Sodium in PDB 3umj: Crystal Structure of D311E Lipase

All present enzymatic activity of Crystal Structure of D311E Lipase:
3.1.1.3;

The structure of Crystal Structure of D311E Lipase, PDB code: 3umj was solved by R.Ruslan, R.N.Z.R.A.Rahman, T.C.Leow, M.S.M.Ali, M.Basri, A.B.Salleh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.17 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.323, 81.162, 100.140, 90.00, 96.49, 90.00
R / Rfree (%)	15.5 / 21.2

The structure of Crystal Structure of D311E 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 D311E Lipase (pdb code 3umj). 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 D311E Lipase, PDB code: 3umj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of D311E 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 D311E Lipase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na904 b:26.2 occ:1.00 OH A:TYR29 2.9 4.3 1.0 N A:THR17 3.1 6.1 1.0 OG1 A:THR17 3.3 6.1 1.0 N A:PHE16 3.4 6.7 1.0 O A:THR17 3.5 3.9 1.0 CA A:GLY15 3.6 6.0 1.0 C A:GLY15 3.7 7.0 1.0 OG A:SER113 3.8 11.4 1.0 CZ A:TYR29 3.9 4.5 1.0 N A:GLY15 3.9 5.3 1.0 CB A:SER113 3.9 4.7 1.0 CE2 A:TYR29 3.9 2.0 1.0 CA A:THR17 4.0 5.4 1.0 C A:PHE16 4.1 7.3 1.0 C A:THR17 4.1 5.1 1.0 CB A:THR17 4.2 5.8 1.0 ND1 A:HIS112 4.2 6.1 1.0 CD1 A:PHE16 4.2 11.2 1.0 CA A:PHE16 4.3 6.2 1.0 CE1 A:HIS112 4.4 7.0 1.0 CE1 A:PHE16 4.4 16.9 1.0 CG A:PHE16 4.5 8.0 1.0 CG2 A:THR17 4.5 9.0 1.0 O A:GLY15 4.6 6.3 1.0 NE2 A:HIS358 4.6 4.8 1.0 CZ A:PHE16 4.8 16.6 1.0 CD2 A:PHE16 4.8 13.4 1.0 CE2 A:PHE16 5.0 15.1 1.0 CB A:PHE16 5.0 6.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of D311E 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 D311E Lipase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na904 b:44.2 occ:1.00 O B:HOH550 2.2 10.7 1.0 OG B:SER113 2.4 10.2 1.0 NE2 B:HIS358 3.2 9.5 1.0 CB B:SER113 3.2 7.1 1.0 CZ B:PHE16 3.3 20.6 1.0 CE2 B:PHE16 3.3 16.5 1.0 CE1 B:PHE16 3.4 19.6 1.0 CD2 B:PHE16 3.5 15.9 1.0 CD1 B:PHE16 3.6 14.6 1.0 N B:PHE16 3.6 5.4 1.0 CG B:PHE16 3.6 13.8 1.0 CD2 B:HIS358 3.8 2.4 1.0 N B:THR17 4.2 5.5 1.0 CA B:GLY15 4.3 5.2 1.0 C B:GLY15 4.4 5.0 1.0 CE1 B:HIS358 4.4 8.3 1.0 OH B:TYR29 4.5 4.6 1.0 CA B:PHE16 4.5 7.1 1.0 CB B:PHE16 4.6 7.6 1.0 CA B:SER113 4.7 6.5 1.0 C B:PHE16 4.7 5.9 1.0 CG2 B:THR17 4.7 4.6 1.0 CE1 B:HIS112 4.8 9.1 1.0 N B:GLN114 4.8 6.5 1.0 ND1 B:HIS112 4.9 7.0 1.0

R.Ruslan, R.N.Z.R.A.Rahman, T.C.Leow, M.S.M.Ali, M.Basri, A.B.Salleh. Improvement of Thermal Stability Via Outer-Loop Ion Pair Interaction of Mutated T1 Lipase From Geobacillus Zalihae Strain T1 Int J Mol Sci V. 13 943 2012.
ISSN: ESSN 1422-0067
PubMed: 22312296
DOI: 10.3390/IJMS13010943