Calcium in PDB 3whu: Crystal Structure of Ergic-53/MCFD2, Calcium/MAN2-Bound Form

The structure of Crystal Structure of Ergic-53/MCFD2, Calcium/MAN2-Bound Form, PDB code: 3whu 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)	40.00 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.680, 58.710, 56.430, 90.00, 109.68, 90.00
R / Rfree (%)	22 / 27.3

The binding sites of Calcium atom in the Crystal Structure of Ergic-53/MCFD2, Calcium/MAN2-Bound Form (pdb code 3whu). 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/MAN2-Bound Form, PDB code: 3whu:
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/MAN2-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/MAN2-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:66.2 occ:1.00 OD1 A:ASN156 2.2 84.3 1.0 OD1 A:ASP181 2.2 66.9 1.0 OD1 A:ASP152 2.6 76.3 1.0 O A:PHE154 2.7 50.0 1.0 OD2 A:ASP152 2.7 76.9 1.0 CG A:ASN156 2.9 80.4 1.0 CG A:ASP152 3.0 70.5 1.0 CG A:ASP181 3.4 68.1 1.0 ND2 A:ASN156 3.5 75.0 1.0 C A:PHE154 3.8 64.5 1.0 CB A:ASN156 3.9 79.6 1.0 OD2 A:ASP181 4.0 59.2 1.0 CB A:PHE154 4.2 63.5 1.0 N A:ASN156 4.3 82.1 1.0 O A:HIS178 4.3 74.1 1.0 OH A:TYR176 4.3 66.5 1.0 CA A:PHE154 4.4 65.4 1.0 OD2 A:ASP121 4.4 68.8 1.0 ND2 A:ASN162 4.5 59.3 1.0 CB A:ASP181 4.5 69.8 1.0 CB A:ASP152 4.5 63.9 1.0 CZ A:PHE138 4.5 59.4 1.0 N A:PHE154 4.5 64.3 1.0 CA A:ASP181 4.6 75.6 1.0 NE2 A:HIS178 4.7 89.7 1.0 CA A:ASN156 4.7 83.0 1.0 O A:ASP121 4.9 47.1 1.0 N A:ASP155 4.9 66.6 1.0 CD2 A:HIS178 4.9 88.5 1.0 CD2 A:PHE154 5.0 62.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Calcium/MAN2-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/MAN2-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:73.0 occ:1.00 OD2 A:ASP181 2.2 59.2 1.0 OD1 A:ASP157 2.6 86.3 1.0 OD1 A:ASN161 2.8 54.8 1.0 ND2 A:ASN161 2.8 53.6 1.0 OD1 A:ASN162 3.1 68.7 1.0 CG A:ASP181 3.1 68.1 1.0 CG A:ASN161 3.1 59.2 1.0 CB A:ASP181 3.3 69.8 1.0 CG A:ASP157 3.4 80.3 1.0 OD1 A:ASP155 3.4 73.9 1.0 OD2 A:ASP157 3.5 66.9 1.0 CG A:ASN162 3.9 63.0 1.0 ND2 A:ASN162 4.2 59.3 1.0 OD1 A:ASP181 4.3 66.9 1.0 N A:ASP157 4.5 90.3 1.0 CA A:ASP155 4.5 78.3 1.0 CG A:ASP155 4.5 79.5 1.0 N A:ASN156 4.6 82.1 1.0 CB A:ASN161 4.6 60.4 1.0 CB A:LYS159 4.7 88.5 1.0 CB A:ASP157 4.7 81.4 1.0 CA A:ASP181 4.8 75.6 1.0 C A:ASP155 4.8 81.1 1.0 CA A:ASP157 5.0 82.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Calcium/MAN2-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/MAN2-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:43.6 occ:1.00 OD1 B:ASN85 2.1 34.4 1.0 OD1 B:ASP83 2.4 32.0 1.0 OE1 B:GLU92 2.7 54.2 1.0 OD1 B:ASP81 2.7 31.7 1.0 O B:LEU87 2.7 46.7 1.0 CG B:ASN85 2.7 33.1 1.0 ND2 B:ASN85 2.8 31.0 1.0 OE2 B:GLU92 2.8 53.3 1.0 CD B:GLU92 3.0 47.1 1.0 CG B:ASP83 3.1 31.1 1.0 OD2 B:ASP83 3.1 29.5 1.0 C B:LEU87 3.7 42.0 1.0 CG B:ASP81 3.9 33.0 1.0 CB B:ASN85 4.2 32.3 1.0 CG B:GLU92 4.4 39.8 1.0 CB B:LEU87 4.4 43.9 1.0 N B:LEU87 4.4 47.3 1.0 CA B:LEU87 4.4 45.5 1.0 CB B:ASP83 4.5 29.4 1.0 N B:ASN85 4.5 34.1 1.0 OD2 B:ASP89 4.6 38.8 1.0 N B:LEU88 4.6 36.8 1.0 OD2 B:ASP81 4.7 30.9 1.0 CA B:LEU88 4.8 33.5 1.0 CA B:ASN85 4.8 31.9 1.0 N B:ASP83 4.8 29.4 1.0 CA B:ASP81 4.8 33.9 1.0 N B:ASP89 4.9 36.9 1.0 CG B:ASP89 4.9 34.4 1.0 NZ A:LYS53 4.9 41.5 1.0 CB B:ASP81 5.0 32.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Calcium/MAN2-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/MAN2-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:46.9 occ:1.00 OE1 B:GLU140 2.3 40.1 1.0 O B:TYR135 2.3 41.0 1.0 OD1 B:ASN131 2.4 64.6 1.0 OD1 B:ASP129 2.5 51.9 1.0 OD1 B:ASP133 2.5 42.9 1.0 OE2 B:GLU140 2.5 44.1 1.0 CD B:GLU140 2.8 41.0 1.0 OD2 B:ASP133 3.0 44.6 1.0 CG B:ASP133 3.1 44.5 1.0 CG B:ASN131 3.2 63.4 1.0 ND2 B:ASN131 3.3 63.5 1.0 C B:TYR135 3.4 37.0 1.0 CG B:ASP129 3.7 52.7 1.0 CA B:ILE136 4.1 39.1 1.0 N B:ILE136 4.2 35.5 1.0 CG B:GLU140 4.3 41.1 1.0 N B:TYR135 4.3 35.8 1.0 OD2 B:ASP137 4.3 48.8 1.0 CA B:TYR135 4.4 38.1 1.0 OD2 B:ASP129 4.5 51.0 1.0 CA B:ASP129 4.5 54.1 1.0 CB B:ASP129 4.5 53.1 1.0 N B:ASP137 4.5 40.1 1.0 CB B:ASN131 4.6 61.8 1.0 N B:ASN131 4.6 56.8 1.0 CB B:ASP133 4.6 41.6 1.0 CB B:TYR135 4.6 40.0 1.0 N B:ASP133 4.8 52.7 1.0 C B:ILE136 4.8 41.0 1.0 CG B:ASP137 4.9 52.9 1.0 N B:LYS130 4.9 65.0 1.0 CB B:ILE136 4.9 42.8 1.0 C B:ASP129 5.0 60.4 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