Potassium in PDB 6r3n: Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Butynoic Acid (INT1')

Enzymatic activity of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Butynoic Acid (INT1')

All present enzymatic activity of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Butynoic Acid (INT1'):
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 Butynoic Acid (INT1'), PDB code: 6r3n 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)*	43.86 / 1.02
*Space group*	P 2₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	95.874, 63.892, 87.714, 90.00, 90.00, 90.00
*R / R_free (%)*	13.5 / 14.7

Other elements in 6r3n:

The structure of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Butynoic Acid (INT1') 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 Butynoic Acid (INT1') (pdb code 6r3n). 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 Butynoic Acid (INT1'), PDB code: 6r3n:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6r3n

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Potassium Binding Sites List in 6r3n

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 Butynoic Acid (INT1')

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 Butynoic Acid (INT1') within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:K604 b:7.0 occ:1.00	OE2	A:GLU233	2.8	7.1	1.0
	O9	A:JRK601	2.8	8.0	0.4
	O	A:MET225	2.8	7.0	1.0
	O	A:ALA222	2.8	6.8	1.0
	O9	A:BYN602	2.8	6.4	0.6
	O7	A:BYN602	3.0	7.0	0.6
	O6	A:JRK601	3.1	7.5	0.4
	O	A:TRP169	3.1	6.7	1.0
	O	A:SER223	3.1	7.3	1.0
	O	A:HOH725	3.3	7.3	1.0
	P1	A:BYN602	3.4	6.7	0.6
	P1	A:JRK601	3.4	7.9	0.4
	C	A:SER223	3.5	6.6	1.0
	O8	A:BYN602	3.6	7.2	0.6
	MN	A:MN603	3.6	7.7	1.0
	CD	A:GLU233	3.7	7.0	1.0
	CA	A:SER223	3.7	6.3	1.0
	O7	A:JRK601	3.7	8.1	0.4
	CG	A:GLU233	3.8	7.2	1.0
	C	A:ALA222	3.8	6.3	1.0
	C	A:MET225	3.9	6.5	1.0
	N	A:MET225	4.0	6.5	1.0
	C22	A:BYN602	4.2	7.0	0.6
	N	A:SER223	4.2	6.8	1.0
	C	A:TRP169	4.3	6.6	1.0
	C21	A:BYN602	4.3	6.7	0.6
	O6	A:BYN602	4.3	7.3	0.6
	C17	A:JRK601	4.3	8.1	0.4
	N	A:SER224	4.3	6.5	0.5
	N	A:SER224	4.4	6.3	0.5
	CB	A:SER170	4.4	7.2	1.0
	O5	A:JRK601	4.4	8.7	0.4
	C16	A:JRK601	4.4	7.6	0.4
	CA	A:SER170	4.4	6.8	1.0
	CA	A:MET225	4.5	6.8	1.0
	OE1	A:GLU233	4.7	7.4	1.0
	C	A:SER224	4.8	6.4	0.5
	O10	A:BYN602	4.8	7.1	0.6
	C	A:SER224	4.8	6.6	0.5
	ND2	A:ASN168	4.8	7.2	1.0
	O8	A:JRK601	4.8	8.0	0.4
	N	A:SER170	4.9	6.7	1.0
	CG1	A:ILE227	4.9	8.1	1.0
	N	A:ILE227	4.9	7.1	1.0
	N	A:PRO226	4.9	6.5	1.0
	CA	A:SER224	5.0	6.2	0.5
	CB	A:SER223	5.0	6.7	1.0

Potassium binding site 2 out of 2 in 6r3n

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Potassium Binding Sites List in 6r3n

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 Butynoic Acid (INT1')

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 Butynoic Acid (INT1') within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:K605 b:7.4 occ:1.00	O	A:ARG421	2.7	7.6	1.0
	O	A:LEU461	2.7	8.3	1.0
	O	A:ASP459	2.7	7.2	1.0
	OD2	A:ASP427	2.8	7.9	1.0
	CG	A:ASP427	3.4	7.7	1.0
	C	A:ASP459	3.7	6.9	1.0
	C	A:LEU461	3.8	7.5	1.0
	C	A:ARG421	3.8	6.9	1.0
	CB	A:ASP427	3.9	7.4	1.0
	CA	A:CYS422	4.1	6.4	1.0
	OD1	A:ASP427	4.1	8.5	1.0
	N	A:LEU461	4.2	7.3	1.0
	CA	A:ALA460	4.3	6.6	1.0
	C	A:ALA460	4.4	6.6	1.0
	N	A:CYS422	4.4	6.6	1.0
	N	A:ALA460	4.4	6.4	1.0
	CG	A:ASP459	4.5	8.5	1.0
	CB	A:ASP459	4.5	7.2	1.0
	N	A:MET462	4.6	8.2	1.0
	CA	A:LEU461	4.6	7.5	1.0
	CA	A:MET462	4.6	8.0	1.0
	N	A:ARG423	4.7	6.2	1.0
	OD1	A:ASP459	4.7	8.6	1.0
	CA	A:ASP459	4.8	7.0	1.0
	OD2	A:ASP459	4.9	11.6	1.0
	CA	A:ARG421	4.9	6.7	1.0
	CB	A:CYS422	4.9	6.6	1.0
	C	A:CYS422	5.0	6.5	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 17:27:09 2024

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