Sodium in PDB 3qm1: Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II

The structure of Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II, PDB code: 3qm1 was solved by P.J.Stogios, K.K.Lai, C.Vu, X.Xu, H.Cui, S.Molloy, C.F.Gonzalez, A.Yakunin, A.Savchenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.07 / 1.82
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.872, 85.396, 81.142, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 19

The structure of Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II also contains other interesting chemical elements:

Chlorine

(Cl)

19 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II (pdb code 3qm1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 42 binding sites of Sodium where determined in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II, PDB code: 3qm1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 42 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II


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 the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Na246 b:29.5 occ:1.00 O A:HOH439 2.7 33.3 1.0 O A:HOH469 3.0 22.1 1.0 N A:GLU73 3.1 19.2 1.0 N A:PHE72 3.3 17.2 1.0 CB A:GLU73 3.5 18.9 1.0 CB A:LYS71 3.6 21.2 0.2 CB A:LYS71 3.6 21.1 0.8 NZ A:LYS71 3.7 32.2 0.2 CA A:GLU73 3.8 18.9 1.0 C A:LYS71 3.9 20.3 1.0 CA A:PHE72 3.9 18.9 1.0 CB A:PHE72 3.9 21.8 1.0 C A:PHE72 4.0 19.5 1.0 CA A:LYS71 4.0 19.7 0.8 CA A:LYS71 4.0 20.5 0.2 CG A:LYS71 4.2 24.0 0.8 CD A:LYS71 4.4 30.8 0.8 O A:THR164 4.6 19.8 1.0 OE1 A:GLU73 4.6 34.2 1.0 O A:HOH471 4.6 48.6 1.0 CG A:LYS71 4.6 23.5 0.2 CE A:LYS71 4.7 33.9 0.8 O A:LYS71 4.8 20.0 1.0 CG A:GLU73 4.8 24.6 1.0 O A:HOH386 4.9 34.0 1.0 CE A:LYS71 4.9 31.1 0.2 CD A:LYS71 4.9 27.7 0.2

Sodium binding site 2 out of 42 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II


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 the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Na247 b:59.7 occ:1.00 O A:HOH361 3.4 37.4 1.0 O A:HOH468 3.6 49.3 1.0 O A:ASP9 3.7 27.6 1.0 CB A:GLU7 4.2 25.8 1.0 N A:ASP9 4.3 18.6 1.0 O A:GLU7 4.5 22.4 1.0 O A:HOH364 4.5 29.0 1.0 C A:GLU7 4.7 22.1 1.0 C A:ASP9 4.7 26.5 1.0 CA A:ASP9 4.8 20.1 1.0 N A:ARG8 4.9 19.1 1.0 C A:ARG8 5.0 16.7 1.0

Sodium binding site 3 out of 42 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II


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 the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Na248 b:41.9 occ:1.00 N A:GLU23 3.1 24.5 1.0 CB A:GLU23 3.7 32.5 1.0 CA A:GLY22 3.8 26.6 1.0 CD2 A:LEU-4 3.8 32.5 1.0 C A:GLY22 3.9 25.6 1.0 CA A:GLU23 4.0 25.9 1.0 N A:ILE24 4.7 22.7 1.0 CG A:LEU-4 4.8 31.7 1.0 O A:HOH435 4.8 40.5 1.0 C A:GLU23 4.9 23.2 1.0 OE1 A:GLU23 5.0 42.6 1.0

Sodium binding site 4 out of 42 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II


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 the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Na249 b:48.4 occ:1.00 O A:HOH352 3.1 24.1 1.0 CB A:GLN145 3.9 29.1 1.0 CA A:GLN145 3.9 29.1 1.0 O A:THR198 4.0 24.9 1.0 CG A:GLN145 4.0 28.8 1.0 CA A:VAL199 4.2 20.0 1.0 CG2 A:VAL199 4.2 23.1 1.0 NE2 A:GLN145 4.3 27.5 1.0 CD A:GLN145 4.4 29.7 1.0 C A:GLN145 4.5 32.2 1.0 CG1 A:VAL199 4.5 19.8 1.0 CB A:VAL199 4.6 19.5 1.0 O A:GLN145 4.7 34.1 1.0 C A:THR198 4.7 23.8 1.0 N A:VAL199 4.9 20.6 1.0 NA A:NA283 4.9 61.9 1.0 O A:HOH366 5.0 25.7 1.0

Sodium binding site 5 out of 42 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Na250 b:54.7 occ:1.00 O A:HOH423 2.8 40.8 1.0 O A:HOH476 3.1 28.9 1.0 O A:HOH407 3.2 28.0 1.0 NE2 A:GLN175 3.6 15.5 1.0 CD A:GLN175 3.8 15.5 1.0 CG A:GLN175 4.0 12.7 1.0 OE1 A:GLN174 4.3 15.6 1.0 CD2 A:LEU140 4.4 14.9 1.0 O A:HOH335 4.4 15.6 1.0 OE1 A:GLN175 4.5 17.4 1.0 O A:HOH336 4.5 24.2 1.0 O A:HOH406 4.8 36.7 1.0 CB A:GLN174 4.9 12.0 1.0

Sodium binding site 6 out of 42 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Na251 b:55.9 occ:1.00 O A:LEU217 3.2 17.6 1.0 NE2 A:HIS218 3.8 20.9 1.0 CD2 A:HIS218 3.9 18.2 1.0 CG2 A:THR216 4.0 20.3 1.0 C A:LEU217 4.3 18.5 1.0 O A:HOH426 4.4 33.1 1.0 CE1 A:HIS218 4.5 17.7 1.0 NA A:NA281 4.5 59.2 1.0 CG A:HIS218 4.6 19.7 1.0 N A:LEU217 4.8 17.2 1.0 ND1 A:HIS218 4.9 20.8 1.0

Sodium binding site 7 out of 42 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Na252 b:48.7 occ:1.00 N A:GLU221 3.0 21.2 1.0 O A:LEU219 3.3 23.2 1.0 O A:HOH442 3.5 43.7 1.0 CB A:GLU221 3.6 28.9 1.0 CA A:ILE220 3.7 20.8 1.0 C A:ILE220 3.8 20.2 1.0 CA A:GLU221 3.9 24.5 1.0 C A:LEU219 4.3 21.6 1.0 N A:ILE220 4.5 21.0 1.0 CG2 A:ILE220 4.5 20.1 1.0 CD1 A:ILE220 4.6 21.1 1.0 CB A:ILE220 4.7 20.1 1.0 O A:GLU221 4.9 25.5 1.0 C A:GLU221 4.9 25.0 1.0 CG A:GLU221 4.9 38.1 1.0 O A:ILE220 5.0 17.4 1.0

Sodium binding site 8 out of 42 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Na253 b:30.1 occ:1.00 O A:HOH362 2.8 23.7 1.0 O A:GLN175 2.8 14.4 1.0 O A:HOH344 2.9 17.0 1.0 O A:HOH365 3.6 36.6 1.0 C A:GLN175 3.7 13.9 1.0 CB A:GLN175 3.9 13.1 1.0 CA A:GLN175 4.1 12.8 1.0 OE1 A:GLN175 4.6 17.4 1.0 CD A:PRO177 4.6 11.2 1.0 CB A:PRO177 4.7 10.1 1.0 N A:PRO177 4.7 11.5 1.0 CG A:GLN175 4.8 12.7 1.0 N A:LEU176 4.9 12.9 1.0 C A:LEU176 4.9 9.4 1.0 CG A:PRO177 4.9 14.5 1.0

Sodium binding site 9 out of 42 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Na254 b:58.3 occ:1.00 O A:HOH370 3.0 28.4 1.0 CD2 A:LEU140 3.9 14.9 1.0 CB A:LEU140 4.2 17.9 1.0 CG A:LEU140 4.4 15.9 1.0 O A:LEU140 4.5 18.6 1.0 CD1 A:LEU140 4.6 15.5 1.0 O A:HOH443 4.6 43.4 1.0 O A:HOH427 4.7 41.0 1.0

Sodium binding site 10 out of 42 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ethylferulate, Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Na255 b:46.0 occ:1.00 O A:ASP67 2.8 23.4 1.0 OD1 A:ASP69 2.8 28.1 1.0 OE1 A:GLN12 3.1 35.8 1.0 CG A:ASP69 3.6 27.4 1.0 N A:ASP69 3.6 17.9 1.0 CG2 A:VAL14 3.7 23.2 1.0 CG A:GLN12 3.7 29.6 1.0 C A:SER68 3.8 18.5 1.0 CA A:SER68 3.8 18.4 1.0 CD A:GLN12 3.8 34.8 1.0 O A:GLN12 3.8 21.0 1.0 CB A:GLN12 3.9 25.1 1.0 C A:ASP67 3.9 24.8 1.0 OD2 A:ASP69 4.1 26.8 1.0 CA A:ASP69 4.3 21.8 1.0 N A:SER68 4.3 19.6 1.0 CB A:ASP69 4.4 24.0 1.0 C A:GLN12 4.4 19.6 1.0 O A:SER68 4.5 20.8 1.0 CA A:GLN12 4.7 19.7 1.0 O A:HOH418 4.8 46.8 1.0

K.K.Lai, P.J.Stogios, C.Vu, X.Xu, H.Cui, S.Molloy, A.Savchenko, A.Yakunin, C.F.Gonzalez. An Inserted Alpha/Beta Subdomain Shapes the Catalytic Pocket of Lactobacillus Johnsonii Cinnamoyl Esterase Plos One V. 6 23269 2011.
ISSN: ESSN 1932-6203
PubMed: 21876742
DOI: 10.1371/JOURNAL.PONE.0023269