Zinc in PDB 3vh4: Crystal Structure of ATG7CTD-ATG8-Mgatp Complex

The structure of Crystal Structure of ATG7CTD-ATG8-Mgatp Complex, PDB code: 3vh4 was solved by N.N.Noda, K.Satoo, F.Inagaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.04 / 2.65
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.282, 69.282, 219.605, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 26.7

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

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of ATG7CTD-ATG8-Mgatp Complex (pdb code 3vh4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of ATG7CTD-ATG8-Mgatp Complex, PDB code: 3vh4:

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:75.9 occ:1.00 SG A:CYS569 2.1 72.4 1.0 SG A:CYS572 2.1 61.6 1.0 SG A:CYS488 2.3 70.0 1.0 SG A:CYS485 2.5 70.3 1.0 CB A:CYS569 2.9 75.8 1.0 CB A:CYS572 3.4 63.0 1.0 N A:CYS488 3.5 66.7 1.0 CB A:CYS485 3.5 68.6 1.0 CB A:CYS488 3.6 68.6 1.0 N A:CYS572 3.6 64.3 1.0 CA A:CYS488 3.8 70.0 1.0 N A:CYS485 3.9 69.0 1.0 C A:PHE487 4.0 65.8 1.0 CA A:CYS572 4.1 65.3 1.0 CA A:CYS485 4.1 68.5 1.0 O A:CYS485 4.3 67.7 1.0 CB A:PHE487 4.3 64.9 1.0 CA A:CYS569 4.4 74.3 1.0 C A:CYS485 4.4 67.5 1.0 CA A:PHE487 4.5 65.3 1.0 N A:PHE487 4.5 64.2 1.0 CB A:ALA571 4.5 66.1 1.0 C A:ALA571 4.7 65.2 1.0 O A:PHE487 4.7 64.7 1.0 C A:CYS572 4.8 67.2 1.0 O A:TYR566 4.9 84.0 1.0 C A:GLY484 4.9 69.5 1.0 N A:ALA571 5.0 65.4 1.0 CA A:ALA571 5.0 65.0 1.0 N A:SER573 5.0 69.2 1.0 C A:CYS569 5.0 71.2 1.0

N.N.Noda, K.Satoo, Y.Fujioka, H.Kumeta, K.Ogura, H.Nakatogawa, Y.Ohsumi, F.Inagaki. Structural Basis of ATG8 Activation By A Homodimeric E1, ATG7. Mol.Cell V. 44 462 2011.
ISSN: ISSN 1097-2765
PubMed: 22055191
DOI: 10.1016/J.MOLCEL.2011.08.035