Magnesium 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:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of ATG7CTD-ATG8-Mgatp Complex in Form II, PDB code: 5yec:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg703 b:99.6 occ:1.00 O1A A:ATP702 2.2 0.3 1.0 O1B A:ATP702 2.2 0.6 1.0 O1G A:ATP702 2.4 0.3 1.0 OD1 A:ASP438 2.7 71.3 1.0 CG A:ASP438 3.3 82.2 1.0 PB A:ATP702 3.4 0.0 1.0 PA A:ATP702 3.4 99.2 0.9 O3A A:ATP702 3.6 0.5 1.0 CB A:ASP438 3.6 81.4 1.0 PG A:ATP702 3.7 0.1 1.0 O3B A:ATP702 4.0 0.2 1.0 OD2 A:ASP438 4.2 80.3 1.0 O5' A:ATP702 4.4 90.4 0.9 O2G A:ATP702 4.4 0.5 1.0 C5' A:ATP702 4.5 69.0 0.9 O2A A:ATP702 4.6 98.5 0.9 O2B A:ATP702 4.7 0.5 1.0 O3G A:ATP702 4.9 0.1 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg703 b:52.6 occ:1.00 O1B C:ATP702 2.0 46.7 0.9 O2A C:ATP702 2.1 42.1 0.9 O1G C:ATP702 2.3 51.6 0.9 OD2 C:ASP438 2.4 53.2 1.0 PB C:ATP702 3.2 45.7 0.9 CG C:ASP438 3.3 57.4 1.0 PA C:ATP702 3.4 38.5 0.9 PG C:ATP702 3.5 53.7 0.9 CB C:ASP438 3.6 55.6 1.0 O3A C:ATP702 3.7 43.6 0.9 O3B C:ATP702 3.7 55.7 0.9 O3G C:ATP702 4.0 64.9 0.9 C5' C:ATP702 4.3 36.3 0.9 O5' C:ATP702 4.3 35.6 0.9 O C:HOH840 4.3 52.1 1.0 OD1 C:ASP438 4.5 53.1 1.0 O1A C:ATP702 4.5 44.8 0.9 O C:MET506 4.5 87.1 1.0 O2B C:ATP702 4.6 50.0 0.9 O2G C:ATP702 4.8 64.8 0.9 CG C:MET506 4.9 0.5 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