Zinc in PDB 8jp4: Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A)

The structure of Cryo-Em Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) 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 (Form A) (pdb code 8jp4). 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 (Form A), PDB code: 8jp4:
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 (Form 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 Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn703 b:132.3 occ:1.00 NE2 C:HIS51 2.0 114.4 1.0 NE2 C:HIS99 2.0 89.4 1.0 NE2 C:HIS55 2.0 100.5 1.0 NE2 C:HIS101 2.0 117.4 1.0 CD2 C:HIS99 2.4 89.5 1.0 CE1 C:HIS51 2.8 112.5 1.0 CD2 C:HIS51 2.9 115.3 1.0 CE1 C:HIS55 2.9 100.5 1.0 CE1 C:HIS101 3.0 115.6 1.0 CD2 C:HIS101 3.0 116.5 1.0 CD2 C:HIS55 3.1 100.8 1.0 CE1 C:HIS99 3.2 83.2 1.0 CG C:HIS99 3.6 86.5 1.0 ND1 C:HIS51 3.7 115.7 1.0 CG C:HIS51 3.8 115.8 1.0 ND1 C:HIS99 3.9 80.2 1.0 ND1 C:HIS55 4.1 99.0 1.0 ND1 C:HIS101 4.1 116.7 1.0 CG C:HIS101 4.1 117.9 1.0 CG C:HIS55 4.2 101.2 1.0 CB C:HIS99 4.8 85.6 1.0 CE1 C:HIS80 4.9 73.0 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 (Form 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 Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn703 b:113.7 occ:1.00 NE2 D:HIS51 2.0 111.9 1.0 NE2 D:HIS55 2.0 95.2 1.0 NE2 D:HIS101 2.0 99.9 1.0 NE2 D:HIS99 2.1 84.3 1.0 CD2 D:HIS101 2.5 99.6 1.0 CE1 D:HIS51 2.9 109.7 1.0 CD2 D:HIS55 2.9 95.8 1.0 CE1 D:HIS55 2.9 96.9 1.0 CD2 D:HIS51 2.9 112.7 1.0 CD2 D:HIS99 3.0 74.6 1.0 CE1 D:HIS99 3.1 78.7 1.0 CE1 D:HIS101 3.1 100.1 1.0 CG D:HIS101 3.7 100.0 1.0 ND1 D:HIS55 3.9 96.8 1.0 ND1 D:HIS51 3.9 114.3 1.0 ND1 D:HIS101 4.0 102.2 1.0 CG D:HIS55 4.0 98.1 1.0 CG D:HIS51 4.0 113.0 1.0 ND1 D:HIS99 4.2 78.9 1.0 CG D:HIS99 4.2 72.2 1.0 O D:HIS51 4.9 106.1 1.0 CB D:HIS101 5.0 98.6 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 (Form 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 Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn703 b:132.3 occ:1.00 NE2 G:HIS51 2.0 114.4 1.0 NE2 G:HIS99 2.0 89.4 1.0 NE2 G:HIS55 2.0 100.5 1.0 NE2 G:HIS101 2.0 117.4 1.0 CD2 G:HIS99 2.4 89.5 1.0 CE1 G:HIS51 2.8 112.5 1.0 CD2 G:HIS51 2.9 115.3 1.0 CE1 G:HIS55 2.9 100.5 1.0 CE1 G:HIS101 3.0 115.6 1.0 CD2 G:HIS101 3.0 116.5 1.0 CD2 G:HIS55 3.1 100.8 1.0 CE1 G:HIS99 3.2 83.2 1.0 CG G:HIS99 3.6 86.5 1.0 ND1 G:HIS51 3.7 115.7 1.0 CG G:HIS51 3.8 115.8 1.0 ND1 G:HIS99 3.9 80.2 1.0 ND1 G:HIS55 4.1 99.0 1.0 ND1 G:HIS101 4.1 116.7 1.0 CG G:HIS101 4.1 117.9 1.0 CG G:HIS55 4.2 101.2 1.0 CB G:HIS99 4.8 85.6 1.0 CE1 G:HIS80 4.9 73.0 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 (Form 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 Structure of the Head Region of Full-Length Ergic-53 with MCFD2 (Form A) within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn703 b:113.7 occ:1.00 NE2 H:HIS51 2.0 111.9 1.0 NE2 H:HIS55 2.0 95.2 1.0 NE2 H:HIS101 2.0 99.9 1.0 NE2 H:HIS99 2.1 84.3 1.0 CD2 H:HIS101 2.5 99.6 1.0 CE1 H:HIS51 2.9 109.7 1.0 CD2 H:HIS55 2.9 95.8 1.0 CE1 H:HIS55 2.9 96.9 1.0 CD2 H:HIS51 2.9 112.7 1.0 CD2 H:HIS99 3.0 74.6 1.0 CE1 H:HIS99 3.1 78.7 1.0 CE1 H:HIS101 3.1 100.1 1.0 CG H:HIS101 3.7 100.0 1.0 ND1 H:HIS55 3.9 96.8 1.0 ND1 H:HIS51 3.9 114.3 1.0 ND1 H:HIS101 4.0 102.2 1.0 CG H:HIS55 4.0 98.1 1.0 CG H:HIS51 4.0 113.0 1.0 ND1 H:HIS99 4.2 78.9 1.0 CG H:HIS99 4.2 72.2 1.0 O H:HIS51 4.9 106.1 1.0 CB H:HIS101 5.0 98.6 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