Zinc in PDB 8jp6: Cryo-Em Structures of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate A)

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

Calcium

(Ca)

16 atoms

The binding sites of Zinc atom in the Cryo-Em Structures of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate A) (pdb code 8jp6). 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 Structures of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate A), PDB code: 8jp6:
Jump to Zinc binding site number: 1; 2; 3; 4;

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structures of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn703 b:139.6 occ:1.00 NE2 C:HIS51 2.0 131.0 1.0 NE2 C:HIS55 2.0 121.6 1.0 NE2 C:HIS101 2.0 124.4 1.0 NE2 C:HIS99 2.0 108.1 1.0 CD2 C:HIS99 2.3 108.9 1.0 CE1 C:HIS55 2.6 121.0 1.0 CE1 C:HIS51 2.8 130.5 1.0 CE1 C:HIS99 2.8 107.7 1.0 CD2 C:HIS101 2.8 122.7 1.0 CD2 C:HIS51 2.8 131.2 1.0 CG C:HIS99 3.1 108.1 1.0 CE1 C:HIS101 3.1 123.9 1.0 CD2 C:HIS55 3.2 123.9 1.0 ND1 C:HIS99 3.3 108.2 1.0 ND1 C:HIS51 3.7 133.6 1.0 CG C:HIS51 3.8 132.7 1.0 ND1 C:HIS55 3.8 120.4 1.0 CG C:HIS101 4.0 123.6 1.0 CG C:HIS55 4.1 122.2 1.0 ND1 C:HIS101 4.1 123.5 1.0 CB C:HIS99 4.3 106.8 1.0 CE1 C:HIS80 4.7 86.5 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structures of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate A) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn703 b:144.7 occ:1.00 CE1 D:HIS51 1.9 136.0 1.0 NE2 D:HIS99 2.0 108.4 1.0 NE2 D:HIS101 2.0 127.5 1.0 NE2 D:HIS55 2.0 123.9 1.0 NE2 D:HIS51 2.0 134.9 1.0 CD2 D:HIS101 2.5 128.1 1.0 CE1 D:HIS99 2.8 104.9 1.0 CD2 D:HIS55 2.9 125.3 1.0 ND1 D:HIS51 2.9 139.9 1.0 CE1 D:HIS101 3.0 127.8 1.0 CE1 D:HIS55 3.1 121.3 1.0 CD2 D:HIS51 3.1 133.7 1.0 CD2 D:HIS99 3.2 100.4 1.0 CG D:HIS51 3.6 136.2 1.0 CG D:HIS101 3.6 127.5 1.0 ND1 D:HIS101 3.8 128.6 1.0 ND1 D:HIS99 4.0 102.0 1.0 CG D:HIS55 4.1 121.9 1.0 ND1 D:HIS55 4.1 117.6 1.0 CG D:HIS99 4.2 96.8 1.0 O D:HIS51 4.7 134.4 1.0 CB D:HIS101 4.8 126.4 1.0 CB D:HIS51 5.0 134.7 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structures of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate A) within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn703 b:137.0 occ:1.00 NE2 G:HIS51 2.0 133.8 1.0 NE2 G:HIS55 2.0 124.1 1.0 NE2 G:HIS101 2.0 126.2 1.0 NE2 G:HIS99 2.0 107.7 1.0 CD2 G:HIS99 2.3 108.4 1.0 CE1 G:HIS55 2.6 123.7 1.0 CE1 G:HIS51 2.8 133.4 1.0 CE1 G:HIS99 2.8 106.9 1.0 CD2 G:HIS101 2.8 124.6 1.0 CD2 G:HIS51 2.8 134.0 1.0 CG G:HIS99 3.1 107.6 1.0 CE1 G:HIS101 3.1 125.9 1.0 CD2 G:HIS55 3.2 126.2 1.0 ND1 G:HIS99 3.3 107.3 1.0 ND1 G:HIS51 3.7 136.1 1.0 CG G:HIS51 3.8 135.2 1.0 ND1 G:HIS55 3.8 123.2 1.0 CG G:HIS101 4.0 125.5 1.0 CG G:HIS55 4.1 124.7 1.0 ND1 G:HIS101 4.1 125.6 1.0 CB G:HIS99 4.3 106.6 1.0 CE1 G:HIS80 4.7 82.6 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structures of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate A) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn703 b:143.8 occ:1.00 CE1 H:HIS51 1.9 136.1 1.0 NE2 H:HIS101 2.0 127.3 1.0 NE2 H:HIS55 2.0 122.7 1.0 NE2 H:HIS99 2.0 106.8 1.0 NE2 H:HIS51 2.0 134.4 1.0 CD2 H:HIS101 2.5 127.3 1.0 CD2 H:HIS55 2.9 124.1 1.0 CE1 H:HIS99 2.9 103.2 1.0 CE1 H:HIS101 2.9 127.6 1.0 ND1 H:HIS51 3.0 139.3 1.0 CE1 H:HIS55 3.1 119.4 1.0 CD2 H:HIS99 3.1 99.8 1.0 CD2 H:HIS51 3.2 133.6 1.0 CG H:HIS101 3.6 127.0 1.0 CG H:HIS51 3.6 135.5 1.0 ND1 H:HIS101 3.7 128.4 1.0 CG H:HIS55 4.1 120.4 1.0 ND1 H:HIS99 4.1 100.7 1.0 ND1 H:HIS55 4.2 115.7 1.0 CG H:HIS99 4.2 96.1 1.0 O H:HIS51 4.8 133.5 1.0 CB H:HIS101 4.8 125.8 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