Calcium in PDB 4ygd: Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2

The structure of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2, PDB code: 4ygd 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 / 2.51
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	103.063, 58.765, 119.386, 90.00, 109.01, 90.00
R / Rfree (%)	19.3 / 23.2

The structure of Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2 also contains other interesting chemical elements:

Chlorine

(Cl)

3 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 2 (pdb code 4ygd). 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 2, PDB code: 4ygd:
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 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:37.6 occ:1.00 OD1 A:ASN156 2.3 38.6 1.0 O A:PHE154 2.3 29.8 1.0 OD1 A:ASP152 2.3 31.4 1.0 OD1 A:ASP181 2.3 34.8 1.0 O A:HOH615 2.4 29.1 1.0 OD2 A:ASP152 2.7 31.8 1.0 CG A:ASP152 2.9 27.5 1.0 CG A:ASP181 3.4 35.8 1.0 CG A:ASN156 3.4 40.3 1.0 C A:PHE154 3.5 33.0 1.0 CB A:ASN156 4.0 42.1 1.0 OD2 A:ASP181 4.2 36.8 1.0 N A:ASN156 4.2 39.0 1.0 CA A:PHE154 4.2 33.3 1.0 CB A:ASP181 4.2 37.3 1.0 N A:PHE154 4.3 29.0 1.0 CB A:ASP152 4.3 27.7 1.0 CA A:ASP181 4.4 40.5 1.0 CB A:PHE154 4.4 35.3 1.0 O A:HIS178 4.4 50.0 1.0 ND2 A:ASN156 4.5 37.6 1.0 OH A:TYR176 4.6 37.8 1.0 N A:ASP155 4.6 35.4 1.0 ND2 A:ASN162 4.7 43.3 1.0 CA A:ASN156 4.7 43.5 1.0 O A:HOH618 4.8 26.1 1.0 CZ A:PHE138 4.9 25.6 1.0 N A:ASP181 4.9 39.9 1.0 CD2 A:PHE154 5.0 39.0 1.0 CA A:ASP155 5.0 40.5 1.0 O A:ASP121 5.0 25.5 1.0 OD2 A:ASP121 5.0 38.5 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:42.7 occ:1.00 OD2 A:ASP181 2.2 36.8 1.0 OD1 A:ASP155 2.3 49.0 1.0 OD1 A:ASN161 2.4 34.3 1.0 OD1 A:ASN162 2.4 47.8 1.0 OD1 A:ASP157 2.6 56.2 1.0 CG A:ASN161 3.4 34.5 1.0 CG A:ASP181 3.4 35.8 1.0 CG A:ASN162 3.5 42.4 1.0 CG A:ASP155 3.5 47.2 1.0 CG A:ASP157 3.6 55.0 1.0 ND2 A:ASN161 3.7 34.4 1.0 ND2 A:ASN162 3.9 43.3 1.0 OD2 A:ASP157 3.9 57.6 1.0 CB A:ASP181 3.9 37.3 1.0 CA A:ASP155 4.0 40.5 1.0 CB A:ASP155 4.2 40.9 1.0 CB A:LYS159 4.3 53.5 1.0 O A:ASN161 4.4 33.4 1.0 OD1 A:ASP181 4.4 34.8 1.0 OD2 A:ASP155 4.4 53.4 1.0 N A:LYS159 4.5 45.4 1.0 C A:ASP155 4.5 38.9 1.0 C A:ASN161 4.5 38.2 1.0 N A:ASN156 4.6 39.0 1.0 N A:ASN161 4.6 43.1 1.0 CB A:ASN161 4.7 35.8 1.0 N A:ASP157 4.8 49.7 1.0 CA A:LYS159 4.8 49.7 1.0 CB A:ASN162 4.8 38.8 1.0 CA A:ASN161 4.8 41.9 1.0 CG A:LYS159 4.9 63.1 1.0 N A:ASN162 5.0 37.2 1.0

Calcium binding site 3 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:22.7 occ:1.00 O B:LEU87 2.2 26.1 1.0 OD1 B:ASP81 2.3 22.8 1.0 O B:HOH609 2.3 16.0 1.0 OD1 B:ASP83 2.3 21.0 1.0 OD1 B:ASN85 2.3 22.9 1.0 OE2 B:GLU92 2.4 24.2 1.0 OE1 B:GLU92 2.5 23.6 1.0 CD B:GLU92 2.8 23.9 1.0 CG B:ASN85 3.3 26.1 1.0 CG B:ASP83 3.3 21.0 1.0 C B:LEU87 3.4 26.1 1.0 CG B:ASP81 3.5 25.0 1.0 OD2 B:ASP83 3.7 18.9 1.0 ND2 B:ASN85 3.8 29.2 1.0 N B:LEU87 4.1 29.0 1.0 CA B:ASP81 4.2 27.3 1.0 CA B:LEU87 4.2 28.0 1.0 CG B:GLU92 4.3 22.7 1.0 OD2 B:ASP89 4.3 27.4 1.0 N B:ASN85 4.3 26.6 1.0 N B:LEU88 4.4 24.9 1.0 OD2 B:ASP81 4.4 25.7 1.0 C B:ASP81 4.4 26.7 1.0 N B:ASP83 4.4 21.3 1.0 CB B:ASP81 4.4 25.4 1.0 CA B:LEU88 4.5 23.6 1.0 CB B:LEU87 4.6 26.1 1.0 O B:HOH606 4.6 17.3 1.0 CB B:ASN85 4.6 26.9 1.0 N B:TYR82 4.6 25.8 1.0 N B:GLY84 4.7 28.1 1.0 CB B:ASP83 4.7 21.6 1.0 N B:ASP89 4.8 21.6 1.0 O B:ASP81 4.8 27.6 1.0 N B:ASN86 4.9 25.4 1.0 CA B:ASN85 4.9 26.4 1.0 CA B:ASP83 4.9 22.1 1.0 C B:ASP83 5.0 25.3 1.0

Calcium binding site 4 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:27.1 occ:1.00 OD1 B:ASP129 2.3 26.2 1.0 OE1 B:GLU140 2.3 30.6 1.0 O B:HOH607 2.3 22.5 1.0 OD1 B:ASN131 2.3 45.4 1.0 O B:TYR135 2.4 33.6 1.0 OD1 B:ASP133 2.4 29.7 1.0 OE2 B:GLU140 2.5 34.7 1.0 CD B:GLU140 2.7 32.0 1.0 CG B:ASP133 3.2 29.7 1.0 CG B:ASN131 3.3 39.1 1.0 OD2 B:ASP133 3.5 28.3 1.0 CG B:ASP129 3.5 28.4 1.0 C B:TYR135 3.5 28.9 1.0 ND2 B:ASN131 3.7 40.3 1.0 CA B:ASP129 4.1 28.8 1.0 CG B:GLU140 4.2 29.1 1.0 N B:TYR135 4.3 24.7 1.0 CA B:ILE136 4.3 29.6 1.0 CB B:ASP129 4.3 27.4 1.0 CA B:TYR135 4.3 28.4 1.0 OD2 B:ASP129 4.4 26.9 1.0 N B:ILE136 4.4 28.2 1.0 N B:ASP133 4.4 33.9 1.0 N B:ASP137 4.4 29.6 1.0 N B:ASN131 4.5 31.2 1.0 C B:ASP129 4.5 30.5 1.0 OD2 B:ASP137 4.5 32.7 1.0 CB B:TYR135 4.5 28.0 1.0 CB B:ASP133 4.5 27.2 1.0 N B:LYS130 4.6 32.3 1.0 O B:HOH614 4.6 46.5 1.0 CB B:ASN131 4.6 36.4 1.0 N B:ASN132 4.8 35.4 1.0 C B:ILE136 4.9 30.5 1.0 CA B:ASN131 4.9 34.0 1.0 CA B:ASP133 4.9 30.4 1.0 CG B:ASP137 5.0 34.1 1.0

Calcium binding site 5 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:38.1 occ:1.00 OD1 C:ASN156 2.1 53.9 1.0 O C:PHE154 2.4 36.5 1.0 OD1 C:ASP181 2.4 31.1 1.0 OD1 C:ASP152 2.4 49.8 1.0 O C:HOH646 2.7 26.2 1.0 OD2 C:ASP152 2.8 43.3 1.0 CG C:ASP152 2.9 50.1 1.0 CG C:ASN156 3.3 50.9 1.0 CG C:ASP181 3.5 38.2 1.0 C C:PHE154 3.6 41.6 1.0 CB C:ASN156 4.0 47.2 1.0 N C:ASN156 4.2 44.8 1.0 CA C:PHE154 4.3 38.7 1.0 OD2 C:ASP181 4.3 35.5 1.0 N C:PHE154 4.3 33.5 1.0 O C:HIS178 4.3 56.6 1.0 CB C:ASP181 4.3 40.4 1.0 ND2 C:ASN156 4.4 54.7 1.0 CB C:PHE154 4.4 39.8 1.0 CA C:ASP181 4.4 40.8 1.0 CB C:ASP152 4.5 45.0 1.0 OH C:TYR176 4.6 34.2 1.0 N C:ASP155 4.7 42.9 1.0 CA C:ASN156 4.7 49.1 1.0 ND2 C:ASN162 4.9 47.2 1.0 CD2 C:PHE154 4.9 40.9 1.0 CZ C:PHE138 4.9 32.2 1.0 N C:ASP181 5.0 50.4 1.0 OD2 C:ASP121 5.0 39.3 1.0 O C:ASP121 5.0 29.7 1.0

Calcium binding site 6 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:49.3 occ:1.00 OD2 C:ASP181 2.1 35.5 1.0 OD1 C:ASP155 2.5 41.6 1.0 OD1 C:ASN162 2.5 62.0 1.0 OD1 C:ASN161 2.5 40.7 1.0 OD1 C:ASP157 2.7 64.9 1.0 CG C:ASP181 3.2 38.2 1.0 CG C:ASN161 3.3 37.1 1.0 CG C:ASN162 3.5 49.0 1.0 ND2 C:ASN161 3.5 35.7 1.0 CG C:ASP155 3.6 47.7 1.0 CG C:ASP157 3.7 66.6 1.0 ND2 C:ASN162 3.8 47.2 1.0 CB C:ASP181 3.8 40.4 1.0 OD2 C:ASP157 3.9 73.7 1.0 CA C:ASP155 4.0 46.6 1.0 OD1 C:ASP181 4.3 31.1 1.0 CB C:ASP155 4.3 44.6 1.0 O C:ASN161 4.4 44.4 1.0 CB C:LYS159 4.5 63.4 1.0 C C:ASN161 4.5 43.1 1.0 C C:ASP155 4.5 45.2 1.0 OD2 C:ASP155 4.6 48.8 1.0 N C:ASN156 4.6 44.8 1.0 CB C:ASN161 4.6 37.5 1.0 N C:LYS159 4.7 55.8 1.0 N C:ASN161 4.7 40.4 1.0 N C:ASP157 4.8 58.7 1.0 CB C:ASN162 4.8 46.4 1.0 CA C:ASN161 4.9 38.7 1.0 CA C:LYS159 5.0 57.7 1.0

Calcium binding site 7 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca501 b:25.7 occ:1.00 O D:LEU87 2.2 33.0 1.0 OD1 D:ASP81 2.3 35.8 1.0 OE2 D:GLU92 2.3 27.5 1.0 OD1 D:ASP83 2.4 28.6 1.0 OE1 D:GLU92 2.5 31.2 1.0 OD1 D:ASN85 2.5 25.0 1.0 CD D:GLU92 2.8 26.8 1.0 C D:LEU87 3.4 31.0 1.0 CG D:ASP83 3.4 27.3 1.0 CG D:ASN85 3.5 24.7 1.0 CG D:ASP81 3.5 30.1 1.0 OD2 D:ASP83 3.7 32.8 1.0 ND2 D:ASN85 3.9 26.0 1.0 CA D:ASP81 4.2 30.3 1.0 N D:LEU87 4.2 32.2 1.0 CA D:LEU87 4.3 31.6 1.0 CG D:GLU92 4.3 26.6 1.0 N D:LEU88 4.3 30.3 1.0 OD2 D:ASP89 4.4 27.3 1.0 CA D:LEU88 4.4 28.5 1.0 CB D:ASP81 4.4 28.7 1.0 C D:ASP81 4.4 31.2 1.0 OD2 D:ASP81 4.4 27.1 1.0 N D:ASP83 4.4 26.6 1.0 N D:ASN85 4.5 24.7 1.0 N D:TYR82 4.6 29.1 1.0 CB D:LEU87 4.6 32.3 1.0 O D:HOH609 4.6 16.4 1.0 CB D:ASP83 4.7 24.6 1.0 N D:GLY84 4.7 25.8 1.0 CB D:ASN85 4.7 26.4 1.0 N D:ASP89 4.7 26.1 1.0 O D:ASP81 4.9 31.8 1.0 N D:ASN86 4.9 28.4 1.0 CA D:ASP83 5.0 25.2 1.0 C D:LEU88 5.0 26.9 1.0 CA D:ASN85 5.0 27.1 1.0

Calcium binding site 8 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca502 b:40.3 occ:1.00 OD1 D:ASN131 2.3 36.5 1.0 OD1 D:ASP133 2.3 33.6 1.0 O D:TYR135 2.4 38.0 1.0 OD1 D:ASP129 2.4 35.5 1.0 OE1 D:GLU140 2.4 42.4 1.0 OE2 D:GLU140 2.6 40.3 1.0 CD D:GLU140 2.9 40.1 1.0 CG D:ASP133 3.1 34.5 1.0 CG D:ASN131 3.3 39.4 1.0 OD2 D:ASP133 3.3 35.7 1.0 C D:TYR135 3.5 37.8 1.0 CG D:ASP129 3.6 38.2 1.0 ND2 D:ASN131 3.7 37.0 1.0 N D:TYR135 4.2 36.4 1.0 CA D:ILE136 4.3 36.6 1.0 CA D:TYR135 4.3 35.6 1.0 CA D:ASP129 4.3 34.8 1.0 N D:ILE136 4.4 35.9 1.0 N D:ASP133 4.4 36.9 1.0 CG D:GLU140 4.4 37.1 1.0 OD2 D:ASP129 4.4 42.0 1.0 CB D:ASP129 4.4 36.4 1.0 N D:ASP137 4.4 38.3 1.0 CB D:TYR135 4.5 34.4 1.0 CB D:ASP133 4.5 32.9 1.0 N D:ASN131 4.5 43.0 1.0 C D:ASP129 4.6 37.0 1.0 OD2 D:ASP137 4.6 47.0 1.0 CB D:ASN131 4.6 38.2 1.0 N D:LYS130 4.7 41.1 1.0 N D:ASN132 4.8 39.5 1.0 C D:ILE136 4.9 37.8 1.0 CA D:ASP133 4.9 35.3 1.0 CA D:ASN131 4.9 40.4 1.0

Calcium binding site 9 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca501 b:41.9 occ:1.00 OD1 E:ASN156 2.2 44.1 1.0 OD1 E:ASP181 2.3 45.1 1.0 O E:PHE154 2.3 30.1 1.0 OD1 E:ASP152 2.4 33.8 1.0 O E:HOH621 2.5 24.7 1.0 OD2 E:ASP152 2.7 36.0 1.0 CG E:ASP152 2.9 32.9 1.0 CG E:ASN156 3.4 43.4 1.0 CG E:ASP181 3.4 44.8 1.0 C E:PHE154 3.6 35.6 1.0 CB E:ASN156 4.0 43.8 1.0 N E:ASN156 4.1 41.3 1.0 OD2 E:ASP181 4.1 42.4 1.0 CB E:ASP181 4.2 42.4 1.0 CA E:PHE154 4.3 35.2 1.0 N E:PHE154 4.3 32.8 1.0 CA E:ASP181 4.3 45.5 1.0 O E:HIS178 4.4 55.5 1.0 CB E:ASP152 4.4 32.3 1.0 ND2 E:ASN156 4.5 42.8 1.0 CB E:PHE154 4.5 37.1 1.0 OH E:TYR176 4.6 33.7 1.0 N E:ASP155 4.6 36.3 1.0 CA E:ASN156 4.7 44.2 1.0 ND2 E:ASN162 4.7 40.9 1.0 N E:ASP181 4.9 51.1 1.0 CZ E:PHE138 4.9 29.6 1.0 CD2 E:PHE154 5.0 36.1 1.0 CA E:ASP155 5.0 39.6 1.0

Calcium binding site 10 out of 16 in the Crystal Structure of Ergic-53/MCFD2, Monoclinic Calcium-Bound Form 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca502 b:50.5 occ:1.00 OD2 E:ASP181 2.2 42.4 1.0 OD1 E:ASN161 2.4 39.1 1.0 OD1 E:ASP155 2.4 38.4 1.0 OD1 E:ASN162 2.4 48.6 1.0 OD1 E:ASP157 2.7 62.7 1.0 CG E:ASN161 3.2 36.8 1.0 CG E:ASP181 3.4 44.8 1.0 CG E:ASN162 3.4 41.6 1.0 ND2 E:ASN161 3.5 35.4 1.0 CG E:ASP155 3.6 47.4 1.0 CG E:ASP157 3.7 58.3 1.0 ND2 E:ASN162 3.8 40.9 1.0 CB E:ASP181 3.9 42.4 1.0 OD2 E:ASP157 4.0 49.9 1.0 CA E:ASP155 4.1 39.6 1.0 O E:ASN161 4.3 38.9 1.0 CB E:ASP155 4.3 41.4 1.0 CB E:LYS159 4.4 67.4 1.0 C E:ASN161 4.4 41.1 1.0 OD1 E:ASP181 4.4 45.1 1.0 OD2 E:ASP155 4.5 53.5 1.0 CB E:ASN161 4.6 38.5 1.0 N E:ASN161 4.6 48.2 1.0 N E:LYS159 4.6 63.6 1.0 C E:ASP155 4.6 38.3 1.0 N E:ASN156 4.7 41.3 1.0 CA E:ASN161 4.8 41.4 1.0 CB E:ASN162 4.8 40.8 1.0 N E:ASP157 4.9 48.8 1.0 N E:ASN162 4.9 42.6 1.0 CA E:LYS159 4.9 62.4 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.