Zinc in PDB 8jp8: Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate C)

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

Calcium

(Ca)

16 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate C) (pdb code 8jp8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate C), PDB code: 8jp8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate C)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate C) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn703 b:190.5 occ:1.00 NE2 C:HIS99 2.0 136.5 1.0 NE2 C:HIS101 2.0 167.3 1.0 NE2 C:HIS51 2.0 157.7 1.0 NE2 C:HIS55 2.0 151.6 1.0 CE1 C:HIS51 2.4 156.1 1.0 CD2 C:HIS101 2.4 166.1 1.0 CD2 C:HIS99 2.5 135.1 1.0 CD2 C:HIS55 2.8 153.5 1.0 CD2 C:HIS51 2.9 158.4 1.0 CE1 C:HIS99 3.0 130.8 1.0 CE1 C:HIS101 3.1 165.5 1.0 CE1 C:HIS55 3.2 148.0 1.0 ND1 C:HIS51 3.2 158.1 1.0 CG C:HIS51 3.5 158.9 1.0 CG C:HIS99 3.6 133.3 1.0 CG C:HIS101 3.6 165.8 1.0 ND1 C:HIS99 3.8 129.2 1.0 ND1 C:HIS101 3.9 165.1 1.0 CG C:HIS55 4.0 150.9 1.0 ND1 C:HIS55 4.2 147.5 1.0 O C:HIS51 4.6 157.4 1.0 CB C:HIS101 4.8 165.3 1.0 CB C:HIS99 4.8 131.5 1.0 CB C:HIS51 4.8 158.8 1.0 OE1 C:GLU54 4.9 169.1 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate C)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate C) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn703 b:193.2 occ:1.00 NE2 D:HIS101 2.0 167.6 1.0 NE2 D:HIS51 2.0 173.4 1.0 NE2 D:HIS55 2.0 158.2 1.0 NE2 D:HIS99 2.1 136.4 1.0 CD2 D:HIS101 2.4 168.6 1.0 CE1 D:HIS55 2.6 157.0 1.0 CD2 D:HIS51 2.7 173.3 1.0 CD2 D:HIS55 2.9 157.2 1.0 CD2 D:HIS99 3.0 131.5 1.0 CE1 D:HIS99 3.0 132.2 1.0 CE1 D:HIS51 3.2 173.1 1.0 CE1 D:HIS101 3.2 168.1 1.0 ND1 D:HIS55 3.5 157.2 1.0 CG D:HIS101 3.6 170.3 1.0 CG D:HIS55 3.7 158.2 1.0 CG D:HIS51 3.9 175.4 1.0 ND1 D:HIS101 4.0 169.7 1.0 ND1 D:HIS51 4.1 177.2 1.0 ND1 D:HIS99 4.1 129.0 1.0 CG D:HIS99 4.1 128.4 1.0 O D:HIS51 4.9 166.4 1.0 CB D:HIS101 4.9 171.3 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate C)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate C) within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn703 b:163.2 occ:1.00 NE2 G:HIS99 2.0 122.5 1.0 NE2 G:HIS101 2.0 142.9 1.0 NE2 G:HIS51 2.0 147.2 1.0 NE2 G:HIS55 2.0 132.2 1.0 CE1 G:HIS51 2.4 146.0 1.0 CD2 G:HIS101 2.4 142.1 1.0 CD2 G:HIS99 2.5 121.3 1.0 CD2 G:HIS55 2.8 133.2 1.0 CD2 G:HIS51 2.9 148.3 1.0 CE1 G:HIS99 3.0 115.1 1.0 CE1 G:HIS101 3.1 141.7 1.0 CE1 G:HIS55 3.2 128.1 1.0 ND1 G:HIS51 3.2 149.4 1.0 CG G:HIS51 3.5 150.3 1.0 CG G:HIS99 3.6 117.0 1.0 CG G:HIS101 3.6 142.5 1.0 ND1 G:HIS99 3.8 111.4 1.0 ND1 G:HIS101 3.9 142.0 1.0 CG G:HIS55 4.0 131.2 1.0 ND1 G:HIS55 4.2 127.0 1.0 O G:HIS51 4.6 146.5 1.0 CB G:HIS101 4.8 141.0 1.0 CB G:HIS99 4.8 113.8 1.0 CB G:HIS51 4.8 150.1 1.0 OE1 G:GLU54 4.9 155.1 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate C)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate C) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn703 b:221.1 occ:1.00 CD2 H:HIS101 2.0 163.7 1.0 NE2 H:HIS51 2.0 178.4 1.0 NE2 H:HIS101 2.0 163.8 1.0 NE2 H:HIS55 2.0 165.7 1.0 NE2 H:HIS99 2.1 139.6 1.0 CD2 H:HIS51 2.7 178.3 1.0 CE1 H:HIS55 2.7 164.1 1.0 CD2 H:HIS55 2.9 165.3 1.0 CE1 H:HIS99 3.0 137.3 1.0 CD2 H:HIS99 3.1 136.3 1.0 CE1 H:HIS51 3.2 176.5 1.0 CG H:HIS101 3.3 162.5 1.0 CE1 H:HIS101 3.3 162.0 1.0 ND1 H:HIS55 3.6 164.5 1.0 CG H:HIS55 3.7 165.1 1.0 CG H:HIS51 3.9 178.1 1.0 ND1 H:HIS101 3.9 162.1 1.0 ND1 H:HIS51 4.1 177.7 1.0 ND1 H:HIS99 4.1 136.3 1.0 CG H:HIS99 4.2 134.8 1.0 CB H:HIS101 4.4 161.2 1.0 O H:HIS51 4.9 173.8 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