Sodium in PDB 4q05: Crystal Structure of An Esterase E25

The structure of Crystal Structure of An Esterase E25, PDB code: 4q05 was solved by P.Y.Li, C.Y.Li, Y.Z.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.81 / 2.05
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	138.796, 138.796, 49.247, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 19

The binding sites of Sodium atom in the Crystal Structure of An Esterase E25 (pdb code 4q05). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of An Esterase E25, PDB code: 4q05:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of An Esterase E25


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 An Esterase E25 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:30.3 occ:1.00 ND1 A:HIS292 2.8 23.1 1.0 O B:VAL306 2.9 19.8 1.0 N B:VAL306 2.9 20.4 1.0 CD2 A:LEU304 3.3 22.6 1.0 CG1 A:ILE293 3.5 22.1 1.0 CD1 A:ILE293 3.5 24.3 1.0 O A:VAL289 3.5 23.0 1.0 C B:VAL306 3.6 24.7 1.0 CA B:VAL306 3.6 19.2 1.0 CG A:HIS292 3.6 20.8 1.0 CE1 A:HIS292 3.7 23.4 1.0 CB A:VAL289 3.7 21.3 1.0 CB B:VAL306 3.7 23.2 1.0 CB A:HIS292 3.8 19.6 1.0 CA A:VAL289 3.9 23.3 1.0 C B:PHE305 3.9 22.5 1.0 CA B:PHE305 4.0 24.2 1.0 C A:VAL289 4.1 20.8 1.0 CG1 A:VAL289 4.2 22.4 1.0 N A:ILE293 4.4 19.6 1.0 CG2 B:VAL306 4.4 19.7 1.0 CG A:LEU304 4.5 22.6 1.0 O B:LEU304 4.6 23.2 1.0 CB A:ILE293 4.7 20.7 1.0 CB A:LEU304 4.7 19.0 1.0 CD2 A:HIS292 4.7 18.8 1.0 NE2 A:HIS292 4.7 21.0 1.0 C A:HIS292 4.8 21.6 1.0 N B:TYR307 4.8 22.6 1.0 CA A:ILE293 4.8 22.2 1.0 CG2 A:VAL289 4.9 21.0 1.0 CA A:HIS292 4.9 22.3 1.0 CB B:PHE305 4.9 21.9 1.0 CG1 B:VAL306 5.0 20.8 1.0 N B:PHE305 5.0 19.8 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of An Esterase E25


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 An Esterase E25 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:31.1 occ:1.00 ND1 B:HIS292 2.7 24.4 1.0 O A:VAL306 2.9 19.6 1.0 N A:VAL306 2.9 21.7 1.0 CD2 B:LEU304 3.4 22.0 1.0 CD1 B:ILE293 3.4 23.0 1.0 CG1 B:ILE293 3.5 21.7 1.0 O B:VAL289 3.5 24.4 1.0 CG B:HIS292 3.6 23.1 1.0 C A:VAL306 3.6 21.1 1.0 CA A:VAL306 3.6 20.0 1.0 CE1 B:HIS292 3.7 24.6 1.0 CB B:VAL289 3.7 20.7 1.0 CB B:HIS292 3.8 20.3 1.0 CB A:VAL306 3.8 22.5 1.0 CA B:VAL289 3.9 21.9 1.0 C A:PHE305 3.9 21.3 1.0 CA A:PHE305 4.0 23.7 1.0 C B:VAL289 4.1 22.2 1.0 CG1 B:VAL289 4.3 22.5 1.0 N B:ILE293 4.3 19.1 1.0 CG2 A:VAL306 4.5 20.2 1.0 CG B:LEU304 4.6 24.9 1.0 O A:LEU304 4.6 21.7 1.0 CB B:ILE293 4.7 20.3 1.0 CD2 B:HIS292 4.7 19.6 1.0 NE2 B:HIS292 4.7 22.6 1.0 C B:HIS292 4.8 20.9 1.0 CB B:LEU304 4.8 19.6 1.0 CA B:ILE293 4.8 22.5 1.0 CA B:HIS292 4.8 19.7 1.0 N A:TYR307 4.9 20.1 1.0 CG2 B:VAL289 4.9 19.5 1.0 CB A:PHE305 4.9 20.6 1.0 O A:HOH536 4.9 25.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of An Esterase E25


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of An Esterase E25 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:32.8 occ:1.00 NE2 B:HIS117 2.7 23.9 1.0 O B:TYR149 2.7 27.6 1.0 OD1 B:ASP148 2.8 29.4 1.0 N B:TYR149 3.2 24.8 1.0 C B:ASP148 3.4 26.7 1.0 CD2 B:HIS117 3.6 26.4 1.0 O B:HOH518 3.6 24.6 1.0 CA B:ASP148 3.6 24.8 1.0 CE B:MET151 3.6 25.1 1.0 C B:TYR149 3.7 26.6 1.0 CE1 B:HIS117 3.7 29.0 1.0 CA B:GLY125 3.8 27.2 1.0 CG B:ASP148 3.9 28.2 1.0 CA B:TYR149 3.9 23.0 1.0 CD1 B:TYR149 4.0 23.1 1.0 O B:ASP148 4.0 27.2 1.0 O B:HOH706 4.1 42.5 1.0 SD B:MET151 4.1 25.9 1.0 CG B:TYR149 4.1 25.4 1.0 CE1 B:TYR149 4.2 26.8 1.0 CG B:MET151 4.2 27.7 1.0 CB B:ASP148 4.3 23.5 1.0 O B:ASN124 4.3 26.1 1.0 N B:GLY126 4.4 30.6 1.0 O B:ILE147 4.4 23.1 1.0 CD2 B:TYR149 4.4 24.0 1.0 CZ B:TYR149 4.5 25.4 1.0 N B:GLY125 4.6 28.7 1.0 C B:GLY125 4.6 33.8 1.0 CB B:TYR149 4.6 22.1 1.0 CE2 B:TYR149 4.7 25.2 1.0 CG B:HIS117 4.8 24.6 1.0 C B:ASN124 4.8 25.7 1.0 ND1 B:HIS117 4.8 25.1 1.0 N B:ASP148 4.8 23.9 1.0 N B:ARG150 4.9 25.8 1.0 OD2 B:ASP148 4.9 29.9 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of An Esterase E25


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of An Esterase E25 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:35.3 occ:1.00 O B:LEU123 2.8 27.4 1.0 O B:HOH555 2.8 33.0 1.0 O B:GLY118 3.0 25.2 1.0 N B:PHE121 3.2 22.6 1.0 N B:LEU123 3.2 25.5 1.0 C B:GLY119 3.3 33.6 1.0 O B:GLY119 3.4 31.6 1.0 N B:VAL122 3.4 26.4 1.0 CA B:PHE121 3.6 28.6 1.0 C B:LEU123 3.6 27.2 1.0 CE1 B:HIS117 3.6 29.0 1.0 C B:PHE121 3.6 26.8 1.0 CA B:GLY119 3.6 32.0 1.0 SD B:MET151 3.7 25.9 1.0 CA B:LEU123 3.8 27.3 1.0 C B:GLY118 3.8 29.6 1.0 N B:ALA120 3.8 26.2 1.0 ND1 B:HIS117 3.9 25.1 1.0 C B:ALA120 3.9 26.9 1.0 C B:VAL122 4.0 29.1 1.0 N B:GLY119 4.2 31.6 1.0 CB B:LEU123 4.2 27.5 1.0 OH B:TYR149 4.2 27.3 1.0 CA B:VAL122 4.2 25.9 1.0 O B:PHE121 4.4 25.8 1.0 CA B:ALA120 4.4 30.0 1.0 O B:ALA120 4.6 26.8 1.0 N B:ASN124 4.8 28.1 1.0 NE2 B:HIS117 4.8 23.9 1.0 O B:HIS117 4.9 25.1 1.0 CE B:MET151 4.9 25.1 1.0 O B:HOH564 4.9 30.8 1.0 CB B:ASN124 4.9 26.4 1.0 ND2 B:ASN124 4.9 29.1 1.0 O B:VAL122 4.9 27.6 1.0 CA B:GLY118 5.0 29.4 1.0

P.Y.Li, P.Ji, C.Y.Li, Y.Zhang, G.L.Wang, X.Y.Zhang, B.B.Xie, Q.L.Qin, X.L.Chen, B.C.Zhou, Y.Z.Zhang. Structural Basis For Dimerization and Catalysis of A Novel Esterase From the Gtsag Motif Subfamily of the Bacterial Hormone-Sensitive Lipase Family J.Biol.Chem. V. 289 19031 2014.
ISSN: ISSN 0021-9258
PubMed: 24867954
DOI: 10.1074/JBC.M114.574913