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Sodium in PDB 3pfc: Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ferulic Acid

Protein crystallography data

The structure of Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ferulic Acid, PDB code: 3pfc 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) 17.65 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 72.046, 85.402, 80.981, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 17.9

Other elements in 3pfc:

The structure of Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ferulic Acid also contains other interesting chemical elements:

Chlorine (Cl) 11 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ferulic Acid (pdb code 3pfc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ferulic Acid, PDB code: 3pfc:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3pfc

Go back to Sodium Binding Sites List in 3pfc
Sodium binding site 1 out of 3 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ferulic Acid


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 Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na251

b:21.6
occ:1.00
O A:HOH358 3.1 43.8 1.0
OG1 A:THR198 3.1 31.3 1.0
N A:HIS225 3.3 21.1 1.0
N A:THR198 3.3 24.5 1.0
CB A:HIS225 3.6 20.7 1.0
CB A:ASP224 3.6 26.9 1.0
O A:ASP196 3.8 25.0 1.0
CB A:THR198 4.0 32.8 1.0
CA A:ASP224 4.0 23.0 1.0
CA A:ASP197 4.0 23.1 1.0
CA A:HIS225 4.1 19.5 1.0
C A:ASP224 4.1 21.5 1.0
CA A:THR198 4.1 24.5 0.8
C A:ASP197 4.2 25.6 1.0
CG2 A:VAL199 4.2 22.4 1.0
CG2 A:THR198 4.2 36.4 1.0
OD1 A:ASP197 4.3 22.6 1.0
N A:VAL199 4.3 21.1 1.0
C A:THR198 4.6 23.5 1.0
CG A:ASP224 4.7 33.6 1.0
C A:ASP196 4.8 27.1 1.0
CG A:ASP197 4.8 22.6 1.0
N A:ASP197 4.9 23.8 1.0
CG A:HIS225 4.9 19.5 1.0
OD2 A:ASP224 4.9 42.0 1.0

Sodium binding site 2 out of 3 in 3pfc

Go back to Sodium Binding Sites List in 3pfc
Sodium binding site 2 out of 3 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ferulic Acid


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 Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na252

b:54.7
occ:1.00
O A:HOH478 3.6 49.3 1.0
CE A:LYS206 3.7 33.8 1.0
CD1 A:LEU219 3.8 33.8 1.0
CD2 A:LEU217 3.9 28.4 1.0
CG A:LYS206 4.1 26.0 1.0
CD A:LYS206 4.2 30.2 1.0
NZ A:LYS206 4.4 37.3 1.0
O A:HOH363 4.9 45.3 1.0
CG A:LEU219 5.0 24.7 1.0

Sodium binding site 3 out of 3 in 3pfc

Go back to Sodium Binding Sites List in 3pfc
Sodium binding site 3 out of 3 in the Crystal Structure of the Lactobacillus Johnsonii Cinnamoyl Esterase LJ0536 S106A Mutant in Complex with Ferulic Acid


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 Ferulic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na253

b:65.9
occ:1.00
O A:HOH364 2.9 44.8 1.0
O A:ARG98 3.4 22.1 1.0
C A:ARG98 3.9 20.5 1.0
CA A:ARG98 4.1 21.0 1.0
CG A:ARG98 4.1 28.1 1.0
O A:HOH349 4.5 33.5 1.0
CB A:ARG98 4.7 21.3 1.0
O A:VAL97 4.8 23.7 1.0
OD1 A:ASN99 4.8 23.3 1.0
N A:ASN99 5.0 18.1 1.0

Reference:

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
Page generated: Tue Dec 15 06:21:05 2020

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