Calcium in PDB 4ygb: Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Free Form

The structure of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Free Form, PDB code: 4ygb was solved by T.Satoh, M.Nishio, M.Yagi-Utsumi, K.Suzuki, T.Anzai, T.Mizushima, Y.Kamiya, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.924, 116.930, 58.065, 90.00, 120.13, 90.00
R / Rfree (%)	18 / 19.9

The binding sites of Calcium atom in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Free Form (pdb code 4ygb). 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, Monoclinic Calcium-Free Form, PDB code: 4ygb:
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, Monoclinic 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, Monoclinic Calcium-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:20.5 occ:1.00 O B:LEU87 2.2 23.6 1.0 OD1 B:ASP81 2.3 23.7 1.0 OD1 B:ASP83 2.3 20.7 1.0 O B:HOH621 2.4 22.8 1.0 OD1 B:ASN85 2.4 23.0 1.0 OE1 B:GLU92 2.5 21.2 1.0 OE2 B:GLU92 2.5 21.5 1.0 CD B:GLU92 2.9 21.9 1.0 CG B:ASP83 3.3 23.8 1.0 CG B:ASN85 3.4 24.1 1.0 C B:LEU87 3.5 24.4 1.0 CG B:ASP81 3.5 23.2 1.0 OD2 B:ASP83 3.7 24.4 1.0 ND2 B:ASN85 3.8 25.4 1.0 N B:LEU87 4.2 22.5 1.0 CA B:ASP81 4.2 21.4 1.0 N B:ASN85 4.3 23.5 1.0 CA B:LEU87 4.3 22.6 1.0 CG B:GLU92 4.3 20.7 1.0 CB B:ASP81 4.3 22.7 1.0 OD2 B:ASP81 4.4 23.2 1.0 N B:LEU88 4.4 21.9 1.0 OD2 B:ASP89 4.4 24.4 1.0 CA B:LEU88 4.4 22.3 1.0 N B:ASP83 4.5 22.1 1.0 C B:ASP81 4.5 22.0 1.0 CB B:ASN85 4.6 25.0 1.0 CB B:ASP83 4.6 24.0 1.0 CB B:LEU87 4.6 24.8 1.0 N B:GLY84 4.7 22.5 1.0 N B:TYR82 4.7 21.8 1.0 N B:ASP89 4.8 21.5 1.0 CA B:ASN85 4.8 23.7 1.0 N B:ASN86 4.8 24.1 1.0 O B:HOH612 4.8 24.6 1.0 CA B:ASP83 4.9 23.7 1.0 C B:ASN85 4.9 24.4 1.0 O B:ASP81 5.0 22.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic 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, Monoclinic Calcium-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:26.8 occ:1.00 O B:TYR135 2.3 24.7 1.0 OD1 B:ASN131 2.3 29.8 1.0 OD1 B:ASP129 2.3 29.7 1.0 O B:HOH627 2.4 35.2 1.0 OD1 B:ASP133 2.4 26.8 1.0 OE1 B:GLU140 2.5 27.6 1.0 OE2 B:GLU140 2.5 27.0 1.0 CD B:GLU140 2.9 30.0 1.0 CG B:ASP133 3.3 26.5 1.0 CG B:ASP129 3.4 28.7 1.0 C B:TYR135 3.5 25.4 1.0 CG B:ASN131 3.5 33.2 1.0 OD2 B:ASP133 3.6 30.7 1.0 ND2 B:ASN131 4.1 36.1 1.0 CA B:ASP129 4.1 29.5 1.0 N B:TYR135 4.2 22.6 1.0 OD2 B:ASP129 4.2 30.2 1.0 CB B:ASP129 4.2 29.4 1.0 CA B:TYR135 4.3 23.6 1.0 N B:ASP133 4.3 29.7 1.0 N B:ASN131 4.4 35.0 1.0 CG B:GLU140 4.4 28.0 1.0 N B:ILE136 4.4 23.7 1.0 C B:ASP129 4.5 31.5 1.0 N B:LYS130 4.5 31.9 1.0 CA B:ILE136 4.5 23.6 1.0 OD2 B:ASP137 4.5 38.3 1.0 CB B:TYR135 4.5 25.0 1.0 N B:ASP137 4.5 25.6 1.0 CB B:ASP133 4.5 27.7 1.0 N B:ASN132 4.7 32.2 1.0 CB B:ASN131 4.7 33.0 1.0 CA B:ASN131 4.8 33.4 1.0 CA B:ASP133 4.9 28.2 1.0 C B:ASN131 4.9 33.5 1.0 CG B:ASP137 5.0 34.0 1.0 C B:ILE136 5.0 23.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Free 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, Monoclinic Calcium-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca501 b:20.7 occ:1.00 O D:LEU87 2.2 23.5 1.0 OD1 D:ASP81 2.3 23.6 1.0 OD1 D:ASP83 2.4 21.0 1.0 OD1 D:ASN85 2.4 21.9 1.0 O D:HOH613 2.4 23.4 1.0 OE1 D:GLU92 2.5 21.7 1.0 OE2 D:GLU92 2.5 21.3 1.0 CD D:GLU92 2.8 21.3 1.0 CG D:ASP83 3.3 24.1 1.0 CG D:ASN85 3.4 23.2 1.0 C D:LEU87 3.5 24.7 1.0 CG D:ASP81 3.5 23.5 1.0 OD2 D:ASP83 3.7 25.0 1.0 ND2 D:ASN85 3.8 24.8 1.0 N D:LEU87 4.2 22.3 1.0 CA D:ASP81 4.2 21.2 1.0 N D:ASN85 4.3 22.6 1.0 CA D:LEU87 4.3 23.4 1.0 CG D:GLU92 4.3 19.8 1.0 CB D:ASP81 4.3 22.6 1.0 N D:LEU88 4.4 21.9 1.0 OD2 D:ASP81 4.4 23.0 1.0 OD2 D:ASP89 4.4 24.7 1.0 CA D:LEU88 4.4 21.8 1.0 C D:ASP81 4.5 22.4 1.0 N D:ASP83 4.5 21.5 1.0 CB D:ASN85 4.5 24.3 1.0 CB D:LEU87 4.6 24.7 1.0 CB D:ASP83 4.6 24.0 1.0 N D:GLY84 4.6 22.7 1.0 N D:TYR82 4.7 21.2 1.0 CA D:ASN85 4.7 23.1 1.0 N D:ASP89 4.8 20.3 1.0 O D:HOH614 4.8 23.9 1.0 N D:ASN86 4.8 24.3 1.0 CA D:ASP83 4.9 22.9 1.0 C D:ASN85 4.9 23.6 1.0 O D:ASP81 5.0 22.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Free 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, Monoclinic Calcium-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca502 b:26.4 occ:1.00 O D:TYR135 2.3 24.5 1.0 OD1 D:ASN131 2.3 29.9 1.0 OD1 D:ASP129 2.4 29.5 1.0 O D:HOH626 2.4 35.0 1.0 OD1 D:ASP133 2.5 25.6 1.0 OE1 D:GLU140 2.5 28.5 1.0 OE2 D:GLU140 2.5 28.2 1.0 CD D:GLU140 2.8 29.5 1.0 CG D:ASP133 3.3 25.6 1.0 CG D:ASP129 3.4 28.4 1.0 C D:TYR135 3.4 24.7 1.0 CG D:ASN131 3.5 33.8 1.0 OD2 D:ASP133 3.6 29.9 1.0 ND2 D:ASN131 4.1 36.0 1.0 CA D:ASP129 4.1 29.3 1.0 N D:TYR135 4.2 23.4 1.0 CB D:ASP129 4.3 28.5 1.0 OD2 D:ASP129 4.3 29.1 1.0 CA D:TYR135 4.3 24.3 1.0 CG D:GLU140 4.4 28.5 1.0 N D:ASP133 4.4 29.2 1.0 N D:ASN131 4.4 34.4 1.0 N D:ILE136 4.4 23.9 1.0 C D:ASP129 4.5 30.9 1.0 CA D:ILE136 4.5 23.8 1.0 N D:LYS130 4.5 33.1 1.0 OD2 D:ASP137 4.5 36.9 1.0 N D:ASP137 4.5 25.1 1.0 CB D:TYR135 4.5 26.0 1.0 CB D:ASP133 4.6 27.8 1.0 O D:HOH632 4.6 43.7 1.0 N D:ASN132 4.7 31.0 1.0 CB D:ASN131 4.7 33.4 1.0 CA D:ASN131 4.8 33.1 1.0 C D:ASN131 4.9 32.8 1.0 CA D:ASP133 4.9 28.0 1.0 CG D:ASP137 4.9 32.5 1.0 C D:ILE136 5.0 23.6 1.0

T.Satoh, M.Nishio, M.Yagi-Utsumi, K.Suzuki, T.Anzai, T.Mizushima, Y.Kamiya, K.Kato. Interaction Mode of Coagulation Factors V and VIII with the Cargo Receptor MCFD2/Ergic-53 Complex To Be Published.