Zinc in PDB 4gsl: Crystal Structure of An ATG7-ATG3 Crosslinked Complex

The structure of Crystal Structure of An ATG7-ATG3 Crosslinked Complex, PDB code: 4gsl was solved by S.E.Kaiser, K.Mao, A.M.Taherbhoy, S.Yu, J.L.Olszewski, D.M.Duda, I.Kurinov, A.Deng, T.D.Fenn, D.J.Klionsky, B.A.Schulman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.07 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	281.556, 125.083, 71.079, 90.00, 103.32, 90.00
R / Rfree (%)	19.3 / 24.6

The binding sites of Zinc atom in the Crystal Structure of An ATG7-ATG3 Crosslinked Complex (pdb code 4gsl). 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 An ATG7-ATG3 Crosslinked Complex, PDB code: 4gsl:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of An ATG7-ATG3 Crosslinked 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 An ATG7-ATG3 Crosslinked Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn700 b:74.1 occ:1.00 SG A:CYS569 2.4 67.7 1.0 SG A:CYS485 2.4 74.6 1.0 CB A:CYS572 2.5 77.1 1.0 SG A:CYS488 2.5 80.9 1.0 SG A:CYS572 3.1 97.5 1.0 CB A:CYS569 3.3 69.4 1.0 CB A:CYS485 3.6 67.5 1.0 N A:CYS488 3.6 70.2 1.0 N A:CYS485 3.6 72.0 1.0 CA A:CYS572 3.7 86.3 1.0 CB A:CYS488 3.7 70.1 1.0 N A:CYS572 3.7 84.9 1.0 CA A:CYS488 3.8 73.5 1.0 CA A:CYS485 4.1 71.5 1.0 C A:PHE487 4.3 74.8 1.0 C A:CYS485 4.5 73.0 1.0 C A:ALA571 4.5 76.6 1.0 O A:CYS485 4.6 67.4 1.0 CA A:CYS569 4.7 68.6 1.0 N A:PHE487 4.7 74.7 1.0 C A:GLY484 4.7 84.0 1.0 CB A:PHE487 4.8 62.3 1.0 C A:CYS572 4.8 76.8 1.0 CA A:PHE487 4.8 71.1 1.0 CA A:GLY484 4.8 92.6 1.0 CB A:ALA571 4.8 76.2 1.0 N A:ALA571 4.8 71.0 1.0 CA A:ALA571 5.0 71.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of An ATG7-ATG3 Crosslinked Complex


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 An ATG7-ATG3 Crosslinked Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn700 b:86.3 occ:1.00 SG B:CYS488 2.4 79.6 1.0 SG B:CYS569 2.5 78.2 1.0 SG B:CYS485 2.5 74.6 1.0 SG B:CYS572 2.5 80.6 1.0 CB B:CYS569 3.3 73.5 1.0 N B:CYS488 3.5 78.4 1.0 CB B:CYS485 3.6 53.5 1.0 CB B:CYS488 3.6 62.9 1.0 CA B:CYS488 3.6 75.8 1.0 N B:CYS485 3.7 67.1 1.0 CB B:CYS572 3.7 98.0 1.0 N B:CYS572 4.0 0.9 1.0 CA B:CYS485 4.1 60.0 1.0 C B:PHE487 4.2 73.2 1.0 CA B:CYS572 4.3 0.1 1.0 O B:CYS485 4.4 67.3 1.0 C B:CYS485 4.5 67.1 1.0 N B:PHE487 4.7 72.2 1.0 CA B:CYS569 4.7 78.4 1.0 C B:ALA571 4.7 92.4 1.0 CA B:PHE487 4.8 74.9 1.0 CB B:PHE487 4.8 77.2 1.0 N B:TYR566 4.8 66.7 1.0 C B:CYS572 4.8 91.3 1.0 CB B:ALA571 4.8 79.0 1.0 C B:GLY484 4.9 70.9 1.0 O B:PHE487 4.9 78.2 1.0 N B:SER573 4.9 86.6 1.0 N B:ALA571 4.9 92.7 1.0

S.E.Kaiser, K.Mao, A.M.Taherbhoy, S.Yu, J.L.Olszewski, D.M.Duda, I.Kurinov, A.Deng, T.D.Fenn, D.J.Klionsky, B.A.Schulman. Noncanonical E2 Recruitment By the Autophagy E1 Revealed By ATG7-ATG3 and ATG7-ATG10 Structures. Nat.Struct.Mol.Biol. V. 19 1242 2012.
ISSN: ISSN 1545-9993
PubMed: 23142976
DOI: 10.1038/NSMB.2415