Sodium in PDB 4bn4: Structure of Human SIRT3 in Complex with Adp-Ribose

The structure of Structure of Human SIRT3 in Complex with Adp-Ribose, PDB code: 4bn4 was solved by G.T.T.Nguyen, S.Schaefer, M.Gertz, M.Weyand, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.21 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.900, 66.670, 66.850, 90.00, 90.00, 90.00
R / Rfree (%)	13.781 / 17.95

The structure of Structure of Human SIRT3 in Complex with Adp-Ribose also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Structure of Human SIRT3 in Complex with Adp-Ribose (pdb code 4bn4). 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 Structure of Human SIRT3 in Complex with Adp-Ribose, PDB code: 4bn4:

Sodium binding site 1 out of 1 in the Structure of Human SIRT3 in Complex with Adp-Ribose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human SIRT3 in Complex with Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1394 b:16.4 occ:1.00 HE2 A:HIS210 2.1 10.4 1.0 HG A:SER149 2.6 12.4 0.0 OD1 A:ASP231 2.7 11.3 1.0 OE2 A:GLU234 2.8 11.5 1.0 HB2 A:LEU233 2.9 11.4 1.0 OD1 A:ASN229 2.9 13.7 1.0 NE2 A:HIS210 3.0 10.4 1.0 OG A:SER149 3.0 11.8 1.0 HD12 A:ILE148 3.2 10.9 1.0 HB2 A:ASN229 3.3 10.4 1.0 OD2 A:ASP231 3.3 15.0 1.0 CD A:GLU234 3.3 12.0 1.0 CG A:ASP231 3.4 12.4 1.0 HG13 A:ILE148 3.5 9.9 1.0 H A:LEU233 3.5 10.5 1.0 HB3 A:ASN229 3.6 10.3 1.0 HD2 A:HIS210 3.7 10.5 1.0 CD2 A:HIS210 3.7 10.7 1.0 OE1 A:GLU234 3.7 12.6 1.0 CB A:ASN229 3.7 10.2 1.0 CG A:ASN229 3.8 9.1 1.0 H A:GLU234 3.8 10.2 1.0 CD1 A:ILE148 3.9 10.7 1.0 CB A:LEU233 3.9 11.2 1.0 HD13 A:ILE148 3.9 10.9 1.0 HD13 A:LEU233 3.9 13.1 1.0 CE1 A:HIS210 4.0 10.1 1.0 HG1 A:THR227 4.0 10.1 0.0 CG1 A:ILE148 4.0 10.2 1.0 HG3 A:GLU234 4.0 10.6 1.0 HG12 A:ILE148 4.1 10.2 1.0 N A:LEU233 4.2 9.9 1.0 HE1 A:HIS210 4.2 9.7 1.0 N A:GLU234 4.3 10.5 1.0 CG A:GLU234 4.3 10.3 1.0 HB3 A:LEU233 4.4 11.2 1.0 CA A:LEU233 4.4 10.2 1.0 CB A:SER149 4.4 10.8 1.0 HG A:LEU233 4.5 11.2 1.0 HB2 A:SER149 4.6 11.6 1.0 C A:LEU233 4.6 9.8 1.0 CG A:LEU233 4.6 10.8 1.0 CD1 A:LEU233 4.7 13.2 1.0 OG1 A:THR227 4.7 9.6 1.0 HD11 A:ILE148 4.7 10.6 1.0 HB3 A:SER149 4.8 11.2 1.0 O A:HOH2119 4.8 14.7 1.0 HG22 A:VAL144 4.8 9.8 1.0 CB A:ASP231 4.9 12.2 1.0 HG23 A:VAL144 4.9 9.8 1.0 HG2 A:GLU234 5.0 10.3 1.0 CG A:HIS210 5.0 9.4 1.0 H A:ASP231 5.0 11.3 1.0 ND2 A:ASN229 5.0 9.1 1.0 HD11 A:LEU233 5.0 12.7 1.0

G.T.T.Nguyen, S.Schaefer, M.Gertz, M.Weyand, C.Steegborn. Structures of Human Sirtuin 3 Complexes with Adp-Ribose and with Carba-Nad+ and SRT1720: Binding Details and Inhibition Mechanism Acta Crystallogr.,Sect.D V. 69 1423 2013.
ISSN: ISSN 0907-4449
PubMed: 23897466
DOI: 10.1107/S0907444913015448