Sodium in PDB 5kc1: Structure of the C-Terminal Dimerization Domain of ATG38

The structure of Structure of the C-Terminal Dimerization Domain of ATG38, PDB code: 5kc1 was solved by Y.Ohashi, N.Soler, M.Garcia-Ortegon, L.Zhang, O.Perisic, G.R.Masson, C.M.Johnson, R.J.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.00 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.383, 249.385, 50.197, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.1

The structure of Structure of the C-Terminal Dimerization Domain of ATG38 also contains other interesting chemical elements:

Iodine	(I)	1 atom
Chlorine	(Cl)	6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Structure of the C-Terminal Dimerization Domain of ATG38 (pdb code 5kc1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Structure of the C-Terminal Dimerization Domain of ATG38, PDB code: 5kc1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:74.3 occ:1.00 ND2 C:ASN141 3.3 34.9 1.0 CA C:LEU138 3.5 27.5 1.0 CD1 C:LEU138 3.8 38.9 1.0 N C:LEU138 3.9 36.1 1.0 CB C:LEU138 4.1 42.9 1.0 OE2 D:GLU173 4.1 60.4 1.0 O C:ARG137 4.2 35.4 1.0 C C:ARG137 4.2 37.5 1.0 OE1 D:GLU173 4.3 76.9 1.0 CG C:ASN141 4.3 43.7 1.0 CB C:ASN141 4.4 41.3 1.0 CD D:ARG166 4.4 54.7 1.0 CD D:GLU173 4.5 50.0 1.0 NH1 D:ARG166 4.6 49.2 1.0 CG C:LEU138 4.6 49.7 1.0 CG C:ARG137 4.6 44.3 1.0 NH1 C:ARG137 4.7 43.5 1.0 C C:LEU138 4.7 36.6 1.0 O D:ARG166 4.7 44.6 1.0 O C:LEU138 4.8 36.6 1.0 CG D:GLN169 4.9 70.9 1.0 CB D:PHE170 5.0 42.7 1.0 CB C:ARG137 5.0 36.7 1.0

Sodium binding site 2 out of 14 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:93.2 occ:1.00 OE1 D:GLU168 3.2 95.3 1.0 OE2 D:GLU168 3.3 88.3 1.0 CD D:GLU168 3.6 88.9 1.0 CD1 D:LEU165 4.3 56.0 1.0

Sodium binding site 3 out of 14 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:94.1 occ:1.00 CE D:LYS162 3.1 96.2 1.0 NZ D:LYS162 3.5 96.4 1.0 CD1 F:LEU165 3.6 84.4 1.0 CG F:LYS162 3.8 84.9 1.0 O2 A:EDO304 3.9 0.6 1.0 CE F:LYS162 4.1 94.9 1.0 O A:HOH409 4.3 80.9 1.0 CD F:LYS162 4.5 98.9 1.0 CD D:LYS162 4.6 88.1 1.0 NE2 A:GLN147 4.6 0.4 1.0 CB F:LYS162 4.8 63.1 1.0 CA F:LYS162 4.9 73.4 1.0 O A:HOH403 5.0 74.5 1.0

Sodium binding site 4 out of 14 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:87.5 occ:1.00 OE1 B:GLU168 2.8 76.8 1.0 O2 C:EDO304 3.5 81.5 1.0 NZ B:LYS171 3.5 62.6 1.0 CD B:GLU168 3.6 82.0 1.0 OE2 B:GLU168 3.8 85.2 1.0 OE1 C:GLN139 4.0 46.0 1.0 C2 C:EDO304 4.1 84.5 1.0 C1 C:EDO304 4.4 62.5 1.0 NE2 C:GLN139 4.5 43.0 1.0 CE B:LYS171 4.6 53.3 1.0 CD C:GLN139 4.6 58.3 1.0 CG B:GLU168 4.9 90.8 1.0 OD1 C:ASN136 4.9 65.2 1.0

Sodium binding site 5 out of 14 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ K:Na301 b:63.2 occ:1.00 OD2 K:ASP145 2.7 52.4 1.0 OD1 K:ASP145 2.9 94.0 1.0 CG K:ASP145 3.0 69.6 1.0 O2 K:SO4309 3.1 52.6 1.0 O3 K:SO4309 3.2 54.6 1.0 S K:SO4309 3.4 65.7 1.0 O4 K:SO4309 3.4 59.6 1.0 ND2 K:ASN141 4.1 36.8 1.0 CE2 K:PHE140 4.1 53.6 1.0 CB K:ASP145 4.3 77.3 1.0 CD2 K:PHE140 4.6 44.8 1.0 O1 K:SO4309 4.8 77.2 1.0

Sodium binding site 6 out of 14 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ K:Na302 b:76.5 occ:1.00 O3 K:NO3305 3.0 83.8 1.0 OD1 K:ASN136 3.1 45.1 1.0 N K:NO3305 3.8 1.0 1.0 O2 K:NO3305 3.9 89.5 1.0 CG K:ASN136 3.9 45.2 1.0 O K:HOH402 4.1 50.3 1.0 ND2 K:ASN136 4.2 29.1 1.0 NZ J:LYS171 4.2 64.9 1.0 SD K:MET132 4.4 71.2 1.0 O1 K:NO3305 4.8 93.5 1.0 OE1 K:GLN139 4.8 65.2 1.0

Sodium binding site 7 out of 14 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ K:Na303 b:73.1 occ:1.00 OD2 K:ASP128 3.5 57.7 1.0 OD1 K:ASP128 3.7 52.2 1.0 CB K:LEU130 3.8 34.7 1.0 CG K:PRO129 3.9 40.2 1.0 CG K:ASP128 3.9 52.7 1.0 N K:LEU130 4.0 34.0 1.0 CD K:PRO129 4.2 37.8 1.0 CA K:LEU130 4.5 39.4 1.0 N K:PRO129 4.7 33.8 1.0 CB K:PRO129 4.9 43.7 1.0 CD2 K:LEU130 5.0 36.6 1.0 C K:PRO129 5.0 30.3 1.0

Sodium binding site 8 out of 14 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na301 b:69.3 occ:1.00 CL E:CL302 3.2 0.8 1.0 OD2 E:ASP128 3.6 68.0 1.0 CG E:PRO129 3.6 37.9 1.0 OD1 E:ASP128 3.9 58.2 1.0 CD E:PRO129 4.0 41.1 1.0 CG E:ASP128 4.0 51.0 1.0 CB E:LEU130 4.0 39.5 1.0 N E:LEU130 4.0 28.1 1.0 N E:PRO129 4.6 39.2 1.0 CA E:LEU130 4.7 32.2 1.0 CB E:PRO129 4.8 39.7 1.0 C E:PRO129 5.0 28.3 1.0

Sodium binding site 9 out of 14 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na301 b:50.1 occ:1.00 ND2 A:ASN136 2.8 44.0 1.0 O F:GLN169 2.9 39.8 1.0 O1 A:NO3302 3.2 84.6 1.0 N F:GLU173 3.6 31.4 1.0 C F:GLN169 3.7 42.0 1.0 CG A:MET132 3.8 79.5 1.0 N A:NO3302 3.8 91.7 1.0 CG A:ASN136 3.8 35.3 1.0 CB F:LYS172 3.8 50.9 1.0 O2 A:NO3302 3.9 76.8 1.0 CA F:GLN169 3.9 38.2 1.0 CB F:GLU173 4.0 44.5 1.0 OD1 A:ASN136 4.0 43.3 1.0 CA F:GLU173 4.1 31.2 1.0 CB F:GLN169 4.2 44.6 1.0 O3 F:NO3305 4.2 50.7 1.0 C F:LYS172 4.3 34.5 1.0 OE1 F:GLU173 4.4 43.4 1.0 CA F:LYS172 4.6 39.9 1.0 SD A:MET132 4.7 68.0 1.0 O3 A:NO3302 4.7 75.0 1.0 CD F:LYS172 4.8 70.0 1.0 CG F:LYS172 4.8 51.6 1.0 O1 F:NO3305 4.8 47.7 1.0 CG F:GLN169 4.8 49.6 1.0 N F:PHE170 4.9 38.9 1.0 N F:NO3305 4.9 61.4 1.0

Sodium binding site 10 out of 14 in the Structure of the C-Terminal Dimerization Domain of ATG38


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of the C-Terminal Dimerization Domain of ATG38 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na302 b:98.6 occ:1.00 CD F:GLU168 3.9 69.0 1.0 OE2 F:GLU168 4.0 72.8 1.0 CG F:GLU168 4.2 62.3 1.0 OE1 F:GLU168 4.2 86.5 1.0

Y.Ohashi, N.Soler, M.Garcia Ortegon, L.Zhang, M.L.Kirsten, O.Perisic, G.R.Masson, J.E.Burke, A.J.Jakobi, A.A.Apostolakis, C.M.Johnson, M.Ohashi, N.T.Ktistakis, C.Sachse, R.L.Williams. Characterization of ATG38 and NRBF2, A Fifth Subunit of the Autophagic VPS34/PIK3C3 Complex. Autophagy V. 12 2129 2016.
ISSN: ESSN 1554-8635
PubMed: 27630019
DOI: 10.1080/15548627.2016.1226736