Sodium in PDB 3pf9: Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant

The structure of Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant, PDB code: 3pf9 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)	50.00 / 1.75
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.740, 85.702, 81.889, 90.00, 90.00, 90.00
R / Rfree (%)	14.2 / 19.9

The binding sites of Sodium atom in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant (pdb code 3pf9). 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 the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant, PDB code: 3pf9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na250 b:29.1 occ:1.00 O A:GLY66 2.3 30.6 1.0 O A:HOH293 2.4 37.8 1.0 C A:GLY66 3.4 29.6 1.0 N A:GLY66 3.7 29.3 1.0 CA A:GLY66 3.8 29.7 1.0 O A:HOH524 3.9 52.4 1.0 C A:HIS65 4.2 27.7 1.0 O A:HOH336 4.4 50.9 1.0 O A:HOH414 4.4 37.7 1.0 N A:ASP67 4.5 30.7 1.0 O A:HIS65 4.6 26.4 1.0 CA A:ASP67 5.0 31.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na251 b:37.5 occ:1.00 O A:HOH326 2.7 32.0 1.0 O A:HOH316 2.8 44.6 1.0 CB A:PRO177 3.8 23.7 1.0 O A:HOH290 4.1 39.3 1.0 OE2 A:GLU180 4.4 38.2 1.0 CA A:PRO177 4.4 20.4 0.5 CD A:GLU180 4.5 36.5 1.0 O A:GLN175 4.7 23.4 1.0 OE1 A:GLU180 4.8 32.4 1.0 CG A:PRO177 4.8 23.8 1.0 CG A:GLU180 4.9 32.5 1.0 N A:PRO177 5.0 23.6 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na252 b:55.9 occ:1.00 NA A:NA253 2.3 44.9 1.0 O A:HOH457 2.8 56.9 1.0 O A:HOH366 2.9 51.1 1.0 N A:SER215 3.1 32.4 1.0 O A:HOH297 3.3 45.8 1.0 O A:SER215 3.3 32.7 1.0 O A:GLN213 3.7 33.0 1.0 CA A:ASN214 3.8 32.5 1.0 OG A:SER215 3.8 33.4 1.0 C A:ASN214 3.9 32.6 1.0 C A:GLN213 3.9 30.9 1.0 N A:ASN214 4.0 31.6 1.0 O A:TYR212 4.0 29.8 1.0 CA A:SER215 4.0 31.0 1.0 C A:SER215 4.1 32.1 1.0 O A:HOH435 4.2 47.0 1.0 CB A:SER215 4.5 30.9 1.0 O A:HOH477 4.7 52.1 1.0 O A:ASP209 4.8 29.2 1.0 OD1 A:ASP209 4.9 33.3 1.0 C A:TYR212 4.9 28.2 1.0 CA A:GLN213 5.0 29.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na253 b:44.9 occ:1.00 NA A:NA252 2.3 55.9 1.0 O A:TYR212 2.5 29.8 1.0 OG A:SER215 2.6 33.4 1.0 O A:HOH435 2.7 47.0 1.0 O A:ASP209 2.8 29.2 1.0 O A:HOH297 3.5 45.8 1.0 C A:TYR212 3.6 28.2 1.0 N A:SER215 3.6 32.4 1.0 CB A:SER215 3.8 30.9 1.0 C A:ASP209 3.9 30.8 1.0 OD1 A:ASP209 4.0 33.3 1.0 CB A:TYR212 4.1 26.9 1.0 CA A:SER215 4.1 31.0 1.0 O A:HOH477 4.2 52.1 1.0 O A:SER215 4.2 32.7 1.0 C A:GLN213 4.2 30.9 1.0 N A:ASN214 4.2 31.6 1.0 CA A:TYR212 4.3 27.1 1.0 N A:TYR212 4.4 28.1 1.0 O A:GLN213 4.4 33.0 1.0 N A:GLN213 4.5 27.6 1.0 C A:ASN214 4.5 32.6 1.0 O A:HOH457 4.5 56.9 1.0 O A:HOH366 4.5 51.1 1.0 CA A:ASP209 4.6 29.1 1.0 C A:SER215 4.6 32.1 1.0 CG A:ASP209 4.6 31.2 1.0 CA A:GLN213 4.6 29.2 1.0 CA A:ASN214 4.6 32.5 1.0 O A:GLN210 4.7 37.5 1.0 C A:GLN210 4.9 34.7 1.0 N A:GLN210 5.0 32.3 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