3 1.0 CA B:LEU88 4.3 60.5 1.0 N B:LEU87 4.3 65.4 1.0 CA B:LEU87 4.4 60.1 1.0 CB B:ASP83 4.4 63.1 1.0 OD2 B:ASP81 4.5 61.9 1.0 CB B:ASP81 4.5 61.2 1.0 N B:ASP83 4.5 61.0 1.0 CB B:LEU87 4.6 59.2 1.0 NZ A:LYS53 4.6 72.8 1.0 C B:ASP81 4.7 60.9 1.0 N B:GLY84 4.7 60.9 1.0 CA B:ASN85 4.7 60.0 1.0 N B:TYR82 4.8 61.5 1.0 N B:ASP89 4.8 68.1 1.0 CA B:ASP83 4.9 63.3 1.0 OD1 B:ASP89 4.9 69.2 1.0 C B:LEU88 4.9 65.6 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Calcium/MAN3-Bound Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Ergic-53/MCFD2, Calcium/MAN3-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:73.3 occ:1.00 OD1 B:ASN131 2.1 82.7 1.0 OE1 B:GLU140 2.3 61.2 1.0 O B:TYR135 2.5 66.9 1.0 OD1 B:ASP129 2.5 65.7 1.0 OD1 B:ASP133 2.6 68.2 1.0 OE2 B:GLU140 2.6 71.5 1.0 CD B:GLU140 2.8 71.4 1.0 CG B:ASN131 3.1 79.5 1.0 CG B:ASP133 3.2 69.7 1.0 OD2 B:ASP133 3.3 60.2 1.0 ND2 B:ASN131 3.5 81.7 1.0 CG B:ASP129 3.6 66.8 1.0 C B:TYR135 3.6 69.1 1.0 OD2 B:ASP129 4.3 73.7 1.0 N B:ASP133 4.3 76.3 1.0 CA B:ASP129 4.3 69.8 1.0 CG B:GLU140 4.4 74.1 1.0 CA B:ILE136 4.4 74.0 1.0 N B:TYR135 4.4 67.0 1.0 N B:ASN132 4.4 78.9 1.0 N B:ILE136 4.4 71.1 1.0 CB B:ASP129 4.4 65.0 1.0 CB B:ASN131 4.5 74.9 1.0 N B:ASN131 4.5 79.8 1.0 CA B:TYR135 4.5 70.1 1.0 CB B:ASP133 4.5 65.0 1.0 N B:LYS130 4.7 86.8 1.0 C B:ASP129 4.7 75.7 1.0 CB B:TYR135 4.8 71.6 1.0 CA B:ASN131 4.8 77.7 1.0 N B:ASP137 4.8 68.7 1.0 C B:ASN131 4.8 82.0 1.0 CA B:ASP133 5.0 68.2 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