Zinc in PDB 4i5i: Crystal Structure of the SIRT1 Catalytic Domain Bound to Nad and An EX527 Analog

The structure of Crystal Structure of the SIRT1 Catalytic Domain Bound to Nad and An EX527 Analog, PDB code: 4i5i was solved by X.Zhao, D.Allison, B.Condon, F.Zhang, T.Gheyi, A.Zhang, S.Ashok, M.Russell, I.Macewan, Y.Qian, J.A.Jamison, J.G.Luz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.50
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	106.513, 106.513, 80.663, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 19.5

The structure of Crystal Structure of the SIRT1 Catalytic Domain Bound to Nad and An EX527 Analog also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the SIRT1 Catalytic Domain Bound to Nad and An EX527 Analog (pdb code 4i5i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the SIRT1 Catalytic Domain Bound to Nad and An EX527 Analog, PDB code: 4i5i:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the SIRT1 Catalytic Domain Bound to Nad and An EX527 Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the SIRT1 Catalytic Domain Bound to Nad and An EX527 Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:34.3 occ:1.00 SG A:CYS374 2.1 35.6 1.0 SG A:CYS395 2.2 33.1 1.0 SG A:CYS398 2.4 43.7 1.0 SG A:CYS371 2.4 36.0 1.0 CB A:CYS395 3.2 32.5 1.0 CB A:CYS371 3.3 33.6 1.0 CB A:CYS374 3.4 37.1 1.0 CB A:CYS398 3.4 45.7 1.0 N A:CYS398 3.8 46.8 1.0 N A:CYS374 3.9 39.6 1.0 CA A:CYS374 4.2 37.8 1.0 CA A:CYS398 4.2 47.9 1.0 CB A:ARG397 4.5 44.9 1.0 CA A:CYS395 4.6 34.5 1.0 CB A:TYR376 4.7 30.6 1.0 CB A:ALA405 4.7 45.7 1.0 CA A:CYS371 4.7 33.0 1.0 CB A:ILE373 4.8 42.7 1.0 C A:ARG397 4.8 46.9 1.0 C A:CYS374 4.9 39.7 1.0 C A:ILE373 5.0 40.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the SIRT1 Catalytic Domain Bound to Nad and An EX527 Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the SIRT1 Catalytic Domain Bound to Nad and An EX527 Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:33.9 occ:1.00 SG B:CYS374 2.1 37.6 1.0 SG B:CYS395 2.3 32.4 1.0 SG B:CYS398 2.4 40.4 1.0 SG B:CYS371 2.4 35.5 1.0 CB B:CYS395 3.2 32.4 1.0 CB B:CYS371 3.2 34.4 1.0 CB B:CYS374 3.3 38.9 1.0 CB B:CYS398 3.4 44.7 1.0 N B:CYS374 3.8 42.1 1.0 N B:CYS398 3.8 46.2 1.0 CA B:CYS374 4.1 39.2 1.0 CA B:CYS398 4.2 47.9 1.0 CB B:ARG397 4.4 43.7 1.0 CB B:TYR376 4.6 31.6 1.0 CA B:CYS395 4.6 35.5 1.0 CA B:CYS371 4.7 33.0 1.0 CB B:ALA405 4.7 46.5 1.0 CB B:ILE373 4.8 45.9 1.0 C B:CYS374 4.8 40.0 1.0 C B:ARG397 4.8 45.9 1.0 C B:ILE373 5.0 43.5 1.0

X.Zhao, D.Allison, B.Condon, F.Zhang, T.Gheyi, A.Zhang, S.Ashok, M.Russell, I.Macewan, Y.Qian, J.A.Jamison, J.G.Luz. The 2.5 Angstrom Crystal Structure of the SIRT1 Catalytic Domain Bound to Nicotinamide Adenine Dinucleotide (Nad+) and An Indole (EX527 Analogue) Reveals A Novel Mechanism of Histone Deacetylase Inhibition. J.Med.Chem. V. 56 963 2013.
ISSN: ISSN 0022-2623
PubMed: 23311358
DOI: 10.1021/JM301431Y