Sodium in PDB 4ue8: Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor

The structure of Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor, PDB code: 4ue8 was solved by D.Peter, O.Weichenrieder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.645 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.450, 73.290, 38.260, 90.00, 112.49, 90.00
R / Rfree (%)	14.52 / 16.14

The binding sites of Sodium atom in the Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor (pdb code 4ue8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor, PDB code: 4ue8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1235 b:43.9 occ:1.00 OD2 A:ASP178 2.4 37.3 1.0 HD2 A:HIS176 2.5 25.6 1.0 OD1 A:ASP178 2.7 36.7 1.0 CG A:ASP178 2.9 33.1 1.0 HB3 A:HIS176 3.2 22.9 1.0 CD2 A:HIS176 3.3 21.3 1.0 HA A:HIS176 3.3 21.9 1.0 HG2 A:GLN179 3.3 23.6 1.0 CB A:HIS176 3.8 19.0 1.0 CG A:HIS176 3.8 18.6 1.0 HG3 A:GLN179 3.9 23.6 1.0 CA A:HIS176 4.0 18.2 1.0 CG A:GLN179 4.0 19.6 1.0 HB3 A:ALA206 4.1 19.4 1.0 H A:GLN179 4.2 23.7 1.0 HD22 A:ASN203 4.3 27.6 1.0 CB A:ASP178 4.4 24.4 1.0 NE2 A:HIS176 4.4 23.1 1.0 HB2 A:GLN179 4.5 20.7 1.0 O A:HIS176 4.5 19.1 1.0 C A:HIS176 4.6 18.9 1.0 HE21 A:GLN179 4.6 29.2 1.0 HB2 A:HIS176 4.7 22.9 1.0 N A:GLN179 4.7 19.8 1.0 H A:ASP178 4.7 23.2 1.0 HB2 A:ASP178 4.7 29.2 1.0 CB A:GLN179 4.8 17.2 1.0 HB2 A:ALA206 4.8 19.4 1.0 HB3 A:ASP178 4.8 29.2 1.0 ND2 A:ASN203 4.9 23.0 1.0 CB A:ALA206 4.9 16.2 1.0

Sodium binding site 2 out of 2 in the Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex of D. Melanogaster EIF4E with the 4E Binding Protein Thor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1236 b:34.2 occ:1.00 OD1 A:ASN160 2.2 28.4 1.0 O A:HOH2114 2.4 33.3 1.0 HA A:ASN160 2.4 17.6 1.0 O A:HOH2112 2.7 29.7 1.0 CG A:ASN160 2.8 26.7 1.0 HD21 A:LEU163 2.9 15.6 1.0 O A:HOH2160 3.2 28.1 1.0 CA A:ASN160 3.2 14.7 1.0 CB A:ASN160 3.3 19.5 1.0 HB3 A:ASN160 3.3 23.4 1.0 HB3 A:LEU163 3.7 12.5 1.0 H83 B:P4G1084 3.7 42.3 1.0 CD2 A:LEU163 3.8 13.0 1.0 ND2 A:ASN160 3.8 29.9 1.0 HD23 A:LEU163 3.9 15.6 1.0 N A:ASN160 4.0 12.8 1.0 H72 B:P4G1084 4.0 43.0 1.0 HD22 A:ASN160 4.1 35.9 1.0 O A:HOH2055 4.1 24.3 1.0 HB2 A:ASN160 4.2 23.4 1.0 H A:ASN160 4.4 15.4 1.0 HD22 A:LEU163 4.4 15.6 1.0 C A:ASN160 4.4 11.6 1.0 HH12 B:ARG63 4.4 17.1 1.0 CB A:LEU163 4.4 10.4 1.0 O B:HOH2015 4.4 43.2 1.0 HB2 A:LEU163 4.4 12.5 1.0 O A:ASN160 4.4 12.0 1.0 HZ1 B:LYS60 4.5 26.4 1.0 HD21 A:ASN160 4.5 35.9 1.0 C8 B:P4G1084 4.5 35.2 1.0 C7 B:P4G1084 4.6 35.9 1.0 C A:ASP159 4.6 11.8 1.0 O A:ASP159 4.6 12.3 1.0 H62 B:P4G1084 4.6 42.3 1.0 HZ2 B:LYS60 4.6 26.4 1.0 O A:HOH2116 4.6 46.3 1.0 O4 B:P4G1084 4.6 36.5 1.0 CG A:LEU163 4.6 10.6 1.0 H81 B:P4G1084 4.8 42.3 1.0 HG A:LEU163 4.8 12.7 1.0 HE2 B:LYS60 4.9 21.0 1.0 NZ B:LYS60 4.9 22.0 1.0

D.Peter, C.Igreja, R.Weber, L.Wohlbold, C.Weiler, L.Ebertsch, O.Weichenrieder, E.Izaurralde. Molecular Architecture of 4E-Bp Translational Inhibitors Bound to EIF4E Mol.Cell 2015.
ISSN: ESSN 1097-4164
PubMed: 25702871
DOI: 10.1016/J.MOLCEL.2015.01.017