Calcium in PDB 4ygc: Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1

The structure of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1, PDB code: 4ygc 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 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.616, 168.892, 73.955, 90.00, 119.86, 90.00
R / Rfree (%)	20.5 / 24.6

The structure of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1 (pdb code 4ygc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1, PDB code: 4ygc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1


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-Bound Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:29.7 occ:1.00 OD1 A:ASP181 2.2 27.5 1.0 OD1 A:ASP152 2.3 30.7 1.0 OD1 A:ASN156 2.3 34.5 1.0 O A:HOH641 2.3 23.3 1.0 O A:HOH649 2.3 32.9 1.0 O A:PHE154 2.4 36.0 1.0 OD2 A:ASP152 2.5 30.0 1.0 CG A:ASP152 2.7 30.0 1.0 CG A:ASP181 3.3 27.5 1.0 CG A:ASN156 3.5 32.2 1.0 C A:PHE154 3.5 36.7 1.0 CB A:ASN156 4.1 33.0 1.0 OD2 A:ASP181 4.1 28.1 1.0 N A:ASN156 4.1 37.0 1.0 CB A:ASP181 4.2 31.8 1.0 CA A:PHE154 4.2 35.8 1.0 CB A:ASP152 4.3 28.9 1.0 N A:PHE154 4.3 35.6 1.0 CB A:PHE154 4.4 38.0 1.0 CA A:ASP181 4.4 30.3 1.0 O A:HIS178 4.5 36.6 1.0 ND2 A:ASN156 4.6 30.1 1.0 N A:ASP155 4.6 42.1 1.0 ND2 A:ASN162 4.6 35.3 1.0 OH A:TYR176 4.7 29.2 1.0 O A:ASP121 4.8 28.3 1.0 CA A:ASN156 4.8 35.2 1.0 CD2 A:PHE154 4.8 37.9 1.0 OD2 A:ASP121 4.8 35.8 1.0 O A:HOH651 4.9 26.1 1.0 CE1 A:HIS178 4.9 63.6 1.0 CA A:ASP155 5.0 41.2 1.0 CZ A:PHE138 5.0 31.9 1.0 N A:ASP181 5.0 29.8 1.0

Calcium binding site 2 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1


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-Bound Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:36.8 occ:1.00 OD2 A:ASP181 2.3 28.1 1.0 OD1 A:ASN161 2.3 29.3 1.0 OD1 A:ASP155 2.4 41.3 1.0 OD1 A:ASN162 2.5 45.2 1.0 OD1 A:ASP157 2.5 45.7 1.0 CG A:ASN161 3.2 35.1 1.0 CG A:ASP181 3.4 27.5 1.0 CG A:ASP157 3.4 42.5 1.0 ND2 A:ASN161 3.4 33.7 1.0 CG A:ASN162 3.5 39.2 1.0 CG A:ASP155 3.5 40.7 1.0 OD2 A:ASP157 3.6 46.6 1.0 ND2 A:ASN162 3.9 35.3 1.0 CB A:ASP181 3.9 31.8 1.0 CA A:ASP155 4.0 41.2 1.0 O A:ASN161 4.2 40.9 1.0 CB A:ASP155 4.3 41.8 1.0 C A:ASN161 4.4 40.4 1.0 CB A:LYS159 4.4 53.4 1.0 OD1 A:ASP181 4.5 27.5 1.0 OD2 A:ASP155 4.5 51.0 1.0 CB A:ASN161 4.5 35.4 1.0 C A:ASP155 4.6 35.3 1.0 N A:LYS159 4.6 45.2 1.0 N A:ASN161 4.6 46.3 1.0 N A:ASP157 4.7 33.1 1.0 CG A:LYS159 4.7 56.8 1.0 N A:ASN156 4.7 37.0 1.0 CA A:ASN161 4.8 40.1 1.0 CB A:ASP157 4.8 41.2 1.0 CB A:ASN162 4.8 38.5 1.0 N A:ASN162 4.9 39.3 1.0 CA A:LYS159 5.0 46.4 1.0

Calcium binding site 3 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1


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-Bound Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:41.3 occ:1.00 OD1 B:ASN131 2.2 41.4 1.0 OD1 B:ASP129 2.3 43.4 1.0 O B:TYR135 2.4 39.7 1.0 OD1 B:ASP133 2.4 44.1 1.0 OE1 B:GLU140 2.5 46.5 1.0 OE2 B:GLU140 2.6 51.4 1.0 CD B:GLU140 2.9 46.4 1.0 CG B:ASP133 3.3 42.2 1.0 CG B:ASN131 3.3 43.1 1.0 CG B:ASP129 3.4 45.2 1.0 C B:TYR135 3.5 42.9 1.0 OD2 B:ASP133 3.6 48.2 1.0 ND2 B:ASN131 3.8 41.0 1.0 OD2 B:ASP129 4.2 45.9 1.0 N B:TYR135 4.2 36.6 1.0 CA B:TYR135 4.3 39.6 1.0 CB B:ASP129 4.3 43.1 1.0 CA B:ASP129 4.3 49.6 1.0 N B:ASP133 4.4 39.8 1.0 CB B:TYR135 4.4 40.5 1.0 N B:ASN131 4.4 46.2 1.0 CG B:GLU140 4.4 48.5 1.0 N B:ILE136 4.4 46.3 1.0 CA B:ILE136 4.5 42.1 1.0 N B:ASP137 4.5 37.3 1.0 CB B:ASP133 4.5 36.3 1.0 C B:ASP129 4.6 51.0 1.0 CB B:ASN131 4.6 38.7 1.0 N B:LYS130 4.6 50.6 1.0 N B:ASN132 4.7 44.8 1.0 CA B:ASN131 4.8 44.1 1.0 CA B:ASP133 4.9 35.7 1.0 OD2 B:ASP137 4.9 53.9 1.0 C B:ASN131 4.9 46.7 1.0 N B:GLY134 5.0 31.0 1.0

Calcium binding site 4 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1


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-Bound Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:31.6 occ:1.00 O B:LEU87 2.2 35.0 1.0 OD1 B:ASP81 2.3 45.5 1.0 OD1 B:ASN85 2.3 33.1 1.0 OD1 B:ASP83 2.4 27.0 1.0 OE2 B:GLU92 2.4 24.5 1.0 OE1 B:GLU92 2.5 29.2 1.0 CD B:GLU92 2.8 25.4 1.0 CG B:ASN85 3.3 32.5 1.0 CG B:ASP83 3.4 30.0 1.0 C B:LEU87 3.4 37.8 1.0 CG B:ASP81 3.5 40.7 1.0 OD2 B:ASP83 3.7 34.3 1.0 ND2 B:ASN85 3.7 38.1 1.0 N B:LEU87 4.1 34.6 1.0 CA B:ASP81 4.1 35.3 1.0 CA B:LEU87 4.3 35.0 1.0 CB B:ASP81 4.3 37.9 1.0 N B:LEU88 4.3 35.0 1.0 CG B:GLU92 4.3 28.9 1.0 CA B:LEU88 4.4 35.4 1.0 OD2 B:ASP81 4.4 47.9 1.0 N B:ASN85 4.4 34.2 1.0 C B:ASP81 4.5 32.5 1.0 N B:ASP83 4.5 27.9 1.0 OD2 B:ASP89 4.6 31.7 1.0 CB B:ASN85 4.6 32.9 1.0 CB B:LEU87 4.6 35.6 1.0 O B:HOH606 4.7 29.7 1.0 N B:TYR82 4.7 35.6 1.0 CB B:ASP83 4.7 28.3 1.0 N B:ASP89 4.7 32.7 1.0 N B:GLY84 4.8 31.1 1.0 CA B:ASN85 4.9 36.7 1.0 N B:ASN86 4.9 38.9 1.0 O B:ASP81 4.9 32.7 1.0 CA B:ASP83 5.0 30.4 1.0

Calcium binding site 5 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:39.1 occ:1.00 OD1 C:ASN156 2.2 36.8 1.0 OD1 C:ASP181 2.2 38.0 1.0 O C:HOH656 2.2 33.9 1.0 O C:PHE154 2.3 47.8 1.0 O C:HOH625 2.3 29.1 1.0 OD1 C:ASP152 2.4 37.2 1.0 OD2 C:ASP152 2.6 39.5 1.0 CG C:ASP152 2.9 38.2 1.0 CG C:ASN156 3.3 36.4 1.0 CG C:ASP181 3.4 42.8 1.0 C C:PHE154 3.4 45.8 1.0 CB C:ASN156 4.0 39.5 1.0 N C:ASN156 4.0 40.7 1.0 OD2 C:ASP181 4.2 36.5 1.0 CA C:PHE154 4.2 46.6 1.0 CB C:ASP181 4.2 37.7 1.0 N C:PHE154 4.3 44.3 1.0 CB C:PHE154 4.3 47.7 1.0 CB C:ASP152 4.4 31.7 1.0 ND2 C:ASN156 4.4 32.9 1.0 CA C:ASP181 4.5 42.0 1.0 N C:ASP155 4.5 49.6 1.0 O C:HIS178 4.6 47.5 1.0 CA C:ASN156 4.6 39.8 1.0 ND2 C:ASN162 4.6 52.1 1.0 CD2 C:PHE154 4.7 51.6 1.0 OH C:TYR176 4.8 41.0 1.0 CA C:ASP155 4.9 48.0 1.0 OD2 C:ASP121 4.9 50.2 1.0 O C:ASP121 4.9 38.3 1.0 C C:ASP155 4.9 44.5 1.0 CG C:PHE154 5.0 47.8 1.0

Calcium binding site 6 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:49.4 occ:1.00 OD2 C:ASP181 2.2 36.5 1.0 OD1 C:ASN161 2.4 42.5 1.0 OD1 C:ASP155 2.4 50.2 1.0 OD1 C:ASP157 2.5 54.1 1.0 OD1 C:ASN162 2.5 40.7 1.0 CG C:ASN161 3.2 46.2 1.0 CG C:ASP181 3.4 42.8 1.0 CG C:ASP157 3.4 57.9 1.0 ND2 C:ASN161 3.5 48.6 1.0 CG C:ASN162 3.5 46.2 1.0 CG C:ASP155 3.5 53.7 1.0 OD2 C:ASP157 3.6 55.4 1.0 ND2 C:ASN162 3.9 52.1 1.0 CB C:ASP181 3.9 37.7 1.0 CA C:ASP155 4.1 48.0 1.0 O C:ASN161 4.2 54.5 1.0 CB C:ASP155 4.3 51.3 1.0 CB C:LYS159 4.4 59.6 1.0 OD1 C:ASP181 4.4 38.0 1.0 C C:ASN161 4.4 51.1 1.0 OD2 C:ASP155 4.5 52.2 1.0 C C:ASP155 4.5 44.5 1.0 CB C:ASN161 4.5 49.3 1.0 N C:LYS159 4.6 51.4 1.0 N C:ASN161 4.6 59.1 1.0 N C:ASP157 4.7 44.7 1.0 N C:ASN156 4.7 40.7 1.0 CB C:ASP157 4.8 56.3 1.0 CG C:LYS159 4.8 65.0 1.0 CA C:ASN161 4.8 53.5 1.0 CB C:ASN162 4.9 44.6 1.0 N C:ASN162 5.0 47.7 1.0 CA C:LYS159 5.0 54.2 1.0

Calcium binding site 7 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca501 b:45.5 occ:1.00 O D:TYR135 2.2 40.0 1.0 OD1 D:ASN131 2.3 44.1 1.0 OD1 D:ASP133 2.4 36.1 1.0 OD1 D:ASP129 2.4 36.4 1.0 OE1 D:GLU140 2.4 59.9 1.0 OE2 D:GLU140 2.6 57.8 1.0 CD D:GLU140 2.9 59.4 1.0 CG D:ASP133 3.2 35.4 1.0 C D:TYR135 3.3 40.2 1.0 CG D:ASN131 3.4 40.1 1.0 CG D:ASP129 3.5 37.1 1.0 OD2 D:ASP133 3.5 35.8 1.0 ND2 D:ASN131 3.8 34.4 1.0 CA D:TYR135 4.2 39.6 1.0 N D:TYR135 4.2 38.1 1.0 CB D:TYR135 4.3 41.5 1.0 N D:ILE136 4.3 41.0 1.0 OD2 D:ASP129 4.3 34.1 1.0 CA D:ILE136 4.4 40.2 1.0 N D:ASP133 4.4 37.9 1.0 CB D:ASP129 4.4 40.0 1.0 CA D:ASP129 4.4 44.3 1.0 N D:ASP137 4.4 39.0 1.0 CG D:GLU140 4.5 55.0 1.0 N D:ASN131 4.5 45.5 1.0 CB D:ASP133 4.5 35.1 1.0 CB D:ASN131 4.7 37.9 1.0 N D:LYS130 4.7 54.0 1.0 C D:ASP129 4.7 51.6 1.0 N D:ASN132 4.8 42.0 1.0 CA D:ASP133 4.9 35.9 1.0 C D:ILE136 4.9 40.4 1.0 CA D:ASN131 4.9 40.2 1.0 OD2 D:ASP137 5.0 47.1 1.0

Calcium binding site 8 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca502 b:28.1 occ:1.00 O D:LEU87 2.3 35.5 1.0 O D:HOH604 2.3 25.2 1.0 OD1 D:ASP81 2.3 36.0 1.0 OD1 D:ASN85 2.3 30.1 1.0 OD1 D:ASP83 2.3 30.5 1.0 OE2 D:GLU92 2.4 31.0 1.0 OE1 D:GLU92 2.6 29.1 1.0 CD D:GLU92 2.9 29.0 1.0 CG D:ASN85 3.3 34.4 1.0 CG D:ASP83 3.3 33.2 1.0 C D:LEU87 3.5 32.9 1.0 CG D:ASP81 3.6 36.4 1.0 OD2 D:ASP83 3.6 37.4 1.0 ND2 D:ASN85 3.7 35.2 1.0 N D:LEU87 4.1 34.6 1.0 CA D:ASP81 4.2 30.0 1.0 CA D:LEU87 4.3 33.5 1.0 N D:LEU88 4.4 32.3 1.0 CG D:GLU92 4.4 29.9 1.0 CB D:ASP81 4.4 32.4 1.0 N D:ASN85 4.4 35.9 1.0 CA D:LEU88 4.4 32.2 1.0 OD2 D:ASP81 4.5 34.4 1.0 C D:ASP81 4.5 29.7 1.0 O D:HOH608 4.5 29.8 1.0 OD2 D:ASP89 4.5 36.0 1.0 N D:ASP83 4.5 34.4 1.0 CB D:ASN85 4.5 32.2 1.0 CB D:LEU87 4.6 33.0 1.0 CB D:ASP83 4.7 32.1 1.0 N D:TYR82 4.7 35.0 1.0 N D:ASP89 4.8 27.4 1.0 N D:GLY84 4.8 36.8 1.0 CA D:ASN85 4.9 34.0 1.0 NZ C:LYS53 4.9 38.7 1.0 N D:ASN86 4.9 35.1 1.0 CA D:ASP83 4.9 33.6 1.0 O D:ASP81 5.0 31.2 1.0

Calcium binding site 9 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca501 b:57.0 occ:1.00 OD2 E:ASP181 2.2 59.5 1.0 O E:HOH620 2.3 41.6 1.0 OD1 E:ASN161 2.4 53.2 1.0 OD1 E:ASP155 2.4 44.1 1.0 OD1 E:ASP157 2.5 61.2 1.0 OD1 E:ASN162 2.5 71.4 1.0 CG E:ASN161 3.2 50.2 1.0 CG E:ASP157 3.4 56.8 1.0 CG E:ASP181 3.4 47.7 1.0 ND2 E:ASN161 3.4 47.6 1.0 OD2 E:ASP157 3.5 52.3 1.0 CG E:ASN162 3.6 68.4 1.0 CG E:ASP155 3.6 57.3 1.0 CB E:ASP181 3.9 50.1 1.0 ND2 E:ASN162 3.9 63.2 1.0 CA E:ASP155 4.1 53.9 1.0 O E:ASN161 4.2 73.8 1.0 CB E:ASP155 4.3 53.7 1.0 CB E:LYS159 4.4 71.2 1.0 OD1 E:ASP181 4.4 48.4 1.0 C E:ASN161 4.5 65.9 1.0 OD2 E:ASP155 4.5 55.4 1.0 CB E:ASN161 4.6 56.9 1.0 C E:ASP155 4.6 52.0 1.0 N E:LYS159 4.6 60.9 1.0 N E:ASP157 4.7 54.9 1.0 N E:ASN161 4.7 62.7 1.0 N E:ASN156 4.7 50.8 1.0 CG E:LYS159 4.7 79.6 1.0 CB E:ASP157 4.8 54.1 1.0 CA E:ASN161 4.9 62.3 1.0 CB E:ASN162 4.9 69.2 1.0 CA E:LYS159 5.0 65.3 1.0

Calcium binding site 10 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca502 b:46.3 occ:1.00 OD1 E:ASP181 2.2 48.4 1.0 OD1 E:ASN156 2.2 46.6 1.0 OD1 E:ASP152 2.3 54.8 1.0 O E:HOH619 2.4 30.0 1.0 O E:PHE154 2.4 44.7 1.0 OD2 E:ASP152 2.5 56.7 1.0 CG E:ASP152 2.8 52.2 1.0 CG E:ASP181 3.3 47.7 1.0 CG E:ASN156 3.4 55.3 1.0 C E:PHE154 3.6 50.8 1.0 CB E:ASN156 4.1 52.6 1.0 N E:ASN156 4.1 50.8 1.0 CB E:ASP181 4.2 50.1 1.0 OD2 E:ASP181 4.2 59.5 1.0 CB E:ASP152 4.3 47.6 1.0 CA E:PHE154 4.3 50.8 1.0 N E:PHE154 4.4 50.2 1.0 CA E:ASP181 4.4 49.8 1.0 CB E:PHE154 4.4 50.7 1.0 O E:HIS178 4.5 61.2 1.0 ND2 E:ASN156 4.5 46.0 1.0 OH E:TYR176 4.6 54.2 1.0 N E:ASP155 4.7 55.1 1.0 ND2 E:ASN162 4.7 63.2 1.0 CA E:ASN156 4.7 53.0 1.0 O E:ASP121 4.8 36.3 1.0 CD2 E:PHE154 4.9 53.6 1.0 CZ E:PHE138 4.9 52.5 1.0 OD2 E:ASP121 4.9 53.5 1.0 N E:ASP181 5.0 54.8 1.0 CA E:ASP155 5.0 53.9 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.