Zinc in PDB 3vh2: Crystal Structure of Saccharomyces Cerevisiae ATG7 (1-613)

The structure of Crystal Structure of Saccharomyces Cerevisiae ATG7 (1-613), PDB code: 3vh2 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)	44.04 / 3.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.028, 88.028, 264.249, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 26

The binding sites of Zinc atom in the Crystal Structure of Saccharomyces Cerevisiae ATG7 (1-613) (pdb code 3vh2). 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 Saccharomyces Cerevisiae ATG7 (1-613), PDB code: 3vh2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Saccharomyces Cerevisiae ATG7 (1-613)


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 Saccharomyces Cerevisiae ATG7 (1-613) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:80.9 occ:1.00 SG A:CYS488 2.2 0.8 1.0 SG A:CYS572 2.2 96.4 1.0 SG A:CYS569 2.4 0.3 1.0 SG A:CYS485 2.6 87.2 1.0 CB A:CYS569 3.0 0.4 1.0 CA A:CYS488 3.3 0.6 1.0 CB A:CYS488 3.3 0.3 1.0 N A:CYS488 3.3 0.5 1.0 CB A:CYS572 3.6 98.7 1.0 N A:CYS485 3.8 91.8 1.0 CB A:CYS485 3.8 91.0 1.0 C A:PHE487 3.9 0.2 1.0 N A:CYS572 4.0 0.1 1.0 CA A:CYS485 4.2 92.1 1.0 O A:PHE487 4.3 0.9 1.0 CA A:CYS572 4.3 0.9 1.0 CA A:CYS569 4.5 0.4 1.0 O A:CYS485 4.6 92.8 1.0 C A:CYS485 4.6 93.5 1.0 CA A:PHE487 4.7 0.8 1.0 C A:CYS488 4.7 0.6 1.0 N A:TYR566 4.8 0.4 1.0 N A:PHE487 4.8 0.5 1.0 CB A:PHE487 4.8 99.9 1.0 C A:GLY484 4.9 91.8 1.0 C A:CYS572 4.9 1.0 1.0 CB A:ALA571 4.9 0.3 1.0 O A:TYR566 4.9 0.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Saccharomyces Cerevisiae ATG7 (1-613)


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 Saccharomyces Cerevisiae ATG7 (1-613) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:95.7 occ:1.00 OD1 A:ASP193 2.3 77.9 1.0 SG A:CYS195 2.4 77.4 1.0 CG A:ASP193 3.2 77.0 1.0 OD2 A:ASP193 3.5 79.1 1.0 CG A:LYS194 3.9 79.2 1.0 CB A:CYS195 3.9 76.6 1.0 N A:CYS195 3.9 74.5 1.0 N A:LYS194 4.5 74.1 1.0 CA A:CYS195 4.6 75.0 1.0 CB A:ASP193 4.6 74.5 1.0 CD A:LYS194 4.8 79.8 1.0 C A:ASP193 4.8 73.3 1.0 C A:LYS194 5.0 75.1 1.0 CA A:ASP193 5.0 72.8 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