Sodium in PDB 5l3g: LSD1-COREST1 in Complex with Polymyxin E (Colistin)

The structure of LSD1-COREST1 in Complex with Polymyxin E (Colistin), PDB code: 5l3g was solved by V.Speranzini, D.Rotili, G.Ciossani, S.Pilotto, M.Forgione, A.Lucidi, F.Forneris, S.Velankar, A.Mai, A.Mattevi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.78 / 3.10
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	119.864, 179.490, 236.985, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 19.7

The binding sites of Sodium atom in the LSD1-COREST1 in Complex with Polymyxin E (Colistin) (pdb code 5l3g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the LSD1-COREST1 in Complex with Polymyxin E (Colistin), PDB code: 5l3g:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the LSD1-COREST1 in Complex with Polymyxin E (Colistin)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of LSD1-COREST1 in Complex with Polymyxin E (Colistin) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:73.0 occ:1.00 OG1 A:THR624 2.3 81.9 1.0 N A:GLY290 2.9 69.4 1.0 CB A:THR624 2.9 71.2 1.0 OG A:SER289 3.1 62.8 1.0 N A:GLY287 3.2 90.9 1.0 CA A:GLY290 3.3 75.2 1.0 CA A:GLY287 3.4 99.5 1.0 O1P A:FAD901 3.5 76.1 1.0 C5B A:FAD901 3.6 89.5 1.0 O A:GLY285 3.6 72.1 1.0 CG2 A:THR624 3.6 71.4 1.0 O5B A:FAD901 3.7 93.5 1.0 C A:GLY287 3.8 96.1 1.0 O A:THR624 3.8 71.0 1.0 C A:GLY285 3.8 74.8 1.0 O A:GLY287 3.9 82.6 1.0 C A:SER289 4.0 83.4 1.0 N A:SER289 4.1 71.2 1.0 C A:SER286 4.2 0.7 1.0 C4B A:FAD901 4.2 86.3 1.0 CB A:SER289 4.2 76.6 1.0 CA A:THR624 4.2 83.6 1.0 CA A:GLY285 4.3 71.2 1.0 O A:ILE284 4.3 62.8 1.0 CA A:SER289 4.3 78.9 1.0 N A:SER286 4.4 70.4 1.0 P A:FAD901 4.4 89.7 1.0 C A:THR624 4.4 83.6 1.0 CA A:SER286 4.5 81.1 1.0 O3P A:FAD901 4.5 76.9 1.0 N A:VAL288 4.5 0.1 1.0 C A:GLY290 4.7 80.3 1.0 PA A:FAD901 4.8 0.8 1.0 O4B A:FAD901 4.8 83.5 1.0 O2P A:FAD901 4.9 83.1 1.0 N A:LEU291 4.9 71.3 1.0 C A:VAL288 5.0 81.6 1.0

Sodium binding site 2 out of 2 in the LSD1-COREST1 in Complex with Polymyxin E (Colistin)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of LSD1-COREST1 in Complex with Polymyxin E (Colistin) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na903 b:88.6 occ:1.00 NH1 A:ARG688 3.2 0.7 1.0 NH2 A:ARG526 3.3 0.6 1.0 NH2 A:ARG688 3.4 0.1 1.0 CZ A:ARG688 3.8 0.2 1.0 CG A:GLU413 3.9 0.7 1.0 CD A:GLU413 4.1 0.9 1.0 OE2 A:GLU413 4.1 1.0 1.0 CE2 A:PHE533 4.1 95.5 1.0 CD2 A:PHE533 4.2 0.5 1.0 CZ A:ARG526 4.4 0.9 1.0 O A:GLY409 4.6 0.5 1.0 OE1 A:GLU413 4.6 0.1 1.0 NH1 A:ARG526 4.7 0.8 1.0 CZ A:PHE533 4.8 95.0 1.0 CG A:PHE533 4.8 0.6 1.0

V.Speranzini, D.Rotili, G.Ciossani, S.Pilotto, B.Marrocco, M.Forgione, A.Lucidi, F.Forneris, P.Mehdipour, S.Velankar, A.Mai, A.Mattevi. Polymyxins and Quinazolines Are LSD1/KDM1A Inhibitors with Unusual Structural Features. Sci Adv V. 2 01017 2016.
ISSN: ESSN 2375-2548
PubMed: 27626075
DOI: 10.1126/SCIADV.1601017