Sodium 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:

Zinc

(Zn)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 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 Sodium with other atoms in the Na 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:Na404 b:41.4 occ:1.00 OE1 A:GLU288 2.3 71.9 1.0 H3B A:KXG403 3.0 50.8 1.0 O A:HOH557 3.3 59.5 1.0 HO3A A:KXG403 3.3 52.0 1.0 O3B A:KXG403 3.4 43.4 1.0 CD A:GLU288 3.4 69.0 1.0 HB3 A:SER263 3.4 60.7 1.0 HO2A A:KXG403 3.4 42.6 1.0 O A:HOH536 3.6 33.7 1.0 C3B A:KXG403 3.7 42.3 1.0 O2B A:KXG403 3.8 35.5 1.0 OE2 A:GLU288 4.0 67.3 1.0 HB2 A:SER263 4.0 60.7 1.0 O B:HOH504 4.1 48.4 1.0 C2B A:KXG403 4.1 43.9 1.0 H2B A:KXG403 4.2 52.6 1.0 CB A:SER263 4.2 50.6 1.0 O A:ARG97 4.3 45.0 1.0 HA A:SER98 4.4 56.5 1.0 CG A:GLU288 4.5 51.5 1.0 HG3 A:GLU288 4.6 61.9 1.0 HE22 A:GLN265 4.6 51.1 1.0 C A:ARG97 4.6 48.1 1.0 HG2 A:GLU288 4.7 61.9 1.0 CB A:ARG97 4.7 29.8 1.0 HG A:SER263 4.7 53.4 1.0 OE1 A:GLN265 4.8 51.0 1.0 HA A:SER263 5.0 55.5 1.0 HD3 A:PRO99 5.0 51.8 1.0 OG A:SER263 5.0 44.5 1.0

Sodium binding site 2 out of 4 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 Sodium with other atoms in the Na 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 A:Na405 b:43.9 occ:1.00 HB2 A:ASP308 3.0 41.1 1.0 HB3 A:ASP308 3.2 41.1 1.0 O A:HOH512 3.5 32.6 1.0 CB A:ASP308 3.5 34.2 1.0 O A:GLY306 3.6 58.4 1.0 HH22 A:ARG282 3.9 48.1 1.0 HA3 A:GLY305 4.1 64.3 1.0 HE1 A:TYR315 4.1 38.1 1.0 OD2 A:ASP308 4.3 48.5 1.0 HH21 A:ARG282 4.4 48.1 1.0 H A:ASP308 4.4 49.6 1.0 H A:GLY306 4.4 82.8 1.0 CG A:ASP308 4.5 45.6 1.0 NH2 A:ARG282 4.5 40.1 1.0 N A:ASP308 4.5 41.3 1.0 HH21 A:ARG316 4.6 56.9 1.0 C A:GLY306 4.6 54.3 1.0 CA A:ASP308 4.7 29.0 1.0 OD1 A:ASP317 4.7 37.0 1.0 N A:GLY306 4.7 69.0 1.0 HE A:ARG316 4.8 32.9 1.0 CE1 A:TYR315 4.8 31.8 1.0 O A:HOH516 4.9 38.9 1.0 CA A:GLY305 4.9 53.6 1.0

Sodium binding site 3 out of 4 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 Sodium with other atoms in the Na binding site number 3 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:Na404 b:49.8 occ:1.00 H3D B:KXG403 2.3 63.5 1.0 O2N B:KXG403 2.7 31.0 1.0 OD1 B:ASN168 2.7 37.4 1.0 HE2 B:PHE96 2.8 44.3 1.0 O B:HOH554 2.9 39.4 1.0 O3D B:KXG403 3.0 49.4 1.0 HA B:ASN168 3.0 50.4 1.0 C3D B:KXG403 3.0 52.9 1.0 HB2 B:ALA85 3.0 34.5 1.0 H B:ALA85 3.1 51.4 1.0 O B:GLN167 3.3 38.3 1.0 HB2 B:GLN167 3.4 37.1 1.0 HB3 B:GLN167 3.4 37.1 1.0 C B:GLN167 3.5 37.1 1.0 N B:ALA85 3.5 42.8 1.0 H2D B:KXG403 3.6 61.2 1.0 N B:ASN168 3.6 35.5 1.0 CE2 B:PHE96 3.7 36.9 1.0 CA B:ASN168 3.7 42.0 1.0 HA2 B:GLY84 3.7 40.2 1.0 CB B:GLN167 3.8 30.9 1.0 HO3N B:KXG403 3.8 59.2 1.0 CG B:ASN168 3.8 37.9 1.0 CB B:ALA85 3.9 28.8 1.0 C2D B:KXG403 3.9 51.0 1.0 HA B:ALA85 3.9 41.0 1.0 H52N B:KXG403 4.0 47.0 1.0 PN B:KXG403 4.0 35.2 1.0 CA B:ALA85 4.0 34.2 1.0 H B:ASN168 4.1 42.5 1.0 C4D B:KXG403 4.2 44.6 1.0 C B:GLY84 4.2 34.5 1.0 CA B:GLN167 4.3 49.2 1.0 HB3 B:ALA85 4.3 34.5 1.0 HD2 B:PHE96 4.3 54.5 1.0 CB B:ASN168 4.3 39.1 1.0 CA B:GLY84 4.4 33.5 1.0 C5D B:KXG403 4.4 39.2 1.0 CD2 B:PHE96 4.4 45.4 1.0 HZ B:PHE96 4.5 68.2 1.0 CZ B:PHE96 4.5 56.9 1.0 O3 B:KXG403 4.6 45.5 1.0 HB1 B:ALA85 4.6 34.5 1.0 HA3 B:GLY84 4.6 40.2 1.0 O5D B:KXG403 4.6 38.5 1.0 H1N B:KXG403 4.7 73.8 1.0 HB3 B:ASN168 4.8 46.9 1.0 C1D B:KXG403 4.8 61.5 1.0 H4D B:KXG403 4.9 53.5 1.0 ND2 B:ASN168 4.9 45.0 1.0 O1N B:KXG403 4.9 44.0 1.0 H B:ILE169 4.9 65.5 1.0 HA B:GLN167 4.9 59.1 1.0 C B:ASN168 4.9 43.4 1.0 O4D B:KXG403 5.0 46.5 1.0 O2D B:KXG403 5.0 61.5 1.0 H B:GLN167 5.0 29.4 1.0

Sodium binding site 4 out of 4 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 Sodium with other atoms in the Na binding site number 4 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:Na405 b:43.1 occ:1.00 OE2 B:GLU288 2.2 66.2 1.0 O B:HOH501 2.5 60.6 1.0 HO3A B:KXG403 2.7 49.3 1.0 H3B B:KXG403 3.0 52.3 1.0 HO2A B:KXG403 3.0 65.2 1.0 CD B:GLU288 3.2 74.3 1.0 O3B B:KXG403 3.4 41.1 1.0 O2B B:KXG403 3.5 54.4 1.0 OE1 B:GLU288 3.5 73.5 1.0 C3B B:KXG403 3.6 43.6 1.0 HA B:SER98 3.8 39.2 1.0 HB3 B:SER263 3.8 56.2 1.0 O B:ARG97 3.9 42.4 1.0 C2B B:KXG403 4.0 40.5 1.0 H2B B:KXG403 4.2 48.6 1.0 C B:ARG97 4.2 39.2 1.0 O B:HOH504 4.3 48.4 1.0 HD3 B:PRO99 4.4 67.6 1.0 HE22 B:GLN265 4.5 62.0 1.0 N B:SER98 4.5 37.7 1.0 CG B:GLU288 4.6 54.0 1.0 CA B:SER98 4.6 32.7 1.0 CB B:ARG97 4.6 38.1 1.0 HB2 B:SER263 4.6 56.2 1.0 CB B:SER263 4.7 46.9 1.0 HG2 B:GLU288 4.7 64.8 1.0 OG B:SER98 4.8 33.2 1.0 O B:HOH512 4.8 44.2 1.0 HG3 B:GLU288 4.8 64.8 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.