Sodium in PDB 4gdl: Crystal Structure of Human ATG12~ATG5 Conjugate in Complex with An N- Terminal Fragment of ATG16L1

The structure of Crystal Structure of Human ATG12~ATG5 Conjugate in Complex with An N- Terminal Fragment of ATG16L1, PDB code: 4gdl was solved by C.Otomo, Z.Metlagel, G.Takaesu, T.Otomo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.22 / 2.88
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.601, 58.399, 91.802, 90.00, 130.04, 90.00
R / Rfree (%)	21.5 / 25.4

The binding sites of Sodium atom in the Crystal Structure of Human ATG12~ATG5 Conjugate in Complex with An N- Terminal Fragment of ATG16L1 (pdb code 4gdl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Human ATG12~ATG5 Conjugate in Complex with An N- Terminal Fragment of ATG16L1, PDB code: 4gdl:

Sodium binding site 1 out of 1 in the Crystal Structure of Human ATG12~ATG5 Conjugate in Complex with An N- Terminal Fragment of ATG16L1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human ATG12~ATG5 Conjugate in Complex with An N- Terminal Fragment of ATG16L1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:0.6 occ:1.00 O B:ALA95 2.2 97.5 1.0 OD1 B:ASN99 2.4 0.9 1.0 O B:PRO97 2.7 82.2 1.0 CG B:ASN99 3.3 92.8 1.0 C B:ALA95 3.5 87.2 1.0 C B:PRO97 3.9 86.4 1.0 N B:ASN99 3.9 81.0 1.0 CB B:ASN99 3.9 92.7 1.0 ND2 B:ASN99 4.2 88.4 1.0 C B:LEU96 4.3 82.6 1.0 CA B:ALA95 4.4 84.4 1.0 N B:LEU96 4.4 86.0 1.0 CA B:LEU96 4.5 81.2 1.0 N B:ALA95 4.5 86.6 1.0 CA B:ASN99 4.5 87.4 1.0 N B:PRO97 4.5 80.8 1.0 CA B:TRP98 4.5 79.6 1.0 C B:TRP98 4.6 81.3 1.0 O B:LEU96 4.6 86.5 1.0 CB B:ALA95 4.6 74.4 1.0 N B:TRP98 4.6 92.6 1.0 CA B:PRO97 4.8 87.5 1.0 C B:SER94 5.0 89.0 1.0 CB B:SER94 5.0 86.5 1.0

C.Otomo, Z.Metlagel, G.Takaesu, T.Otomo. Structure of the Human ATG12~ATG5 Conjugate Required For LC3 Lipidation in Autophagy. Nat.Struct.Mol.Biol. V. 20 59 2013.
ISSN: ISSN 1545-9993
PubMed: 23202584
DOI: 10.1038/NSMB.2431