Manganese in PDB 5lbb: Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R396T Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9)

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R396T Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9)

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R396T Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9):
1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R396T Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9), PDB code: 5lbb was solved by R.Chowdhury, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	36.07 / 1.70
*Space group*	P 6₃
*Cell size a, b, c (Å), α, β, γ (°)*	110.199, 110.199, 39.717, 90.00, 90.00, 120.00
*R / R_free (%)*	15.2 / 17.8

Other elements in 5lbb:

Chlorine

(Cl)

1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R396T Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9) (pdb code 5lbb). 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 Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R396T Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9), PDB code: 5lbb:

Manganese binding site 1 out of 1 in 5lbb

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Manganese Binding Sites List in 5lbb

Manganese binding site 1 out of 1 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R396T Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9)

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) R396T Variant in Complex with Mn(II) and N-[(1-Chloro-4-Hydroxyisoquinolin-3-Yl)Carbonyl]Glycine (IOX3/UN9) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn501 b:23.4 occ:1.00	OD1	A:ASP315	2.2	21.7	1.0
	O13	A:UN9502	2.2	23.2	1.0
	O	A:HOH641	2.2	23.9	1.0
	NE2	A:HIS313	2.2	20.2	1.0
	NE2	A:HIS374	2.2	24.3	1.0
	N8	A:UN9502	2.4	25.2	1.0
	C12	A:UN9502	3.0	22.7	1.0
	CE1	A:HIS313	3.1	24.7	1.0
	HE1	A:HIS313	3.1	29.7	1.0
	C9	A:UN9502	3.2	21.5	1.0
	CE1	A:HIS374	3.2	22.9	1.0
	CG	A:ASP315	3.2	25.9	1.0
	CD2	A:HIS374	3.2	25.7	1.0
	CD2	A:HIS313	3.3	23.8	1.0
	C7	A:UN9502	3.4	24.1	1.0
	HE1	A:HIS374	3.4	27.5	1.0
	HD2	A:HIS374	3.4	30.8	1.0
	CL1	A:UN9502	3.4	28.1	1.0
	OD2	A:ASP315	3.5	23.5	1.0
	HD2	A:HIS313	3.6	28.5	1.0
	HZ	A:PHE366	3.9	28.2	1.0
	N14	A:UN9502	4.2	22.4	1.0
	ND1	A:HIS313	4.2	23.4	1.0
	HZ2	A:TRP389	4.3	31.2	1.0
	O	A:HOH636	4.3	30.1	1.0
	ND1	A:HIS374	4.3	24.1	1.0
	CG	A:HIS374	4.3	24.2	1.0
	CG	A:HIS313	4.4	23.5	1.0
	HA	A:ASP315	4.4	29.5	1.0
	C10	A:UN9502	4.6	26.6	1.0
	CB	A:ASP315	4.6	22.6	1.0
	H151	A:UN9502	4.6	26.2	1.0
	C2	A:UN9502	4.7	24.1	1.0
	CZ	A:PHE366	4.8	23.5	1.0
	HG21	A:THR325	4.8	28.2	1.0
	C15	A:UN9502	4.9	21.9	1.0
	CA	A:ASP315	4.9	24.6	1.0
	HN14	A:UN9502	4.9	26.8	1.0
	HE1	A:PHE366	4.9	29.2	1.0
	H152	A:UN9502	4.9	26.2	1.0
	HD11	A:ILE327	4.9	26.6	1.0
	HD1	A:HIS313	5.0	28.1	1.0

Reference:

R.Chowdhury, I.K.Leung, Y.M.Tian, M.I.Abboud, W.Ge, C.Domene, F.X.Cantrelle, I.Landrieu, A.P.Hardy, C.W.Pugh, P.J.Ratcliffe, T.D.Claridge, C.J.Schofield. Structural Basis For Oxygen Degradation Domain Selectivity of the Hif Prolyl Hydroxylases. Nat Commun V. 7 12673 2016.
ISSN: ESSN 2041-1723
PubMed: 27561929
DOI: 10.1038/NCOMMS12673

Page generated: Sun Oct 6 01:51:00 2024

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