Sodium in PDB 3nvd: Structure of Ybbd in Complex with Pugnac

All present enzymatic activity of Structure of Ybbd in Complex with Pugnac:
3.2.1.52;

The structure of Structure of Ybbd in Complex with Pugnac, PDB code: 3nvd was solved by K.Diederichs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.55 / 1.84
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	58.473, 73.206, 83.788, 79.83, 69.45, 88.22
R / Rfree (%)	18.7 / 24.6

The binding sites of Sodium atom in the Structure of Ybbd in Complex with Pugnac (pdb code 3nvd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Ybbd in Complex with Pugnac, PDB code: 3nvd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Ybbd in Complex with Pugnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Ybbd in Complex with Pugnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Na643 b:20.6 occ:1.00 HG A:SER233 2.0 15.8 1.0 H A:HIS270 2.4 16.9 1.0 OG A:SER233 2.8 13.2 1.0 OD2 A:ASP318 2.8 11.9 1.0 HD2 A:HIS226 2.9 4.8 1.0 HE1 A:MET322 2.9 10.7 1.0 HA A:ALA269 2.9 13.5 1.0 N A:HIS270 3.2 14.1 1.0 HB2 A:HIS270 3.2 12.0 1.0 HB2 A:SER233 3.4 26.3 1.0 CD2 A:HIS226 3.5 4.1 1.0 CB A:SER233 3.6 22.0 1.0 NE2 A:HIS226 3.6 15.1 1.0 CAH A:OAN646 3.7 11.6 1.0 CE A:MET322 3.7 9.0 1.0 HE2 A:MET322 3.7 10.7 1.0 CA A:ALA269 3.8 11.3 1.0 CG A:ASP318 3.8 3.7 1.0 CB A:HIS270 3.8 10.0 1.0 HB3 A:SER233 3.8 26.3 1.0 HB3 A:ASP318 3.9 9.5 1.0 HD2 A:HIS270 3.9 16.2 1.0 HB1 A:ALA269 3.9 7.6 1.0 CG A:HIS270 3.9 7.0 1.0 HG23 A:VAL271 3.9 12.3 1.0 C A:ALA269 3.9 13.3 1.0 HB2 A:ASP318 3.9 9.5 1.0 CD2 A:HIS270 4.0 13.6 1.0 CA A:HIS270 4.0 8.9 1.0 CB A:ASP318 4.1 8.0 1.0 CB A:ALA269 4.3 6.4 1.0 SD A:MET322 4.5 16.4 1.0 HE3 A:MET322 4.5 10.7 1.0 HB3 A:HIS222 4.5 22.0 1.0 C A:HIS270 4.5 9.0 1.0 HD2 A:HIS222 4.5 20.1 1.0 HB2 A:ALA269 4.6 7.6 1.0 NAI A:OAN646 4.6 7.7 1.0 O A:HIS270 4.6 11.7 1.0 O A:THR268 4.6 11.3 1.0 CAG A:OAN646 4.7 15.5 1.0 HB3 A:HIS270 4.7 12.0 1.0 CG2 A:VAL271 4.8 10.3 1.0 ND1 A:HIS270 4.8 7.1 1.0 CD2 A:HIS222 4.8 16.8 1.0 CG A:HIS226 4.8 15.5 1.0 OD1 A:ASP318 4.8 7.4 1.0 NE2 A:HIS270 4.9 10.8 1.0 HA A:HIS270 4.9 10.6 1.0 HB2 A:HIS222 4.9 22.0 1.0 N A:ALA269 4.9 10.9 1.0 CE1 A:HIS226 4.9 15.9 1.0 HG22 A:VAL271 4.9 12.3 1.0 CA A:SER233 5.0 21.4 1.0 HG21 A:VAL271 5.0 12.3 1.0 CG A:HIS222 5.0 16.1 1.0

Sodium binding site 2 out of 2 in the Structure of Ybbd in Complex with Pugnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Ybbd in Complex with Pugnac within 5.0Å range: probe atom residue distance (Å) B Occ B:Na643 b:19.5 occ:1.00 H B:HIS270 2.3 7.9 1.0 HG B:SER233 2.4 25.6 1.0 HA B:ALA269 2.6 18.8 1.0 HD2 B:HIS226 2.8 14.6 1.0 OD2 B:ASP318 2.8 11.1 1.0 N B:HIS270 3.0 6.6 1.0 OG B:SER233 3.2 21.4 1.0 HB2 B:SER233 3.4 14.8 1.0 CD2 B:HIS226 3.4 12.2 1.0 CA B:ALA269 3.4 15.7 1.0 HB1 B:ALA269 3.5 10.0 1.0 HB3 B:SER233 3.6 14.8 1.0 NE2 B:HIS226 3.6 18.7 1.0 HB2 B:HIS270 3.6 17.0 1.0 CB B:SER233 3.6 12.4 1.0 HD2 B:HIS270 3.6 14.3 1.0 HE1 B:MET322 3.7 15.2 1.0 C B:ALA269 3.7 10.5 1.0 CG B:ASP318 3.8 10.0 1.0 CD2 B:HIS270 3.8 12.0 1.0 HG23 B:VAL271 3.8 12.6 1.0 HB3 B:ASP318 3.9 14.3 1.0 HB2 B:ASP318 3.9 14.3 1.0 CAH B:OAN646 3.9 11.9 1.0 CG B:HIS270 3.9 14.7 1.0 CA B:HIS270 3.9 14.0 1.0 CB B:HIS270 4.0 14.2 1.0 CB B:ALA269 4.0 8.4 1.0 CB B:ASP318 4.1 12.0 1.0 HB2 B:ALA269 4.3 10.0 1.0 HB3 B:HIS222 4.3 13.0 1.0 C B:HIS270 4.3 16.0 1.0 CE B:MET322 4.4 12.8 1.0 HE2 B:MET322 4.4 15.2 1.0 O B:THR268 4.5 17.6 1.0 O B:HIS270 4.5 15.6 1.0 HD2 B:HIS222 4.6 10.1 1.0 NE2 B:HIS270 4.6 16.5 1.0 N B:ALA269 4.6 22.7 1.0 CG2 B:VAL271 4.6 10.6 1.0 CG B:HIS226 4.7 7.2 1.0 SD B:MET322 4.7 20.8 1.0 ND1 B:HIS270 4.8 18.2 1.0 HA B:HIS270 4.8 16.7 1.0 CD2 B:HIS222 4.8 8.4 1.0 NAI B:OAN646 4.8 12.9 1.0 HG21 B:VAL271 4.8 12.6 1.0 HB3 B:ALA269 4.8 10.0 1.0 HG22 B:VAL271 4.9 12.6 1.0 OD1 B:ASP318 4.9 12.6 1.0 O B:ALA269 4.9 8.7 1.0 CAG B:OAN646 4.9 11.9 1.0 CE1 B:HIS226 4.9 15.0 1.0 HB3 B:HIS270 4.9 17.0 1.0 CB B:HIS222 5.0 10.9 1.0 C B:THR268 5.0 18.1 1.0 CG B:HIS222 5.0 10.3 1.0

S.Litzinger, S.Fischer, P.Polzer, K.Diederichs, W.Welte, C.Mayer. Structural and Kinetic Analysis of Bacillus Subtilis N-Acetylglucosaminidase Reveals A Unique Asp-His Dyad Mechanism J.Biol.Chem. V. 285 35675 2010.
ISSN: ISSN 0021-9258
PubMed: 20826810
DOI: 10.1074/JBC.M110.131037