Calcium in PDB 8jp4: Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A)

The structure of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) (pdb code 8jp4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A), PDB code: 8jp4:
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 Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:47.0 occ:1.00 OD1 A:ASP152 2.3 50.6 1.0 O A:PHE154 2.3 55.6 1.0 OD1 A:ASP181 2.3 69.5 1.0 OD1 A:ASN156 2.4 56.2 1.0 OD2 A:ASP152 2.4 57.3 1.0 CG A:ASP152 2.7 49.3 1.0 CG A:ASP181 3.2 62.3 1.0 C A:PHE154 3.4 50.7 1.0 CG A:ASN156 3.5 55.7 1.0 OD2 A:ASP181 3.7 66.7 1.0 N A:ASN156 3.9 57.7 1.0 CB A:ASP152 4.1 43.9 1.0 CB A:ASN156 4.2 58.5 1.0 CA A:PHE154 4.2 48.2 1.0 CB A:ASP181 4.2 67.9 1.0 N A:PHE154 4.3 42.4 1.0 N A:ASP155 4.3 55.5 1.0 CB A:PHE154 4.3 46.8 1.0 OD1 A:ASN162 4.5 52.8 1.0 CA A:ASP155 4.5 55.9 1.0 ND2 A:ASN156 4.5 58.1 1.0 CA A:ASP181 4.6 71.7 1.0 O A:HIS178 4.6 89.4 1.0 CA A:ASN156 4.7 61.9 1.0 C A:ASP155 4.7 57.0 1.0 ND2 A:ASN162 4.8 48.5 1.0 CG A:ASN162 4.8 46.0 1.0 CD2 A:PHE154 4.9 51.9 1.0

Calcium binding site 2 out of 16 in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:58.2 occ:1.00 OD1 A:ASP155 2.3 61.1 1.0 OD2 A:ASP181 2.4 66.7 1.0 OD1 A:ASP157 2.4 62.9 1.0 OD2 A:ASP157 2.4 65.7 1.0 OD1 A:ASN161 2.4 52.5 1.0 OD1 A:ASN162 2.4 52.8 1.0 CG A:ASP157 2.7 65.8 1.0 CG A:ASN161 3.4 50.5 1.0 CG A:ASN162 3.4 46.0 1.0 CG A:ASP181 3.4 62.3 1.0 CG A:ASP155 3.5 60.2 1.0 ND2 A:ASN161 3.9 51.9 1.0 CB A:ASP181 3.9 67.9 1.0 ND2 A:ASN162 4.1 48.5 1.0 CB A:ASP157 4.2 62.9 1.0 OD2 A:ASP155 4.3 60.7 1.0 CB A:LYS159 4.3 58.2 1.0 CA A:ASP155 4.4 55.9 1.0 CB A:ASN162 4.5 42.3 1.0 CB A:ASP155 4.5 55.8 1.0 OD1 A:ASP181 4.5 69.5 1.0 N A:ASN161 4.6 56.0 1.0 N A:ASP157 4.6 63.2 1.0 N A:ASN162 4.6 50.4 1.0 N A:LYS159 4.7 60.8 1.0 C A:ASN161 4.7 55.6 1.0 CB A:ASN161 4.7 53.1 1.0 CA A:ASN161 4.9 55.4 1.0 CA A:ASP157 4.9 65.0 1.0 CA A:LYS159 5.0 54.5 1.0

Calcium binding site 3 out of 16 in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:57.4 occ:1.00 OD2 B:ASP152 2.4 52.0 1.0 OD1 B:ASP181 2.4 74.9 1.0 OD1 B:ASP152 2.4 59.7 1.0 O B:PHE154 2.4 65.4 1.0 OD1 B:ASN156 2.4 79.0 1.0 CG B:ASP152 2.7 53.5 1.0 CG B:ASP181 3.1 72.7 1.0 CG B:ASN156 3.5 73.6 1.0 C B:PHE154 3.5 63.4 1.0 OD2 B:ASP181 3.6 73.3 1.0 N B:ASN156 4.0 70.9 1.0 CB B:ASP181 4.1 70.6 1.0 CB B:ASN156 4.1 71.1 1.0 CB B:ASP152 4.2 48.4 1.0 CA B:PHE154 4.3 56.4 1.0 CB B:PHE154 4.4 57.7 1.0 CA B:ASP181 4.4 73.0 1.0 N B:PHE154 4.4 54.8 1.0 ND2 B:ASN156 4.4 71.8 1.0 N B:ASP155 4.5 72.3 1.0 O B:HIS178 4.5 76.7 1.0 CA B:ASN156 4.7 74.9 1.0 CA B:ASP155 4.7 69.9 1.0 C B:ASP155 4.8 70.1 1.0 ND2 B:ASN162 4.9 60.2 1.0 O B:ASP121 4.9 51.2 1.0 OD1 B:ASN162 4.9 66.2 1.0

Calcium binding site 4 out of 16 in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:76.8 occ:1.00 OD1 B:ASP155 2.3 77.5 1.0 OD1 B:ASP157 2.4 81.7 1.0 OD2 B:ASP181 2.4 73.3 1.0 OD1 B:ASN161 2.4 67.4 1.0 OD2 B:ASP157 2.4 79.8 1.0 OD1 B:ASN162 2.4 66.2 1.0 CG B:ASP157 2.7 80.4 1.0 CG B:ASN161 3.3 69.0 1.0 CG B:ASP181 3.4 72.7 1.0 CG B:ASP155 3.4 75.0 1.0 CG B:ASN162 3.5 60.4 1.0 CB B:ASP181 3.7 70.6 1.0 ND2 B:ASN161 3.8 67.0 1.0 OD2 B:ASP155 4.1 73.1 1.0 CB B:ASP157 4.1 76.4 1.0 ND2 B:ASN162 4.1 60.2 1.0 CA B:ASP155 4.4 69.9 1.0 O B:ASN161 4.5 69.0 1.0 CB B:ASP155 4.5 70.4 1.0 OD1 B:ASP181 4.5 74.9 1.0 C B:ASN161 4.5 66.6 1.0 CB B:ASN161 4.6 68.2 1.0 CB B:ASN162 4.6 58.7 1.0 N B:ASP157 4.6 77.2 1.0 N B:ASN161 4.7 65.9 1.0 CB B:LYS159 4.7 77.7 1.0 N B:LYS159 4.8 74.4 1.0 CA B:ASN161 4.8 65.1 1.0 N B:ASN162 4.9 64.2 1.0 CA B:ASP157 4.9 75.7 1.0 C B:ASP155 5.0 70.1 1.0

Calcium binding site 5 out of 16 in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca701 b:65.6 occ:1.00 O C:TYR135 2.3 47.7 1.0 OD1 C:ASP129 2.3 55.1 1.0 OD1 C:ASN131 2.4 69.8 1.0 OE1 C:GLU140 2.4 65.7 1.0 OD2 C:ASP133 2.4 52.6 1.0 OE2 C:GLU140 2.4 55.9 1.0 OD1 C:ASP133 2.4 55.1 1.0 CD C:GLU140 2.7 59.6 1.0 CG C:ASP133 2.7 54.5 1.0 ND2 C:ASN131 2.8 64.6 1.0 CG C:ASN131 2.9 63.3 1.0 C C:TYR135 3.2 40.7 1.0 OD1 C:ASP137 3.3 69.4 1.0 CG C:ASP129 3.5 48.4 1.0 CA C:ILE136 3.9 35.2 1.0 N C:ILE136 3.9 37.2 1.0 N C:ASP137 4.1 66.1 1.0 CA C:TYR135 4.2 34.1 1.0 CB C:ASP133 4.3 48.5 1.0 CG C:GLU140 4.3 60.0 1.0 N C:TYR135 4.3 24.2 1.0 CB C:ASP129 4.3 49.6 1.0 CG C:ASP137 4.4 71.4 1.0 OD2 C:ASP129 4.4 47.2 1.0 CB C:ASN131 4.4 53.0 1.0 C C:ILE136 4.4 48.6 1.0 CB C:TYR135 4.5 32.4 1.0 CA C:ASP129 4.7 48.5 1.0 N C:ASN131 4.8 63.9 1.0 N C:ASP133 4.9 46.8 1.0

Calcium binding site 6 out of 16 in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca702 b:51.5 occ:1.00 OD1 C:ASP83 2.3 66.0 1.0 OE1 C:GLU92 2.3 56.8 1.0 O C:LEU87 2.3 44.1 1.0 OD1 C:ASP81 2.4 54.4 1.0 OD2 C:ASP83 2.4 61.9 1.0 OE2 C:GLU92 2.4 50.6 1.0 OD1 C:ASN85 2.4 58.2 1.0 CG C:ASP83 2.6 61.5 1.0 CD C:GLU92 2.6 48.1 1.0 CG C:ASN85 3.3 55.7 1.0 CG C:ASP81 3.5 56.7 1.0 C C:LEU87 3.6 45.7 1.0 ND2 C:ASN85 3.6 57.0 1.0 CB C:ASP83 4.0 52.6 1.0 CG C:GLU92 4.1 40.3 1.0 OD1 C:ASP89 4.2 34.5 1.0 N C:LEU87 4.3 50.1 1.0 OD2 C:ASP81 4.3 61.5 1.0 CA C:ASP81 4.4 49.3 1.0 CA C:LEU87 4.5 46.2 1.0 CB C:ASP81 4.5 51.9 1.0 N C:ASP83 4.5 52.6 1.0 N C:LEU88 4.5 39.5 1.0 CA C:LEU88 4.6 34.8 1.0 CG C:ASP89 4.6 36.8 1.0 N C:ASP89 4.6 24.1 1.0 N C:ASN85 4.7 55.2 1.0 CB C:ASN85 4.7 52.9 1.0 N C:GLY84 4.8 60.5 1.0 C C:ASP81 4.8 56.3 1.0 CA C:ASP83 4.8 55.6 1.0 CB C:LEU87 4.9 46.4 1.0 N C:TYR82 4.9 48.1 1.0 OD2 C:ASP89 4.9 44.3 1.0 CD2 C:LEU88 4.9 49.9 1.0

Calcium binding site 7 out of 16 in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca701 b:39.6 occ:1.00 CB D:ASN131 2.3 55.2 1.0 O D:TYR135 2.4 48.2 1.0 OD1 D:ASP133 2.4 60.4 1.0 OE2 D:GLU140 2.4 59.1 1.0 OD1 D:ASP129 2.4 54.9 1.0 OD2 D:ASP133 2.5 54.2 1.0 OE1 D:GLU140 2.5 58.7 1.0 OD1 D:ASN131 2.6 60.4 1.0 CG D:ASP133 2.8 51.6 1.0 CG D:ASN131 2.8 60.4 1.0 CD D:GLU140 2.8 60.6 1.0 OD1 D:ASP137 3.0 62.6 1.0 C D:TYR135 3.6 31.4 1.0 CG D:ASP129 3.6 54.1 1.0 CA D:ASN131 3.7 46.9 1.0 OD2 D:ASP129 4.1 48.1 1.0 ND2 D:ASN131 4.1 48.9 1.0 N D:ASN131 4.1 59.6 1.0 CG D:ASP137 4.1 66.9 1.0 N D:ASP137 4.2 61.6 1.0 CB D:ASP133 4.2 35.1 1.0 CG D:GLU140 4.3 56.5 1.0 C D:ASN131 4.4 44.3 1.0 N D:ILE136 4.5 26.1 1.0 CA D:ILE136 4.5 40.9 1.0 CA D:TYR135 4.5 38.8 1.0 N D:ASP133 4.5 40.8 1.0 N D:TYR135 4.5 43.0 1.0 N D:ASN132 4.7 51.0 1.0 C D:ILE136 4.7 45.6 1.0 CB D:TYR135 4.8 33.9 1.0 CB D:ASP137 4.8 58.3 1.0 CB D:ASP129 4.8 58.8 1.0 CA D:ASP133 5.0 35.5 1.0

Calcium binding site 8 out of 16 in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca702 b:54.8 occ:1.00 O D:LEU87 2.1 48.4 1.0 OD1 D:ASP83 2.2 61.8 1.0 OE1 D:GLU92 2.3 35.7 1.0 OD1 D:ASP81 2.4 56.0 1.0 OD2 D:ASP83 2.4 55.2 1.0 OD1 D:ASN85 2.4 40.0 1.0 OE2 D:GLU92 2.5 51.5 1.0 CG D:ASP83 2.6 58.0 1.0 CD D:GLU92 2.7 39.8 1.0 C D:LEU87 3.3 40.9 1.0 CG D:ASN85 3.4 40.6 1.0 CG D:ASP81 3.5 49.2 1.0 ND2 D:ASN85 3.8 50.6 1.0 N D:LEU87 4.1 47.1 1.0 CB D:ASP83 4.1 49.4 1.0 OD2 D:ASP81 4.2 53.7 1.0 N D:LEU88 4.2 34.9 1.0 CG D:GLU92 4.2 35.4 1.0 CA D:LEU87 4.3 39.6 1.0 CA D:LEU88 4.3 32.2 1.0 CA D:ASP81 4.3 44.1 1.0 CD2 D:LEU88 4.4 29.0 1.0 CB D:ASP81 4.4 46.0 1.0 N D:ASP83 4.5 55.1 1.0 N D:ASN85 4.6 42.4 1.0 N D:TYR82 4.7 44.4 1.0 C D:ASP81 4.8 48.7 1.0 CB D:ASN85 4.8 42.5 1.0 N D:GLY84 4.8 54.9 1.0 CA D:ASP83 4.8 52.5 1.0 CB D:LEU87 4.9 35.5 1.0 N D:ASN86 4.9 41.1 1.0 N D:ASP89 4.9 21.8 1.0 OD1 D:ASP89 4.9 35.1 1.0

Calcium binding site 9 out of 16 in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca601 b:47.0 occ:1.00 OD1 E:ASP152 2.3 50.6 1.0 O E:PHE154 2.3 55.6 1.0 OD1 E:ASP181 2.3 69.5 1.0 OD1 E:ASN156 2.4 56.2 1.0 OD2 E:ASP152 2.4 57.3 1.0 CG E:ASP152 2.7 49.3 1.0 CG E:ASP181 3.2 62.3 1.0 C E:PHE154 3.4 50.7 1.0 CG E:ASN156 3.5 55.7 1.0 OD2 E:ASP181 3.7 66.7 1.0 N E:ASN156 3.9 57.7 1.0 CB E:ASP152 4.1 43.9 1.0 CB E:ASN156 4.2 58.5 1.0 CA E:PHE154 4.2 48.2 1.0 CB E:ASP181 4.2 67.9 1.0 N E:PHE154 4.3 42.4 1.0 N E:ASP155 4.3 55.5 1.0 CB E:PHE154 4.3 46.8 1.0 OD1 E:ASN162 4.5 52.8 1.0 CA E:ASP155 4.5 55.9 1.0 ND2 E:ASN156 4.5 58.1 1.0 CA E:ASP181 4.6 71.7 1.0 O E:HIS178 4.6 89.4 1.0 CA E:ASN156 4.7 61.9 1.0 C E:ASP155 4.7 57.0 1.0 ND2 E:ASN162 4.8 48.5 1.0 CG E:ASN162 4.8 46.0 1.0 CD2 E:PHE154 4.9 51.9 1.0

Calcium binding site 10 out of 16 in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca602 b:58.2 occ:1.00 OD1 E:ASP155 2.3 61.1 1.0 OD2 E:ASP181 2.4 66.7 1.0 OD1 E:ASP157 2.4 62.9 1.0 OD2 E:ASP157 2.4 65.7 1.0 OD1 E:ASN161 2.4 52.5 1.0 OD1 E:ASN162 2.4 52.8 1.0 CG E:ASP157 2.7 65.8 1.0 CG E:ASN161 3.4 50.5 1.0 CG E:ASN162 3.4 46.0 1.0 CG E:ASP181 3.4 62.3 1.0 CG E:ASP155 3.5 60.2 1.0 ND2 E:ASN161 3.9 51.9 1.0 CB E:ASP181 3.9 67.9 1.0 ND2 E:ASN162 4.1 48.5 1.0 CB E:ASP157 4.2 62.9 1.0 OD2 E:ASP155 4.3 60.7 1.0 CB E:LYS159 4.3 58.2 1.0 CA E:ASP155 4.4 55.9 1.0 CB E:ASN162 4.5 42.3 1.0 CB E:ASP155 4.5 55.8 1.0 OD1 E:ASP181 4.5 69.5 1.0 N E:ASN161 4.6 56.0 1.0 N E:ASP157 4.6 63.2 1.0 N E:ASN162 4.6 50.4 1.0 N E:LYS159 4.7 60.8 1.0 C E:ASN161 4.7 55.6 1.0 CB E:ASN161 4.7 53.1 1.0 CA E:ASN161 4.9 55.4 1.0 CA E:ASP157 4.9 65.0 1.0 CA E:LYS159 5.0 54.5 1.0

S.Watanabe, Y.Kise, K.Yonezawa, M.Inoue, N.Shimizu, O.Nureki, K.Inaba. Structure of Full-Length Ergic-53 in Complex with MCFD2 For Cargo Transport. Nat Commun V. 15 2404 2024.
ISSN: ESSN 2041-1723
PubMed: 38493152
DOI: 10.1038/S41467-024-46747-1