Sodium in PDB 4naw: Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3

The structure of Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3, PDB code: 4naw was solved by Z.Metlagel, C.Otomo, G.Takaesu, T.Otomo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.83 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.584, 120.097, 189.466, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21.5

The binding sites of Sodium atom in the Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3 (pdb code 4naw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3, PDB code: 4naw:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3


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-ATG16N in Complex with A Fragment of ATG3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:41.6 occ:1.00 O B:PRO97 2.3 34.5 1.0 O B:HOH405 2.3 35.8 1.0 O B:HOH413 2.4 47.1 1.0 OD1 B:ASN99 2.4 43.5 1.0 O B:ALA95 2.4 38.4 1.0 O J:HOH410 2.6 51.9 1.0 CG B:ASN99 3.4 37.2 1.0 H B:ASN99 3.5 33.9 1.0 C B:PRO97 3.5 35.3 1.0 C B:ALA95 3.5 45.0 1.0 O B:HOH440 3.8 39.3 1.0 HA B:LEU96 3.8 42.5 1.0 C B:LEU96 3.9 32.2 1.0 HA B:TRP98 3.9 36.4 1.0 N B:ASN99 4.0 28.2 1.0 O B:LEU96 4.0 37.3 1.0 HB2 B:ASN99 4.0 39.1 1.0 O B:HOH431 4.0 43.7 1.0 N B:PRO97 4.1 35.9 1.0 HB3 B:ALA95 4.1 60.9 1.0 CA B:LEU96 4.2 35.4 1.0 CB B:ASN99 4.2 32.6 1.0 HD2 B:PRO97 4.2 52.8 1.0 HD21 B:ASN99 4.3 41.1 1.0 ND2 B:ASN99 4.3 34.3 1.0 N B:LEU96 4.3 34.7 1.0 N B:TRP98 4.4 29.1 1.0 HB3 B:SER94 4.4 49.0 1.0 CA B:TRP98 4.4 30.4 1.0 CA B:PRO97 4.4 42.8 1.0 C B:TRP98 4.5 27.8 1.0 O B:HOH462 4.5 39.6 1.0 CA B:ALA95 4.5 40.2 1.0 CA B:ASN99 4.7 25.4 1.0 CB B:ALA95 4.7 50.8 1.0 CD B:PRO97 4.7 44.0 1.0 N B:ALA95 4.7 49.6 1.0 H B:ALA95 4.8 59.5 1.0 HB1 B:ALA95 4.9 60.9 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3


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-ATG16N in Complex with A Fragment of ATG3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na303 b:39.3 occ:1.00 O F:PRO97 2.3 35.8 1.0 O F:ALA95 2.4 39.3 1.0 OD1 F:ASN99 2.4 49.0 1.0 O F:HOH412 2.4 42.5 1.0 O F:HOH401 2.5 33.8 1.0 O F:HOH407 2.5 44.6 1.0 CG F:ASN99 3.4 35.9 1.0 H F:ASN99 3.5 39.4 1.0 C F:ALA95 3.5 42.7 1.0 C F:PRO97 3.5 34.9 1.0 HA F:LEU96 3.8 43.1 1.0 HA F:TRP98 3.8 40.4 1.0 C F:LEU96 3.9 37.6 1.0 O F:HOH436 3.9 38.9 1.0 HB2 F:ASN99 3.9 43.5 1.0 N F:ASN99 4.0 32.9 1.0 O F:LEU96 4.0 37.6 1.0 HB3 F:ALA95 4.1 48.7 1.0 N F:PRO97 4.1 34.0 1.0 O F:HOH457 4.1 47.5 1.0 CA F:LEU96 4.2 35.9 1.0 CB F:ASN99 4.2 36.2 1.0 HB3 F:SER94 4.3 62.0 1.0 N F:LEU96 4.3 38.9 1.0 N F:TRP98 4.4 33.0 1.0 ND2 F:ASN99 4.4 40.2 1.0 HD21 F:ASN99 4.4 48.3 1.0 O C:HOH114 4.4 52.4 1.0 CA F:TRP98 4.4 33.7 1.0 CA F:PRO97 4.4 34.8 1.0 CA F:ALA95 4.5 43.8 1.0 HD2 F:PRO97 4.5 44.0 1.0 C F:TRP98 4.5 40.7 1.0 O C:HOH108 4.5 42.5 1.0 N F:ALA95 4.6 41.8 1.0 H F:ALA95 4.7 50.2 1.0 CA F:ASN99 4.7 35.2 1.0 CB F:ALA95 4.7 40.6 1.0 O2 F:SO4301 4.9 0.4 1.0 CD F:PRO97 4.9 36.6 1.0 HB1 F:ALA95 5.0 48.7 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3 within 5.0Å range: probe atom residue distance (Å) B Occ J:Na305 b:72.4 occ:1.00 O J:PRO97 2.4 42.6 1.0 OD1 J:ASN99 2.5 51.8 1.0 O J:HOH514 2.6 56.0 1.0 O J:ALA95 2.8 52.9 1.0 O J:HOH458 3.2 43.4 1.0 CG J:ASN99 3.4 45.6 1.0 C J:PRO97 3.6 34.1 1.0 O J:HOH464 3.8 51.5 1.0 HD2 J:PRO97 3.8 56.8 1.0 HD21 J:ASN99 3.8 60.0 1.0 C J:LEU96 3.8 39.8 1.0 N J:PRO97 3.8 46.6 1.0 C J:ALA95 3.9 59.0 1.0 HA J:LEU96 4.0 52.3 1.0 ND2 J:ASN99 4.0 50.0 1.0 O J:LEU96 4.0 51.3 1.0 H J:ASN99 4.1 37.0 1.0 HB3 J:ALA95 4.2 58.0 1.0 CA J:PRO97 4.3 40.3 1.0 CD J:PRO97 4.3 47.4 1.0 CA J:LEU96 4.4 43.6 1.0 O J:HOH519 4.4 58.3 1.0 HB2 J:ASN99 4.5 44.9 1.0 HA J:TRP98 4.5 45.5 1.0 O J:HOH528 4.5 60.0 1.0 N J:ASN99 4.5 30.8 1.0 N J:LEU96 4.5 53.5 1.0 CB J:ASN99 4.5 37.4 1.0 N J:TRP98 4.7 35.0 1.0 HB2 J:PRO97 4.7 47.8 1.0 HD22 J:ASN99 4.8 60.0 1.0 CA J:ALA95 4.9 53.8 1.0 CB J:ALA95 4.9 48.4 1.0 HD3 J:PRO97 4.9 56.8 1.0 CA J:TRP98 4.9 37.9 1.0 HB1 J:ALA95 5.0 58.0 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human ATG12~ATG5-ATG16N in Complex with A Fragment of ATG3 within 5.0Å range: probe atom residue distance (Å) B Occ N:Na304 b:69.1 occ:1.00 O N:PRO97 2.3 43.7 1.0 O N:ALA95 2.4 50.5 1.0 OD1 N:ASN99 2.4 63.2 1.0 O N:HOH405 2.7 44.0 1.0 CG N:ASN99 3.4 47.9 1.0 C N:PRO97 3.5 36.7 1.0 H N:ASN99 3.5 42.0 1.0 C N:ALA95 3.5 48.4 1.0 HA N:LEU96 3.8 51.6 1.0 C N:LEU96 3.8 40.2 1.0 HB2 N:ASN99 3.9 55.3 1.0 N N:PRO97 3.9 41.6 1.0 HA N:TRP98 4.0 49.7 1.0 N N:ASN99 4.0 35.0 1.0 HB3 N:ALA95 4.0 73.7 1.0 HD2 N:PRO97 4.0 53.9 1.0 O N:LEU96 4.0 51.6 1.0 O N:HOH435 4.0 48.0 1.0 CB N:ASN99 4.2 46.1 1.0 CA N:LEU96 4.2 43.0 1.0 N N:LEU96 4.3 57.1 1.0 ND2 N:ASN99 4.3 51.8 1.0 HD21 N:ASN99 4.3 62.2 1.0 O N:HOH455 4.3 52.4 1.0 CA N:PRO97 4.3 40.7 1.0 N N:TRP98 4.4 39.8 1.0 CA N:TRP98 4.5 41.5 1.0 CA N:ALA95 4.5 50.8 1.0 CD N:PRO97 4.5 44.9 1.0 C N:TRP98 4.5 43.5 1.0 CB N:ALA95 4.6 61.4 1.0 CA N:ASN99 4.7 35.3 1.0 HB3 N:SER94 4.7 69.1 1.0 N N:ALA95 4.8 56.8 1.0 HB1 N:ALA95 4.8 73.7 1.0 H N:ALA95 4.8 68.1 1.0 HA N:ASN99 5.0 42.4 1.0 HB2 N:PRO97 5.0 50.6 1.0

Z.Metlagel, C.Otomo, G.Takaesu, T.Otomo. Structural Basis of ATG3 Recognition By the Autophagic Ubiquitin-Like Protein ATG12. Proc.Natl.Acad.Sci.Usa V. 110 18844 2013.
ISSN: ISSN 0027-8424
PubMed: 24191030
DOI: 10.1073/PNAS.1314755110