Zinc in PDB 6nr0: SIRT2(56-356) with Covalent Intermediate Between Mechanism-Based Inhibitor Glucose-Tm-1BETA and 1'-Sh Adp-Ribose

The structure of SIRT2(56-356) with Covalent Intermediate Between Mechanism-Based Inhibitor Glucose-Tm-1BETA and 1'-Sh Adp-Ribose, PDB code: 6nr0 was solved by I.R.Price, J.Hong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.69 / 2.45
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.310, 76.840, 114.461, 90.00, 95.87, 90.00
R / Rfree (%)	22 / 25.6

The structure of SIRT2(56-356) with Covalent Intermediate Between Mechanism-Based Inhibitor Glucose-Tm-1BETA and 1'-Sh Adp-Ribose also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Zinc atom in the SIRT2(56-356) with Covalent Intermediate Between Mechanism-Based Inhibitor Glucose-Tm-1BETA and 1'-Sh Adp-Ribose (pdb code 6nr0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the SIRT2(56-356) with Covalent Intermediate Between Mechanism-Based Inhibitor Glucose-Tm-1BETA and 1'-Sh Adp-Ribose, PDB code: 6nr0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the SIRT2(56-356) with Covalent Intermediate Between Mechanism-Based Inhibitor Glucose-Tm-1BETA and 1'-Sh Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SIRT2(56-356) with Covalent Intermediate Between Mechanism-Based Inhibitor Glucose-Tm-1BETA and 1'-Sh Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:63.4 occ:1.00 SG A:CYS224 2.3 71.5 1.0 SG A:CYS200 2.3 62.6 1.0 SG A:CYS221 2.3 56.6 1.0 SG A:CYS195 2.3 54.1 1.0 HB2 A:CYS221 2.9 54.1 1.0 HB3 A:CYS221 2.9 54.1 1.0 HB2 A:CYS195 3.0 53.6 1.0 CB A:CYS221 3.0 45.0 1.0 CB A:CYS195 3.1 44.7 1.0 HB3 A:CYS200 3.1 75.8 1.0 H A:CYS224 3.2 69.1 1.0 HB3 A:CYS195 3.2 53.6 1.0 HB3 A:CYS224 3.3 75.8 1.0 CB A:CYS200 3.3 63.1 1.0 CB A:CYS224 3.4 63.1 1.0 HB2 A:CYS200 3.6 75.8 1.0 HB2 A:HIS202 3.8 57.6 1.0 N A:CYS224 3.8 57.6 1.0 HD1 A:HIS202 3.9 70.9 1.0 HB2 A:SER226 3.9 71.2 1.0 H A:SER226 4.0 79.5 1.0 H A:HIS202 4.1 40.4 1.0 HB2 A:ASP223 4.1 70.9 1.0 CA A:CYS224 4.1 60.9 1.0 HB2 A:CYS224 4.2 75.8 1.0 ND1 A:HIS202 4.2 59.1 1.0 HG A:SER226 4.2 79.4 1.0 HB3 A:SER197 4.5 71.6 1.0 CA A:CYS221 4.5 46.4 1.0 CG A:HIS202 4.6 52.2 1.0 CA A:CYS195 4.6 44.3 1.0 CB A:HIS202 4.6 48.0 1.0 H A:ASP223 4.6 60.7 1.0 H A:GLN225 4.7 91.9 1.0 CA A:CYS200 4.7 64.1 1.0 C A:CYS224 4.7 69.1 1.0 HH A:TYR204 4.7 60.9 1.0 H A:SER197 4.8 62.3 1.0 CB A:SER226 4.8 59.3 1.0 HA A:CYS221 4.8 55.7 1.0 N A:SER226 4.8 66.3 1.0 HA A:CYS195 4.8 53.1 1.0 N A:GLN225 4.9 76.6 1.0 HB2 A:SER197 4.9 71.6 1.0 N A:HIS202 4.9 33.6 1.0 OG A:SER226 4.9 66.2 1.0 CE1 A:HIS202 4.9 45.9 1.0 C A:ASP223 4.9 66.2 1.0 N A:ARG201 5.0 55.4 1.0 HE1 A:TYR204 5.0 56.7 1.0 CB A:ASP223 5.0 59.1 1.0 HA A:CYS200 5.0 76.9 1.0 HA A:CYS224 5.0 73.1 1.0

Zinc binding site 2 out of 2 in the SIRT2(56-356) with Covalent Intermediate Between Mechanism-Based Inhibitor Glucose-Tm-1BETA and 1'-Sh Adp-Ribose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SIRT2(56-356) with Covalent Intermediate Between Mechanism-Based Inhibitor Glucose-Tm-1BETA and 1'-Sh Adp-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:87.5 occ:1.00 HB2 B:CYS221 2.2 73.1 1.0 SG B:CYS221 2.3 81.4 1.0 SG B:CYS224 2.3 84.0 1.0 SG B:CYS195 2.3 88.4 1.0 SG B:CYS200 2.3 56.7 1.0 HB3 B:CYS221 2.3 73.1 1.0 CB B:CYS221 2.4 60.9 1.0 HB2 B:CYS195 2.7 72.0 1.0 CB B:CYS195 3.0 60.0 1.0 HB2 B:SER226 3.2 82.2 1.0 HB3 B:CYS200 3.2 80.7 1.0 HB3 B:CYS195 3.3 72.0 1.0 CB B:CYS200 3.4 67.3 1.0 H B:CYS224 3.5 0.3 1.0 H B:SER226 3.7 0.4 1.0 HB2 B:CYS200 3.7 80.7 1.0 CB B:CYS224 3.8 84.7 1.0 HB3 B:CYS224 3.8 0.6 1.0 HG B:SER226 3.9 0.1 1.0 CA B:CYS221 3.9 63.6 1.0 CB B:SER226 4.1 68.5 1.0 H B:HIS202 4.1 62.2 1.0 HB2 B:HIS202 4.1 79.6 1.0 N B:CYS224 4.2 89.5 1.0 HA B:CYS221 4.2 76.3 1.0 OG B:SER226 4.3 88.4 1.0 HD1 B:HIS202 4.3 90.8 1.0 HB3 B:SER197 4.4 0.7 1.0 H B:CYS221 4.4 74.9 1.0 CA B:CYS195 4.4 63.1 1.0 CA B:CYS224 4.5 76.0 1.0 N B:SER226 4.5 91.2 1.0 HB2 B:CYS224 4.5 0.6 1.0 HA B:CYS195 4.5 75.8 1.0 HB2 B:ASP223 4.6 92.3 1.0 H B:GLN225 4.6 0.8 1.0 H B:SER197 4.6 81.4 1.0 ND1 B:HIS202 4.7 75.7 1.0 N B:CYS221 4.7 62.4 1.0 C B:CYS221 4.7 74.5 1.0 HB3 B:SER226 4.7 82.2 1.0 HH B:TYR204 4.7 71.0 1.0 H B:ASP223 4.7 85.3 1.0 CA B:CYS200 4.8 61.6 1.0 HG22 B:VAL228 4.8 65.5 1.0 HG23 B:VAL228 4.8 65.5 1.0 HB2 B:SER197 4.8 0.7 1.0 C B:CYS224 4.8 86.4 1.0 N B:GLN225 4.8 0.3 1.0 CA B:SER226 4.8 65.3 1.0 N B:ARG201 4.9 67.1 1.0 N B:HIS202 4.9 51.9 1.0 CB B:HIS202 4.9 66.3 1.0 H B:VAL196 4.9 75.6 1.0 CG B:HIS202 5.0 54.4 1.0

I.R.Price, J.Hong. SIRT2(56-356) with Covalent Intermediate Between Mechanism-Based Inhibitor Glucose-Tm-1BETA and 1'-Sh Adp-Ribose To Be Published.