Sodium in PDB 6fzp: Ppar Gamma Complex

The structure of Ppar Gamma Complex, PDB code: 6fzp was solved by N.Rochel, S.Beji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.32 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	53.592, 86.268, 122.693, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 25.2

The binding sites of Sodium atom in the Ppar Gamma Complex (pdb code 6fzp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ppar Gamma Complex, PDB code: 6fzp:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Ppar Gamma Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ppar Gamma Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na551 b:59.9 occ:1.00 O A:HOH632 2.7 61.4 1.0 ND2 A:ASN403 3.4 48.4 1.0 NH2 A:ARG262 3.7 79.7 1.0 CB A:ASN403 3.8 48.1 1.0 CA A:ASN363 3.8 54.0 1.0 O A:MET362 4.0 69.4 1.0 CG A:ASN403 4.1 51.9 1.0 N A:LYS364 4.3 66.6 1.0 C A:ASN363 4.3 53.7 1.0 CA A:VAL400 4.3 66.8 1.0 CB A:ASN363 4.4 63.5 1.0 O A:ALA399 4.6 57.0 1.0 CG2 A:VAL400 4.7 71.6 1.0 C A:MET362 4.8 61.0 1.0 N A:ASN363 4.8 54.0 1.0 CZ A:ARG262 4.8 77.2 1.0 O A:VAL400 4.8 66.3 1.0 CB A:VAL400 4.9 70.1 1.0 N A:VAL400 5.0 63.0 1.0

Sodium binding site 2 out of 3 in the Ppar Gamma Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ppar Gamma Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na552 b:81.4 occ:1.00 O A:GLY389 2.8 1.0 1.0 N A:GLU393 3.0 74.3 1.0 O A:LEU381 3.0 85.2 1.0 N A:MET392 3.1 82.9 1.0 CB A:MET392 3.2 77.4 1.0 CA A:MET392 3.4 77.4 1.0 C A:LEU381 3.5 87.6 1.0 C A:MET392 3.5 73.4 1.0 C A:GLY389 3.6 0.1 1.0 CA A:LYS382 3.8 89.2 1.0 N A:LYS382 3.8 88.5 1.0 CA A:GLU393 3.9 78.5 1.0 CB A:GLU393 4.0 90.0 1.0 CB A:LEU381 4.0 65.8 1.0 N A:PHE391 4.0 93.9 1.0 CG A:MET392 4.2 80.5 1.0 C A:PHE391 4.2 81.4 1.0 N A:ASP390 4.2 0.4 1.0 CA A:ASP390 4.3 97.2 1.0 C A:ASP390 4.3 93.7 1.0 CA A:LEU381 4.4 77.3 1.0 CB A:LYS382 4.4 90.8 1.0 CA A:GLY389 4.5 0.0 1.0 O A:MET392 4.6 77.5 1.0 CA A:PHE391 4.7 83.0 1.0 O A:PHE388 4.8 91.5 1.0 CG A:LYS382 4.8 95.7 1.0 OE2 A:GLU393 4.8 94.8 1.0

Sodium binding site 3 out of 3 in the Ppar Gamma Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ppar Gamma Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na553 b:80.3 occ:1.00 NZ A:LYS395 2.9 71.8 1.0 O A:ILE473 3.1 62.3 1.0 N A:HIS477 3.5 75.4 1.0 CG2 A:ILE473 3.5 79.4 1.0 CE A:LYS395 3.7 65.1 1.0 CB A:GLU476 3.7 88.9 1.0 CB A:HIS477 3.8 77.3 1.0 CA A:HIS477 3.8 74.3 1.0 C A:ILE473 3.9 59.8 1.0 CB A:PRO394 3.9 63.4 1.0 C A:GLU476 3.9 84.7 1.0 CA A:ILE473 4.0 63.9 1.0 CG A:PRO394 4.1 69.6 1.0 CD A:LYS395 4.3 65.0 1.0 CB A:ILE473 4.3 64.2 1.0 CA A:GLU476 4.4 87.1 1.0 O A:PHE391 4.5 78.9 1.0 O A:GLU476 4.6 84.4 1.0 ND1 A:HIS477 4.6 80.2 1.0 CG A:HIS477 4.7 80.8 1.0 CG A:GLU476 4.9 0.9 1.0 N A:GLU476 4.9 76.3 1.0 CG1 A:ILE473 5.0 56.9 1.0

N.Rochel, C.Krucker, L.Coutos-Thevenot, J.Osz, R.Zhang, E.Guyon, W.Zita, S.Vanthong, O.A.Hernandez, M.Bourguet, K.A.Badawy, F.Dufour, C.Peluso-Iltis, S.Heckler-Beji, A.Dejaegere, A.Kamoun, A.De Reynies, Y.Neuzillet, S.Rebouissou, C.Beraud, H.Lang, T.Massfelder, Y.Allory, S.Cianferani, R.H.Stote, F.Radvanyi, I.Bernard-Pierrot. Recurrent Activating Mutations of Ppar Gamma Associated with Luminal Bladder Tumors. Nat Commun V. 10 253 2019.
ISSN: ESSN 2041-1723
PubMed: 30651555
DOI: 10.1038/S41467-018-08157-Y