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Potassium in PDB 6r34: Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Phenyl Acetylene (INT3')

Enzymatic activity of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Phenyl Acetylene (INT3')

All present enzymatic activity of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Phenyl Acetylene (INT3'):
4.1.1.102;

Protein crystallography data

The structure of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Phenyl Acetylene (INT3'), PDB code: 6r34 was solved by S.S.Bailey, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.51 / 1.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.000, 63.960, 87.720, 90.00, 90.00, 90.00
R / Rfree (%) 11.6 / 14.1

Other elements in 6r34:

The structure of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Phenyl Acetylene (INT3') also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Phenyl Acetylene (INT3') (pdb code 6r34). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Phenyl Acetylene (INT3'), PDB code: 6r34:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6r34

Go back to Potassium Binding Sites List in 6r34
Potassium binding site 1 out of 2 in the Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Phenyl Acetylene (INT3')


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Phenyl Acetylene (INT3') within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:7.9
occ:1.00
 OE2 A:GLU233 2.8 7.3 1.0
O A:MET225 2.8 7.5 1.0
O A:ALA222 2.8 7.3 1.0
O5 A:JQH604 2.9 6.9 1.0
O3 A:JQH604 3.0 6.7 1.0
O A:TRP169 3.1 6.8 1.0
O A:SER223 3.1 8.6 1.0
O A:HOH746 3.3 7.2 1.0
P1 A:JQH604 3.4 6.7 1.0
C A:SER223 3.5 7.1 1.0
O6 A:JQH604 3.6 7.0 1.0
CD A:GLU233 3.6 7.1 1.0
MN A:MN601 3.7 7.4 1.0
CA A:SER223 3.7 6.5 1.0
CG A:GLU233 3.8 7.3 1.0
C A:ALA222 3.9 6.9 1.0
C A:MET225 3.9 7.3 1.0
N A:MET225 4.1 7.2 1.0
C30 A:JQH604 4.2 7.2 1.0
N A:SER223 4.3 7.0 1.0
C A:TRP169 4.3 6.5 1.0
C21 A:JQH604 4.3 6.7 1.0
O9 A:JQH604 4.3 7.8 1.0
N A:SER224 4.4 6.6 0.5
CB A:SER170 4.4 7.2 1.0
N A:SER224 4.4 6.8 0.5
CA A:SER170 4.5 6.6 1.0
CA A:MET225 4.6 7.5 1.0
OE1 A:GLU233 4.7 7.6 1.0
C A:SER224 4.8 7.2 0.5
ND2 A:ASN168 4.8 7.6 1.0
O4 A:JQH604 4.8 7.2 1.0
C A:SER224 4.9 7.1 0.5
CG1 A:ILE227 4.9 9.1 1.0
N A:SER170 4.9 6.6 1.0
N A:ILE227 4.9 7.3 1.0
N A:PRO226 4.9 7.1 1.0
CA A:SER224 5.0 6.8 0.5
CB A:SER223 5.0 6.8 1.0

Potassium binding site 2 out of 2 in 6r34

Go back to Potassium Binding Sites List in 6r34
Potassium binding site 2 out of 2 in the Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Phenyl Acetylene (INT3')


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Phenyl Acetylene (INT3') within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:7.9
occ:1.00
 O A:ARG421 2.7 8.0 1.0
O A:LEU461 2.7 9.4 1.0
O A:ASP459 2.7 7.8 1.0
OD2 A:ASP427 2.8 8.5 1.0
CG A:ASP427 3.4 8.5 1.0
C A:LEU461 3.7 7.8 1.0
C A:ASP459 3.7 7.2 1.0
C A:ARG421 3.8 7.1 1.0
CB A:ASP427 3.9 7.5 1.0
OD1 A:ASP427 4.1 9.7 1.0
CA A:CYS422 4.1 7.1 1.0
N A:LEU461 4.2 7.6 1.0
CA A:ALA460 4.3 6.9 1.0
C A:ALA460 4.4 6.9 1.0
N A:CYS422 4.4 7.0 1.0
N A:ALA460 4.4 7.1 1.0
CG A:ASP459 4.5 9.7 1.0
CB A:ASP459 4.5 8.0 1.0
CA A:LEU461 4.6 7.3 1.0
N A:MET462 4.6 8.2 1.0
CA A:MET462 4.7 8.2 1.0
N A:ARG423 4.7 6.7 1.0
OD1 A:ASP459 4.7 9.6 1.0
CA A:ASP459 4.8 7.2 1.0
OD2 A:ASP459 4.8 13.6 1.0
CA A:ARG421 5.0 7.0 1.0
CB A:CYS422 5.0 7.6 1.0

Reference:

S.S.Bailey, K.A.P.Payne, A.Saaret, S.A.Marshall, I.Gostimskaya, I.Kosov, K.Fisher, S.Hay, D.Leys. Atomic Description of An Enzyme Reaction Dependent on Reversible 1,3-Dipolar Cycloaddition To Be Published.
Page generated: Sat Aug 9 12:00:42 2025

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