Magnesium in PDB 9ifq: Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 5-Hydroxymethylfurfural

Enzymatic activity of Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 5-Hydroxymethylfurfural

All present enzymatic activity of Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 5-Hydroxymethylfurfural:
1.11.2.1;

Protein crystallography data

The structure of Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 5-Hydroxymethylfurfural, PDB code: 9ifq was solved by A.Fernandez-Garcia, J.Sanz-Aparicio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	48.35 / 2.00
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	272.213, 75.112, 105.385, 90, 111.68, 90
*R / R_free (%)*	19.5 / 22.1

Other elements in 9ifq:

The structure of Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 5-Hydroxymethylfurfural also contains other interesting chemical elements:

Iron

(Fe)

3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 5-Hydroxymethylfurfural (pdb code 9ifq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 5-Hydroxymethylfurfural, PDB code: 9ifq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 9ifq

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Magnesium Binding Sites List in 9ifq

Magnesium binding site 1 out of 3 in the Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 5-Hydroxymethylfurfural

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 5-Hydroxymethylfurfural within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg412 b:35.7 occ:1.00	OE2	A:GLU138	2.0	34.3	1.0
	O	A:HOH534	2.0	26.0	1.0
	O2A	A:HEM401	2.1	34.2	1.0
	O	A:HOH503	2.1	49.2	1.0
	O	A:GLY139	2.2	32.4	1.0
	O	A:HOH613	2.2	42.5	1.0
	CGA	A:HEM401	3.0	42.6	1.0
	CD	A:GLU138	3.1	38.4	1.0
	O1A	A:HEM401	3.3	46.6	1.0
	C	A:GLY139	3.4	36.9	1.0
	CG	A:GLU138	3.6	36.3	1.0
	N	A:GLY139	3.8	33.3	1.0
	O	A:HOH596	3.8	28.2	1.0
	O	A:HOH608	4.0	28.2	1.0
	CA	A:GLY139	4.2	35.9	1.0
	O	A:ASN153	4.2	29.9	1.0
	OE1	A:GLU138	4.2	37.6	1.0
	O	A:HOH520	4.2	28.8	1.0
	CBA	A:HEM401	4.4	32.5	1.0
	N	A:ASP140	4.5	39.7	1.0
	NH2	A:ARG205	4.7	39.0	1.0
	CB	A:ARG145	4.7	34.1	1.0
	C	A:GLU138	4.7	34.4	1.0
	CA	A:ASP140	4.7	35.1	1.0
	O	A:ALA146	4.8	28.3	1.0
	CAA	A:HEM401	4.9	29.8	1.0
	CB	A:GLU138	4.9	34.6	1.0
	CB	A:ASN153	4.9	32.9	1.0
	CZ	A:ARG205	4.9	38.7	1.0
	CA	A:GLU138	5.0	33.8	1.0

Magnesium binding site 2 out of 3 in 9ifq

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Magnesium Binding Sites List in 9ifq

Magnesium binding site 2 out of 3 in the Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 5-Hydroxymethylfurfural

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 5-Hydroxymethylfurfural within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg416 b:37.9 occ:1.00	OE2	B:GLU138	2.0	40.2	1.0
	O	B:HOH565	2.1	30.1	1.0
	O	B:HOH517	2.1	46.2	1.0
	O	B:GLY139	2.1	36.2	1.0
	O1A	B:HEM414	2.1	37.2	1.0
	O	B:HOH618	2.1	39.3	1.0
	CGA	B:HEM414	3.1	41.1	1.0
	CD	B:GLU138	3.1	42.2	1.0
	O2A	B:HEM414	3.3	42.8	1.0
	C	B:GLY139	3.3	38.4	1.0
	CG	B:GLU138	3.7	40.4	1.0
	N	B:GLY139	3.7	37.1	1.0
	O	B:HOH527	3.9	30.4	1.0
	O	B:HOH579	4.0	32.0	1.0
	CA	B:GLY139	4.0	40.2	1.0
	O	B:HOH525	4.1	31.0	1.0
	OE1	B:GLU138	4.2	40.6	1.0
	O	B:ASN153	4.3	35.4	1.0
	N	B:ASP140	4.3	38.0	1.0
	CBA	B:HEM414	4.4	34.1	1.0
	CA	B:ASP140	4.6	41.2	1.0
	NH2	B:ARG205	4.6	40.4	1.0
	C	B:GLU138	4.7	40.6	1.0
	CB	B:ARG145	4.8	34.5	1.0
	O	B:ALA146	4.8	32.2	1.0
	CAA	B:HEM414	4.9	32.7	1.0
	CZ	B:ARG205	4.9	39.1	1.0
	CB	B:GLU138	4.9	40.0	1.0
	CB	B:ASN153	4.9	38.1	1.0
	CA	B:GLU138	5.0	41.3	1.0

Magnesium binding site 3 out of 3 in 9ifq

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Magnesium Binding Sites List in 9ifq

Magnesium binding site 3 out of 3 in the Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 5-Hydroxymethylfurfural

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Unspecific Peroxygenase From Psathyrella Aberdarensis (Pabupo-II) in Complex with 5-Hydroxymethylfurfural within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mg416 b:50.8 occ:1.00	O	C:HOH579	2.0	44.3	1.0
	O	C:GLY139	2.1	40.9	1.0
	OE2	C:GLU138	2.2	41.5	1.0
	O1A	C:HEM414	2.3	43.5	1.0
	CGA	C:HEM414	3.1	45.5	1.0
	O2A	C:HEM414	3.2	44.6	1.0
	C	C:GLY139	3.3	44.7	1.0
	CD	C:GLU138	3.4	45.2	1.0
	O	C:HOH508	3.9	41.0	1.0
	N	C:GLY139	4.0	45.9	1.0
	CG	C:GLU138	4.0	42.2	1.0
	O	C:HOH559	4.1	35.1	1.0
	O	C:HOH520	4.2	38.5	1.0
	CA	C:GLY139	4.2	43.8	1.0
	O	C:ASN153	4.3	46.5	1.0
	N	C:ASP140	4.3	46.2	1.0
	OE1	C:GLU138	4.4	42.1	1.0
	NH2	C:ARG205	4.4	50.4	1.0
	CBA	C:HEM414	4.5	41.0	1.0
	CA	C:ASP140	4.5	49.6	1.0
	CB	C:ARG145	4.6	44.2	1.0
	N	C:GLY142	4.7	49.6	1.0
	O	C:ALA146	4.7	44.2	1.0
	C	C:ASP140	4.8	50.8	1.0
	CZ	C:ARG205	4.8	52.9	1.0
	CA	C:GLY142	4.8	52.3	1.0
	O	C:ARG145	4.9	46.3	1.0
	C	C:GLU138	4.9	39.6	1.0
	CAA	C:HEM414	5.0	36.6	1.0
	CB	C:ASN153	5.0	41.8	1.0

Reference:

A.Fernandez-Garcia, J.Sanz-Aparicio. Unspecific Peroxygenase From Psathyrella Aberdarensis To Be Published.

Page generated: Sat Aug 23 06:02:50 2025

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