Sodium in PDB 2dsn: Crystal Structure of T1 Lipase

All present enzymatic activity of Crystal Structure of T1 Lipase:
3.1.1.3;

The structure of Crystal Structure of T1 Lipase, PDB code: 2dsn was solved by H.Matsumura, Y.Kai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.33 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.731, 81.270, 99.912, 90.00, 97.09, 90.00
R / Rfree (%)	17.4 / 18.8

The structure of Crystal Structure of T1 Lipase also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Calcium	(Ca)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of T1 Lipase (pdb code 2dsn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of T1 Lipase, PDB code: 2dsn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of T1 Lipase


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 T1 Lipase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2101 b:19.8 occ:0.58 O A:HOH2202 2.6 32.0 1.0 OG A:SER113 2.7 17.8 1.0 NE2 A:HIS358 2.8 14.0 1.0 CZ A:PHE16 3.1 18.4 1.0 CE2 A:PHE16 3.2 19.5 1.0 CB A:SER113 3.3 12.9 1.0 CE1 A:PHE16 3.4 18.6 1.0 CD2 A:HIS358 3.4 12.6 1.0 CD2 A:PHE16 3.5 19.0 1.0 CD1 A:PHE16 3.7 17.1 1.0 CG A:PHE16 3.7 15.7 1.0 CE1 A:HIS358 4.0 13.9 1.0 N A:PHE16 4.1 9.4 1.0 CE1 A:HIS112 4.6 11.5 1.0 CA A:SER113 4.7 11.4 1.0 CG A:HIS358 4.7 12.1 1.0 N A:THR17 4.7 13.3 1.0 CG2 A:ILE319 4.8 13.4 1.0 CB A:PHE16 4.8 12.8 1.0 OG1 A:THR17 4.9 25.1 1.0 CA A:PHE16 4.9 11.1 1.0 CA A:GLY15 4.9 9.3 1.0 OH A:TYR29 4.9 12.0 1.0 ND1 A:HIS358 5.0 13.0 1.0 C A:GLY15 5.0 8.8 1.0 ND1 A:HIS112 5.0 10.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of T1 Lipase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of T1 Lipase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2102 b:19.8 occ:0.48 OG B:SER113 2.6 18.6 1.0 O B:HOH2203 2.7 29.6 1.0 NE2 B:HIS358 2.8 12.0 1.0 CZ B:PHE16 2.9 23.7 1.0 CE2 B:PHE16 3.0 23.5 1.0 CE1 B:PHE16 3.2 22.9 1.0 CB B:SER113 3.3 14.3 1.0 CD2 B:PHE16 3.3 21.5 1.0 CD2 B:HIS358 3.4 11.8 1.0 CD1 B:PHE16 3.6 19.3 1.0 CG B:PHE16 3.6 17.6 1.0 CE1 B:HIS358 4.0 13.9 1.0 N B:PHE16 4.2 12.4 1.0 CE1 B:HIS112 4.7 13.0 1.0 CG B:HIS358 4.7 12.4 1.0 CG2 B:ILE319 4.7 12.9 1.0 CA B:SER113 4.7 12.4 1.0 CB B:PHE16 4.8 15.0 1.0 CA B:PHE16 4.9 12.6 1.0 CA B:GLY15 4.9 12.2 1.0 ND1 B:HIS358 4.9 11.1 1.0 OH B:TYR29 5.0 13.4 1.0

H.Matsumura, T.Yamamoto, T.C.Leow, T.Mori, A.B.Salleh, M.Basri, T.Inoue, Y.Kai, R.N.Z.R.A.Rahman. Novel Cation-Pi Interaction Revealed By Crystal Structure of Thermoalkalophilic Lipase Proteins V. 70 592 2007.
ISSN: ISSN 0887-3585
PubMed: 17932933
DOI: 10.1002/PROT.21799