Zinc in PDB 5yec: Crystal Structure of ATG7CTD-ATG8-Mgatp Complex in Form II

The structure of Crystal Structure of ATG7CTD-ATG8-Mgatp Complex in Form II, PDB code: 5yec was solved by M.Yamaguchi, K.Satoo, N.N.Noda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.14 / 2.15
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	138.995, 138.995, 134.368, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 21.9

The structure of Crystal Structure of ATG7CTD-ATG8-Mgatp Complex in Form II also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of ATG7CTD-ATG8-Mgatp Complex in Form II (pdb code 5yec). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of ATG7CTD-ATG8-Mgatp Complex in Form II, PDB code: 5yec:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of ATG7CTD-ATG8-Mgatp Complex in Form II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of ATG7CTD-ATG8-Mgatp Complex in Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:46.5 occ:1.00 SG A:CYS572 2.3 49.1 1.0 SG A:CYS569 2.3 47.8 1.0 SG A:CYS488 2.3 54.0 1.0 SG A:CYS485 2.4 54.7 1.0 CB A:CYS569 3.0 41.7 1.0 CB A:CYS485 3.5 53.6 1.0 CB A:CYS572 3.5 50.2 1.0 N A:CYS488 3.6 53.7 1.0 CB A:CYS488 3.6 67.2 1.0 N A:CYS572 3.8 50.3 1.0 CA A:CYS488 3.8 61.7 1.0 N A:CYS485 3.8 59.5 1.0 CA A:CYS485 4.1 60.9 1.0 C A:PHE487 4.2 58.6 1.0 CA A:CYS572 4.2 52.7 1.0 C A:CYS485 4.4 63.1 1.0 CB A:ALA571 4.4 54.4 1.0 O A:CYS485 4.5 87.3 1.0 CA A:CYS569 4.5 42.4 1.0 N A:PHE487 4.6 48.4 1.0 CB A:PHE487 4.6 58.6 1.0 O A:HOH813 4.6 53.9 1.0 CA A:PHE487 4.7 52.0 1.0 C A:ALA571 4.8 52.0 1.0 O A:PHE487 4.9 63.9 1.0 C A:CYS572 4.9 52.2 1.0 N A:ALA571 4.9 52.1 1.0 C A:GLY484 5.0 51.0 1.0 CA A:ALA571 5.0 52.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of ATG7CTD-ATG8-Mgatp Complex in Form II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of ATG7CTD-ATG8-Mgatp Complex in Form II within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:52.8 occ:1.00 SG C:CYS572 2.3 55.3 1.0 SG C:CYS569 2.3 53.1 1.0 SG C:CYS485 2.4 51.9 1.0 SG C:CYS488 2.4 57.5 1.0 CB C:CYS569 3.1 52.7 1.0 CB C:CYS572 3.3 60.7 1.0 CB C:CYS485 3.4 50.5 1.0 N C:CYS488 3.7 53.6 1.0 CB C:CYS488 3.7 53.8 1.0 N C:CYS485 3.7 54.9 1.0 N C:CYS572 3.8 54.6 1.0 CA C:CYS488 3.9 60.0 1.0 CA C:CYS485 4.0 53.1 1.0 CA C:CYS572 4.1 56.4 1.0 C C:PHE487 4.3 52.7 1.0 C C:CYS485 4.4 54.3 1.0 O C:CYS485 4.4 50.4 1.0 CA C:CYS569 4.6 55.4 1.0 CB C:ALA571 4.6 48.3 1.0 N C:PHE487 4.6 45.6 1.0 CB C:PHE487 4.7 45.6 1.0 O C:HOH834 4.7 52.7 1.0 C C:CYS572 4.8 60.0 1.0 CA C:PHE487 4.8 48.3 1.0 C C:ALA571 4.8 53.6 1.0 C C:GLY484 4.9 52.9 1.0 N C:TYR566 4.9 62.8 1.0 O C:PHE487 5.0 57.5 1.0 N C:ALA571 5.0 50.6 1.0

M.Yamaguchi, K.Satoo, H.Suzuki, Y.Fujioka, Y.Ohsumi, F.Inagaki, N.N.Noda. ATG7 Activates An Autophagy-Essential Ubiquitin-Like Protein ATG8 Through Multi-Step Recognition. J. Mol. Biol. V. 430 249 2018.
ISSN: ESSN 1089-8638
PubMed: 29237558
DOI: 10.1016/J.JMB.2017.12.002