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Sodium in PDB 4bv3: Crystal Structure of SIRT3 in Complex with the Inhibitor Ex-527 and Nad

Protein crystallography data

The structure of Crystal Structure of SIRT3 in Complex with the Inhibitor Ex-527 and Nad, PDB code: 4bv3 was solved by M.Gertz, N.T.T.Nguyen, M.Weyand, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.83 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.940, 63.380, 66.350, 90.00, 90.00, 90.00
R / Rfree (%) 16.308 / 20.942

Other elements in 4bv3:

The structure of Crystal Structure of SIRT3 in Complex with the Inhibitor Ex-527 and Nad also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of SIRT3 in Complex with the Inhibitor Ex-527 and Nad (pdb code 4bv3). 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 Crystal Structure of SIRT3 in Complex with the Inhibitor Ex-527 and Nad, PDB code: 4bv3:

Sodium binding site 1 out of 1 in 4bv3

Go back to Sodium Binding Sites List in 4bv3
Sodium binding site 1 out of 1 in the Crystal Structure of SIRT3 in Complex with the Inhibitor Ex-527 and Nad


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of SIRT3 in Complex with the Inhibitor Ex-527 and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1399

b:40.3
occ:1.00
OE2 A:GLU325 2.6 22.6 1.0
OE2 A:GLU332 3.0 17.7 0.4
CA A:SER329 3.2 18.2 1.0
N A:SER329 3.3 18.1 1.0
CD A:GLU325 3.4 21.8 1.0
OE1 A:GLU325 3.5 19.8 1.0
CB A:SER329 3.6 19.5 1.0
CG A:PRO350 3.6 17.8 1.0
C A:ALA328 3.8 19.1 1.0
CD A:GLU332 4.0 16.0 0.4
O A:ALA328 4.1 19.6 1.0
CB A:ALA328 4.2 18.3 1.0
CD A:PRO350 4.3 18.4 1.0
CL A:CL1400 4.4 48.6 1.0
CG A:GLU332 4.5 15.3 0.4
C A:SER329 4.6 16.6 1.0
CA A:ALA328 4.7 17.4 1.0
CG A:GLU325 4.8 20.1 1.0
OG A:SER329 4.9 21.1 1.0
CB A:PRO350 4.9 18.4 1.0

Reference:

M.Gertz, F.Fischer, G.T.T.Nguyen, M.Lakshminarasimhan, M.Schutkowski, M.Weyand, C.Steegborn. Ex-527 Inhibits Sirtuins By Exploiting Their Unique Nad+-Dependent Deacetylation Mechanism Proc.Natl.Acad.Sci.Usa V. 110 E2772 2013.
ISSN: ISSN 0027-8424
PubMed: 23840057
DOI: 10.1073/PNAS.1303628110
Page generated: Tue Dec 15 06:34:50 2020

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