Manganese in PDB 6btd: Crystal Structure of Deoxyribose-Phosphate Aldolase From Bacillus Thuringiensis Involved in Dispatching the Ubiquitous Radical Sam Enzyme Byproduct 5-Deoxyribose

Enzymatic activity of Crystal Structure of Deoxyribose-Phosphate Aldolase From Bacillus Thuringiensis Involved in Dispatching the Ubiquitous Radical Sam Enzyme Byproduct 5-Deoxyribose

All present enzymatic activity of Crystal Structure of Deoxyribose-Phosphate Aldolase From Bacillus Thuringiensis Involved in Dispatching the Ubiquitous Radical Sam Enzyme Byproduct 5-Deoxyribose:
4.1.2.17;

Protein crystallography data

The structure of Crystal Structure of Deoxyribose-Phosphate Aldolase From Bacillus Thuringiensis Involved in Dispatching the Ubiquitous Radical Sam Enzyme Byproduct 5-Deoxyribose, PDB code: 6btd was solved by Q.Li, S.D.Bruner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	35.55 / 1.55
*Space group*	P 4 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	103.724, 103.724, 48.817, 90.00, 90.00, 90.00
*R / R_free (%)*	16.5 / 18.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Deoxyribose-Phosphate Aldolase From Bacillus Thuringiensis Involved in Dispatching the Ubiquitous Radical Sam Enzyme Byproduct 5-Deoxyribose (pdb code 6btd). 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 Crystal Structure of Deoxyribose-Phosphate Aldolase From Bacillus Thuringiensis Involved in Dispatching the Ubiquitous Radical Sam Enzyme Byproduct 5-Deoxyribose, PDB code: 6btd:

Manganese binding site 1 out of 1 in 6btd

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Manganese Binding Sites List in 6btd

Manganese binding site 1 out of 1 in the Crystal Structure of Deoxyribose-Phosphate Aldolase From Bacillus Thuringiensis Involved in Dispatching the Ubiquitous Radical Sam Enzyme Byproduct 5-Deoxyribose

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Deoxyribose-Phosphate Aldolase From Bacillus Thuringiensis Involved in Dispatching the Ubiquitous Radical Sam Enzyme Byproduct 5-Deoxyribose within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn302 b:8.8 occ:1.00	OE2	A:GLU76	2.0	12.9	1.0
	NE2	A:HIS157	2.0	9.8	1.0
	NE2	A:HIS95	2.1	11.0	1.0
	NE2	A:HIS97	2.1	11.4	1.0
	CD	A:GLU76	2.7	11.9	1.0
	OE1	A:GLU76	2.8	13.8	1.0
	CE1	A:HIS157	3.0	10.6	1.0
	CD2	A:HIS95	3.0	9.9	1.0
	CD2	A:HIS157	3.0	10.6	1.0
	CD2	A:HIS97	3.1	11.0	1.0
	CE1	A:HIS97	3.1	14.1	1.0
	CE1	A:HIS95	3.1	8.2	1.0
	O	A:HOH407	3.8	18.6	1.0
	CE2	A:PHE133	3.9	21.5	1.0
	ND1	A:HIS157	4.1	11.1	1.0
	CG	A:HIS157	4.2	8.9	1.0
	ND1	A:HIS95	4.2	9.7	1.0
	CG	A:HIS95	4.2	8.7	1.0
	ND1	A:HIS97	4.2	13.6	1.0
	CG	A:HIS97	4.2	11.4	1.0
	CG	A:GLU76	4.2	11.8	1.0
	CD2	A:PHE133	4.4	21.2	1.0
	ND2	A:ASN29	4.8	12.7	1.0
	N	A:GLY28	4.8	14.8	1.0
	CZ	A:PHE133	4.9	24.8	1.0
	CA	A:GLY28	4.9	14.2	1.0
	CE	A:MET79	4.9	14.1	1.0

Reference:

G.A.W.Beaudoin, Q.Li, J.Folz, O.Fiehn, J.L.Goodsell, A.Angerhofer, S.D.Bruner, A.D.Hanson. Salvage of the 5-Deoxyribose Byproduct of Radical Sam Enzymes. Nat Commun V. 9 3105 2018.
ISSN: ESSN 2041-1723
PubMed: 30082730
DOI: 10.1038/S41467-018-05589-4

Page generated: Sun Oct 6 03:57:02 2024

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