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Potassium in PDB 6r3j: Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Crotonic Acid Following Decarboxylation (INT3)

Enzymatic activity of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Crotonic Acid Following Decarboxylation (INT3)

All present enzymatic activity of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Crotonic Acid Following Decarboxylation (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 Crotonic Acid Following Decarboxylation (INT3), PDB code: 6r3j 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) 87.74 / 1.39
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.028, 63.815, 87.742, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 17.8

Other elements in 6r3j:

The structure of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Crotonic Acid Following Decarboxylation (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 Crotonic Acid Following Decarboxylation (INT3) (pdb code 6r3j). 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 Crotonic Acid Following Decarboxylation (INT3), PDB code: 6r3j:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6r3j

Go back to Potassium Binding Sites List in 6r3j
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 Crotonic Acid Following Decarboxylation (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 Crotonic Acid Following Decarboxylation (INT3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1103

b:10.0
occ:1.00
 O A:MET225 2.8 9.0 1.0
O A:ALA222 2.8 9.6 1.0
OE2 A:GLU233 2.8 8.7 1.0
O7 A:JRH1101 2.9 9.4 1.0
O6 A:JRH1101 3.0 10.9 1.0
O A:TRP169 3.1 7.9 1.0
O A:SER223 3.1 9.4 1.0
O A:HOH1226 3.3 9.2 1.0
P1 A:JRH1101 3.4 9.7 1.0
C A:SER223 3.5 7.8 1.0
CD A:GLU233 3.6 8.7 1.0
O9 A:JRH1101 3.7 10.0 1.0
MN A:MN1102 3.7 9.1 1.0
CA A:SER223 3.7 8.3 1.0
CG A:GLU233 3.8 8.9 1.0
C A:ALA222 3.9 7.6 1.0
C A:MET225 3.9 7.9 1.0
N A:MET225 4.1 8.5 1.0
C22 A:JRH1101 4.2 12.9 1.0
N A:SER223 4.3 8.1 1.0
O4 A:JRH1101 4.3 13.1 1.0
C21 A:JRH1101 4.3 11.6 1.0
C A:TRP169 4.3 6.9 1.0
N A:SER224 4.4 7.8 0.5
N A:SER224 4.4 7.7 0.5
CB A:SER170 4.4 9.3 1.0
CA A:SER170 4.5 8.2 1.0
CA A:MET225 4.6 7.1 1.0
OE1 A:GLU233 4.7 9.4 1.0
C A:SER224 4.8 9.2 0.5
C A:SER224 4.8 9.2 0.5
O8 A:JRH1101 4.8 11.9 1.0
CG1 A:ILE227 4.9 11.1 1.0
N A:SER170 4.9 7.3 1.0
ND2 A:ASN168 4.9 8.4 1.0
N A:ILE227 4.9 8.7 1.0
N A:PRO226 4.9 8.7 1.0
CA A:SER224 5.0 7.7 0.5
CB A:SER223 5.0 7.9 1.0

Potassium binding site 2 out of 2 in 6r3j

Go back to Potassium Binding Sites List in 6r3j
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 Crotonic Acid Following Decarboxylation (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 Crotonic Acid Following Decarboxylation (INT3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1104

b:10.2
occ:1.00
 O A:ARG421 2.6 10.4 1.0
O A:LEU461 2.7 12.0 1.0
O A:ASP459 2.7 9.1 1.0
OD2 A:ASP427 2.8 9.3 1.0
CG A:ASP427 3.4 11.5 1.0
C A:LEU461 3.7 8.9 1.0
C A:ASP459 3.8 8.6 1.0
C A:ARG421 3.8 8.6 1.0
CB A:ASP427 3.9 9.4 1.0
CA A:CYS422 4.1 9.0 1.0
OD1 A:ASP427 4.1 11.2 1.0
N A:LEU461 4.2 10.8 1.0
CA A:ALA460 4.3 9.3 1.0
C A:ALA460 4.4 9.8 1.0
N A:CYS422 4.4 7.5 1.0
N A:ALA460 4.5 8.6 1.0
CB A:ASP459 4.5 9.3 1.0
CG A:ASP459 4.5 11.4 1.0
CA A:LEU461 4.6 10.0 1.0
N A:MET462 4.6 10.3 1.0
CA A:MET462 4.7 9.8 1.0
N A:ARG423 4.7 8.2 1.0
OD1 A:ASP459 4.8 11.9 1.0
CA A:ASP459 4.8 9.5 1.0
OD2 A:ASP459 4.8 17.3 1.0
CA A:ARG421 4.9 8.6 1.0
CB A:CYS422 5.0 9.1 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: Mon Aug 12 17:26:32 2024

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