Manganese in PDB 6r3l: Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Cinnamic Acid Following Decarboxylation (INT3)

Enzymatic activity of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Cinnamic 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 Cinnamic 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 Cinnamic Acid Following Decarboxylation (INT3), PDB code: 6r3l 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)*	87.77 / 1.24
*Space group*	P 2₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	95.923, 64.219, 87.773, 90.00, 90.00, 90.00
*R / R_free (%)*	13 / 16.7

Other elements in 6r3l:

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

Potassium

(K)

2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Cinnamic Acid Following Decarboxylation (INT3) (pdb code 6r3l). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Cinnamic Acid Following Decarboxylation (INT3), PDB code: 6r3l:

Manganese binding site 1 out of 1 in 6r3l

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Manganese Binding Sites List in 6r3l

Manganese binding site 1 out of 1 in the Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Cinnamic Acid Following Decarboxylation (INT3)

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Aspergillus Niger Ferulic Acid Decarboxylase (Fdc) in Complex with the Covalent Adduct Formed Between Prfmn Cofactor and Cinnamic Acid Following Decarboxylation (INT3) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn601 b:8.3 occ:1.00	OE2	A:GLU233	2.1	7.8	1.0
	OD1	A:ASN168	2.1	7.8	1.0
	O10	A:BYN605	2.2	10.0	0.7
	O	A:HOH736	2.2	8.3	1.0
	O5	A:JSH604	2.2	3.4	0.3
	O	A:HOH833	2.2	8.3	1.0
	ND1	A:HIS191	2.3	8.1	1.0
	CG	A:ASN168	3.1	6.8	1.0
	CE1	A:HIS191	3.2	7.9	1.0
	CD	A:GLU233	3.2	7.6	1.0
	P1	A:BYN605	3.4	10.8	0.7
	CG	A:HIS191	3.4	8.0	1.0
	P1	A:JSH604	3.4	3.2	0.3
	ND2	A:ASN168	3.5	8.7	1.0
	OE1	A:GLU233	3.6	8.3	1.0
	O4	A:JSH604	3.6	3.3	0.3
	O8	A:BYN605	3.6	11.7	0.7
	K	A:K602	3.7	10.0	1.0
	CB	A:HIS191	3.8	7.5	1.0
	O6	A:JSH604	4.2	3.2	0.3
	O9	A:BYN605	4.3	11.3	0.7
	O	A:ILE227	4.3	8.4	1.0
	CZ2	A:TRP166	4.4	9.9	1.0
	NE2	A:HIS191	4.4	7.8	1.0
	CG1	A:ILE227	4.4	9.6	1.0
	O7	A:BYN605	4.4	11.4	0.7
	CB	A:ASN168	4.4	8.3	1.0
	O	A:VAL231	4.4	9.6	1.0
	CG	A:GLU233	4.5	8.5	1.0
	CD2	A:HIS191	4.5	7.9	1.0
	O3	A:JSH604	4.6	2.4	0.3
	O	A:TRP169	4.6	7.8	1.0
	NE1	A:TRP166	4.6	9.7	1.0
	O	A:PRO228	4.7	9.0	1.0
	CE2	A:TRP166	4.9	9.2	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: Sun Oct 6 06:59:03 2024

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