Zinc in PDB 8jp5: Cryo-Em Structures of the Head Region of Full-Length Ergic-53 with MCFD2 (Form B)

The structure of Cryo-Em Structures of the Head Region of Full-Length Ergic-53 with MCFD2 (Form B) 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 (Form B) (pdb code 8jp5). 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 (Form B), PDB code: 8jp5:
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 (Form B)


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 (Form B) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn703 b:132.8 occ:1.00 NE2 C:HIS99 2.0 88.6 1.0 NE2 C:HIS101 2.0 112.6 1.0 NE2 C:HIS51 2.0 127.9 1.0 NE2 C:HIS55 2.1 117.1 1.0 CD2 C:HIS55 2.3 117.6 1.0 CE1 C:HIS99 2.7 89.3 1.0 CD2 C:HIS51 2.7 126.7 1.0 CD2 C:HIS101 2.9 110.0 1.0 CD2 C:HIS99 3.0 85.0 1.0 CE1 C:HIS101 3.1 111.8 1.0 CE1 C:HIS55 3.2 113.6 1.0 CE1 C:HIS51 3.2 127.5 1.0 CG C:HIS55 3.4 117.3 1.0 ND1 C:HIS99 3.8 83.3 1.0 ND1 C:HIS55 3.8 114.3 1.0 CG C:HIS99 4.0 87.7 1.0 CG C:HIS51 4.0 126.4 1.0 CG C:HIS101 4.1 112.0 1.0 ND1 C:HIS101 4.1 112.3 1.0 ND1 C:HIS51 4.2 128.7 1.0 CB C:HIS55 4.6 118.4 1.0 CE C:MET79 4.8 89.0 1.0 CE1 C:HIS80 4.8 78.6 1.0 O C:HIS51 5.0 127.4 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 (Form B)


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 (Form B) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn703 b:129.2 occ:1.00 CE1 D:HIS51 1.5 104.1 1.0 NE2 D:HIS55 2.0 105.5 1.0 NE2 D:HIS51 2.1 103.3 1.0 NE2 D:HIS99 2.1 84.9 1.0 NE2 D:HIS101 2.1 101.6 1.0 CD2 D:HIS99 2.2 86.0 1.0 CE1 D:HIS55 2.3 103.1 1.0 ND1 D:HIS51 2.8 103.3 1.0 CD2 D:HIS101 3.0 96.0 1.0 CE1 D:HIS101 3.2 96.9 1.0 CE1 D:HIS99 3.2 82.9 1.0 CD2 D:HIS55 3.2 106.9 1.0 CG D:HIS99 3.3 82.1 1.0 CD2 D:HIS51 3.4 105.1 1.0 ND1 D:HIS55 3.4 102.6 1.0 CG D:HIS51 3.7 103.9 1.0 ND1 D:HIS99 3.7 80.0 1.0 CG D:HIS55 3.9 105.3 1.0 CG D:HIS101 4.2 96.4 1.0 ND1 D:HIS101 4.2 98.1 1.0 CB D:HIS99 4.4 78.0 1.0 OE2 D:GLU54 4.6 115.8 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 (Form B)


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 (Form B) within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn703 b:132.8 occ:1.00 NE2 G:HIS99 2.0 88.6 1.0 NE2 G:HIS101 2.0 112.6 1.0 NE2 G:HIS51 2.0 127.9 1.0 NE2 G:HIS55 2.1 117.1 1.0 CD2 G:HIS55 2.3 117.6 1.0 CE1 G:HIS99 2.7 89.3 1.0 CD2 G:HIS51 2.7 126.7 1.0 CD2 G:HIS101 2.9 110.0 1.0 CD2 G:HIS99 3.0 85.0 1.0 CE1 G:HIS101 3.1 111.8 1.0 CE1 G:HIS55 3.2 113.6 1.0 CE1 G:HIS51 3.2 127.5 1.0 CG G:HIS55 3.4 117.3 1.0 ND1 G:HIS99 3.8 83.3 1.0 ND1 G:HIS55 3.8 114.3 1.0 CG G:HIS99 4.0 87.7 1.0 CG G:HIS51 4.0 126.4 1.0 CG G:HIS101 4.1 112.0 1.0 ND1 G:HIS101 4.1 112.3 1.0 ND1 G:HIS51 4.2 128.7 1.0 CB G:HIS55 4.6 118.4 1.0 CE G:MET79 4.8 89.0 1.0 CE1 G:HIS80 4.8 78.6 1.0 O G:HIS51 5.0 127.4 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 (Form B)


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 (Form B) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn703 b:129.2 occ:1.00 CE1 H:HIS51 1.5 104.1 1.0 NE2 H:HIS55 2.0 105.5 1.0 NE2 H:HIS51 2.1 103.3 1.0 NE2 H:HIS99 2.1 84.9 1.0 NE2 H:HIS101 2.1 101.6 1.0 CD2 H:HIS99 2.2 86.0 1.0 CE1 H:HIS55 2.3 103.1 1.0 ND1 H:HIS51 2.8 103.3 1.0 CD2 H:HIS101 3.0 96.0 1.0 CE1 H:HIS101 3.2 96.9 1.0 CE1 H:HIS99 3.2 82.9 1.0 CD2 H:HIS55 3.2 106.9 1.0 CG H:HIS99 3.3 82.1 1.0 CD2 H:HIS51 3.4 105.1 1.0 ND1 H:HIS55 3.5 102.6 1.0 CG H:HIS51 3.7 103.9 1.0 ND1 H:HIS99 3.7 80.0 1.0 CG H:HIS55 3.9 105.3 1.0 CG H:HIS101 4.2 96.4 1.0 ND1 H:HIS101 4.2 98.1 1.0 CB H:HIS99 4.4 78.0 1.0 OE2 H:GLU54 4.6 115.8 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