Sodium in PDB 4gdk: 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: 4gdk 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)	44.06 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.757, 113.153, 210.685, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 23.6

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 4gdk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human ATG12~ATG5 Conjugate in Complex with An N- Terminal Fragment of ATG16L1, PDB code: 4gdk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 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:52.2 occ:1.00 OD1 B:ASN99 2.4 53.4 1.0 O B:HOH438 2.4 52.4 1.0 O B:PRO97 2.4 43.1 1.0 O B:HOH424 2.5 47.6 1.0 O B:HOH437 2.5 59.6 1.0 O B:ALA95 2.5 48.7 1.0 CG B:ASN99 3.4 46.0 1.0 C B:ALA95 3.5 44.6 1.0 C B:PRO97 3.6 41.9 1.0 O B:HOH439 3.9 43.2 1.0 N B:ASN99 4.0 40.7 1.0 C B:LEU96 4.0 49.6 1.0 O B:LEU96 4.1 51.8 1.0 N B:PRO97 4.1 50.4 1.0 CB B:ASN99 4.2 37.1 1.0 CA B:ALA95 4.4 42.0 1.0 ND2 B:ASN99 4.4 42.1 1.0 N B:LEU96 4.4 44.7 1.0 CB B:ALA95 4.4 40.0 1.0 CA B:LEU96 4.4 44.4 1.0 CA B:PRO97 4.5 47.4 1.0 N B:TRP98 4.5 41.0 1.0 N B:ALA95 4.6 49.5 1.0 CA B:TRP98 4.6 36.4 1.0 C B:TRP98 4.6 39.8 1.0 CA B:ASN99 4.7 38.1 1.0 CD B:PRO97 4.7 44.9 1.0

Sodium binding site 2 out of 2 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 2 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 E:Na301 b:65.6 occ:1.00 O E:ALA95 2.4 54.6 1.0 OD1 E:ASN99 2.4 51.0 1.0 O E:HOH413 2.4 48.2 1.0 O E:HOH407 2.5 64.4 1.0 O E:PRO97 2.5 48.8 1.0 C E:ALA95 3.5 49.6 1.0 CG E:ASN99 3.6 47.9 1.0 C E:PRO97 3.7 48.5 1.0 O E:HOH410 3.7 46.8 1.0 C E:LEU96 4.1 52.6 1.0 N E:ASN99 4.2 45.2 1.0 O E:LEU96 4.2 57.6 1.0 N E:PRO97 4.2 52.7 1.0 O C:HOH107 4.2 58.6 1.0 N E:LEU96 4.4 50.2 1.0 CB E:ASN99 4.4 42.7 1.0 CA E:LEU96 4.4 50.3 1.0 CA E:ALA95 4.4 46.1 1.0 N E:ALA95 4.5 49.9 1.0 ND2 E:ASN99 4.6 49.2 1.0 CA E:PRO97 4.6 53.2 1.0 N E:TRP98 4.6 41.3 1.0 CB E:ALA95 4.6 46.1 1.0 CA E:TRP98 4.7 40.0 1.0 C E:TRP98 4.7 42.4 1.0 CA E:ASN99 4.9 43.6 1.0 CD E:PRO97 4.9 52.2 1.0 CB E:SER94 4.9 61.4 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