Zinc in PDB 8jp7: Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate B)

The structure of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate B) 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 B) (pdb code 8jp7). 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 B), PDB code: 8jp7:
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 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 Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate B) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn703 b:165.0 occ:1.00 NE2 C:HIS99 2.0 112.6 1.0 NE2 C:HIS55 2.0 145.2 1.0 NE2 C:HIS51 2.0 151.6 1.0 NE2 C:HIS101 2.0 154.4 1.0 CD2 C:HIS55 2.4 145.5 1.0 CD2 C:HIS51 2.6 151.0 1.0 CE1 C:HIS99 2.6 113.2 1.0 CD2 C:HIS101 2.9 151.3 1.0 CE1 C:HIS55 3.0 142.0 1.0 CE1 C:HIS101 3.0 153.9 1.0 CD2 C:HIS99 3.1 111.2 1.0 CE1 C:HIS51 3.2 151.1 1.0 CG C:HIS55 3.5 144.4 1.0 ND1 C:HIS55 3.7 140.5 1.0 ND1 C:HIS99 3.8 109.9 1.0 CG C:HIS51 3.9 149.5 1.0 CG C:HIS99 4.0 112.1 1.0 CG C:HIS101 4.1 152.7 1.0 ND1 C:HIS101 4.1 154.2 1.0 ND1 C:HIS51 4.1 150.5 1.0 CB C:HIS55 4.7 145.5 1.0 OE2 C:GLU54 4.9 159.6 1.0 O C:HIS51 4.9 150.6 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 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 Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate B) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn703 b:202.9 occ:1.00 CE1 D:HIS51 1.9 158.5 1.0 NE2 D:HIS51 2.0 158.8 1.0 NE2 D:HIS55 2.1 160.5 1.0 NE2 D:HIS101 2.1 158.9 1.0 NE2 D:HIS99 2.1 135.9 1.0 CE1 D:HIS55 2.1 161.5 1.0 CD2 D:HIS99 2.3 133.7 1.0 CE1 D:HIS99 2.8 135.1 1.0 CD2 D:HIS101 3.1 157.5 1.0 CG D:HIS99 3.1 133.1 1.0 ND1 D:HIS51 3.2 158.2 1.0 CE1 D:HIS101 3.2 157.9 1.0 ND1 D:HIS99 3.3 132.3 1.0 CD2 D:HIS51 3.4 159.3 1.0 ND1 D:HIS55 3.4 159.6 1.0 CD2 D:HIS55 3.4 159.3 1.0 CG D:HIS51 3.9 159.0 1.0 CG D:HIS55 4.0 158.6 1.0 CB D:HIS99 4.2 132.5 1.0 ND1 D:HIS101 4.2 158.1 1.0 CG D:HIS101 4.2 157.3 1.0 OE2 D:GLU54 4.7 178.4 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 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 Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate B) within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn703 b:177.2 occ:1.00 NE2 G:HIS99 2.0 116.8 1.0 NE2 G:HIS55 2.0 160.9 1.0 NE2 G:HIS51 2.0 176.5 1.0 NE2 G:HIS101 2.0 160.2 1.0 CD2 G:HIS55 2.4 162.1 1.0 CE1 G:HIS99 2.6 118.1 1.0 CD2 G:HIS51 2.6 174.2 1.0 CE1 G:HIS101 2.9 161.5 1.0 CE1 G:HIS55 2.9 158.9 1.0 CD2 G:HIS101 3.0 158.4 1.0 CD2 G:HIS99 3.1 114.6 1.0 CE1 G:HIS51 3.2 176.2 1.0 CG G:HIS55 3.5 161.1 1.0 ND1 G:HIS55 3.7 157.2 1.0 ND1 G:HIS99 3.7 115.8 1.0 CG G:HIS51 3.9 174.0 1.0 CG G:HIS99 3.9 116.6 1.0 ND1 G:HIS101 4.0 162.1 1.0 CG G:HIS101 4.1 160.5 1.0 ND1 G:HIS51 4.1 176.0 1.0 CB G:HIS55 4.7 161.8 1.0 OE2 G:GLU54 4.9 183.1 1.0 O G:HIS51 5.0 172.6 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 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 Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Substate B) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn703 b:190.9 occ:1.00 CE1 H:HIS51 1.6 136.9 1.0 NE2 H:HIS51 2.1 136.5 1.0 NE2 H:HIS101 2.1 149.1 1.0 NE2 H:HIS55 2.1 134.1 1.0 NE2 H:HIS99 2.2 123.3 1.0 CE1 H:HIS55 2.3 132.5 1.0 CD2 H:HIS99 2.5 123.9 1.0 CE1 H:HIS99 2.8 125.9 1.0 ND1 H:HIS51 2.9 133.3 1.0 CD2 H:HIS101 2.9 146.2 1.0 CE1 H:HIS101 3.2 147.0 1.0 CG H:HIS99 3.2 122.4 1.0 CD2 H:HIS55 3.3 133.8 1.0 ND1 H:HIS99 3.3 125.6 1.0 ND1 H:HIS55 3.4 130.9 1.0 CD2 H:HIS51 3.4 135.7 1.0 CG H:HIS51 3.7 135.2 1.0 CG H:HIS55 3.9 132.6 1.0 CG H:HIS101 4.1 145.2 1.0 ND1 H:HIS101 4.2 146.2 1.0 CB H:HIS99 4.3 120.0 1.0 OE2 H:GLU54 4.8 157.5 1.0 CE H:MET79 5.0 118.1 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