Zinc in PDB 8jp9: Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate D)

The structure of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate D) 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 D) (pdb code 8jp9). 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 D), PDB code: 8jp9:
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 D)


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 D) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn703 b:166.6 occ:1.00 NE2 C:HIS99 2.0 123.9 1.0 NE2 C:HIS55 2.0 141.1 1.0 NE2 C:HIS51 2.0 156.9 1.0 NE2 C:HIS101 2.0 159.0 1.0 CD2 C:HIS101 2.5 158.2 1.0 CD2 C:HIS99 2.5 124.3 1.0 CD2 C:HIS51 2.7 156.9 1.0 CD2 C:HIS55 2.8 142.9 1.0 CE1 C:HIS51 2.9 156.2 1.0 CE1 C:HIS99 3.1 117.3 1.0 CE1 C:HIS101 3.1 158.4 1.0 CE1 C:HIS55 3.1 137.6 1.0 CG C:HIS101 3.6 158.4 1.0 CG C:HIS51 3.7 158.8 1.0 CG C:HIS99 3.7 119.5 1.0 ND1 C:HIS51 3.7 158.6 1.0 ND1 C:HIS101 3.9 158.4 1.0 ND1 C:HIS99 3.9 115.5 1.0 CG C:HIS55 4.0 140.4 1.0 ND1 C:HIS55 4.1 136.3 1.0 O C:HIS51 4.7 159.4 1.0 CB C:HIS101 4.9 156.2 1.0 OE1 C:GLU54 4.9 162.7 1.0 CB C:HIS99 5.0 113.2 1.0 CB C:HIS51 5.0 158.9 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 D)


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 D) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn703 b:185.6 occ:1.00 NE2 D:HIS51 2.0 174.0 1.0 NE2 D:HIS101 2.0 145.2 1.0 NE2 D:HIS55 2.0 146.0 1.0 NE2 D:HIS99 2.0 123.8 1.0 CD2 D:HIS101 2.5 145.0 1.0 CD2 D:HIS51 2.7 172.3 1.0 CE1 D:HIS55 2.8 146.2 1.0 CD2 D:HIS55 2.9 145.2 1.0 CD2 D:HIS99 3.0 118.2 1.0 CE1 D:HIS99 3.1 119.8 1.0 CE1 D:HIS51 3.1 172.8 1.0 CE1 D:HIS101 3.2 145.7 1.0 CG D:HIS101 3.8 146.8 1.0 ND1 D:HIS55 3.8 145.3 1.0 CG D:HIS55 3.8 146.0 1.0 CG D:HIS51 3.9 172.5 1.0 ND1 D:HIS101 4.1 147.8 1.0 ND1 D:HIS51 4.1 174.4 1.0 CG D:HIS99 4.1 113.6 1.0 ND1 D:HIS99 4.1 116.3 1.0 O D:HIS51 4.9 167.6 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 D)


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 D) within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn703 b:179.1 occ:1.00 NE2 G:HIS99 2.0 131.2 1.0 NE2 G:HIS51 2.0 161.6 1.0 NE2 G:HIS55 2.0 144.4 1.0 NE2 G:HIS101 2.0 170.3 1.0 CD2 G:HIS101 2.5 168.9 1.0 CD2 G:HIS99 2.6 129.8 1.0 CD2 G:HIS51 2.7 161.9 1.0 CD2 G:HIS55 2.8 145.4 1.0 CE1 G:HIS51 2.9 160.8 1.0 CE1 G:HIS99 3.1 127.0 1.0 CE1 G:HIS101 3.1 170.3 1.0 CE1 G:HIS55 3.1 142.6 1.0 CG G:HIS101 3.7 169.3 1.0 CG G:HIS51 3.7 161.8 1.0 CG G:HIS99 3.7 126.9 1.0 ND1 G:HIS51 3.7 162.3 1.0 ND1 G:HIS101 3.9 170.0 1.0 ND1 G:HIS99 3.9 125.2 1.0 CG G:HIS55 4.0 143.7 1.0 ND1 G:HIS55 4.2 142.1 1.0 O G:HIS51 4.7 161.0 1.0 OE1 G:GLU54 4.9 170.3 1.0 CB G:HIS101 4.9 168.8 1.0 CB G:HIS51 5.0 160.3 1.0 CB G:HIS99 5.0 123.8 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 D)


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 D) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn703 b:183.2 occ:1.00 NE2 H:HIS101 2.0 144.9 1.0 NE2 H:HIS51 2.0 160.8 1.0 NE2 H:HIS55 2.0 148.5 1.0 NE2 H:HIS99 2.0 112.5 1.0 CD2 H:HIS101 2.5 144.8 1.0 CD2 H:HIS51 2.7 159.9 1.0 CE1 H:HIS55 2.8 146.2 1.0 CD2 H:HIS55 2.9 148.2 1.0 CD2 H:HIS99 3.0 105.3 1.0 CE1 H:HIS99 3.1 108.6 1.0 CE1 H:HIS51 3.1 158.2 1.0 CE1 H:HIS101 3.2 145.1 1.0 CG H:HIS101 3.8 146.4 1.0 ND1 H:HIS55 3.8 145.6 1.0 CG H:HIS55 3.8 147.4 1.0 CG H:HIS51 3.9 160.7 1.0 ND1 H:HIS101 4.1 146.7 1.0 ND1 H:HIS51 4.1 160.1 1.0 CG H:HIS99 4.1 101.7 1.0 ND1 H:HIS99 4.1 106.4 1.0 O H:HIS51 4.9 153.1 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