Sodium in PDB 4rmj: Human SIRT2 in Complex with Adp Ribose and Nicotinamide

The structure of Human SIRT2 in Complex with Adp Ribose and Nicotinamide, PDB code: 4rmj was solved by T.Rumpf, M.Schiedel, B.Karaman, C.Roessler, B.J.North, A.Lehotzky, J.Olah, K.I.Ladwein, K.Schmidtkunz, M.Gajer, M.Pannek, C.Steegborn, D.A.Sinclair, S.Gerhardt, J.Ovadi, M.Schutkowski, W.Sippl, O.Einsle, M.Jung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.20 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.600, 77.960, 114.280, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 24

The structure of Human SIRT2 in Complex with Adp Ribose and Nicotinamide also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Human SIRT2 in Complex with Adp Ribose and Nicotinamide (pdb code 4rmj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human SIRT2 in Complex with Adp Ribose and Nicotinamide, PDB code: 4rmj:

Sodium binding site 1 out of 1 in the Human SIRT2 in Complex with Adp Ribose and Nicotinamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human SIRT2 in Complex with Adp Ribose and Nicotinamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:19.2 occ:0.50 OE2 A:GLU173 2.5 28.1 1.0 OD1 A:ASP170 2.7 27.6 1.0 NE2 A:HIS149 2.8 26.1 1.0 ND2 A:ASN168 3.0 25.1 1.0 CD A:GLU173 3.1 30.2 1.0 OG A:SER88 3.2 26.4 1.0 OD2 A:ASP170 3.3 27.5 1.0 CG A:ASP170 3.4 28.6 1.0 OE1 A:GLU173 3.4 32.0 1.0 CB A:ASN168 3.7 25.5 1.0 CE1 A:HIS149 3.7 25.7 1.0 CD2 A:HIS149 3.8 24.4 1.0 CG A:ASN168 3.8 24.4 1.0 CD1 A:ILE87 3.9 21.3 1.0 CB A:LEU172 3.9 28.1 1.0 CG1 A:ILE87 4.1 20.9 1.0 CG A:GLU173 4.2 29.8 1.0 N A:GLU173 4.3 30.3 1.0 N A:LEU172 4.4 30.4 1.0 OG1 A:THR166 4.4 21.9 1.0 O A:HOH529 4.4 34.2 1.0 CA A:LEU172 4.5 29.5 1.0 CB A:SER88 4.6 24.9 1.0 CD1 A:LEU172 4.7 29.4 1.0 CG A:LEU172 4.7 29.9 1.0 C A:LEU172 4.7 29.1 1.0 ND1 A:HIS149 4.9 28.9 1.0 CG A:HIS149 4.9 27.0 1.0 CB A:ASP170 4.9 28.8 1.0

T.Rumpf, M.Schiedel, B.Karaman, C.Roessler, B.J.North, A.Lehotzky, J.Olah, K.I.Ladwein, K.Schmidtkunz, M.Gajer, M.Pannek, C.Steegborn, D.A.Sinclair, S.Gerhardt, J.Ovadi, M.Schutkowski, W.Sippl, O.Einsle, M.Jung. Selective SIRT2 Inhibition By Ligand-Induced Rearrangement of the Active Site. Nat Commun V. 6 6263 2015.
ISSN: ESSN 2041-1723
PubMed: 25672491
DOI: 10.1038/NCOMMS7263