Manganese in PDB 2y1f: X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue, Manganese and Nadph.

Enzymatic activity of X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue, Manganese and Nadph.

All present enzymatic activity of X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue, Manganese and Nadph.:
1.1.1.267;

Protein crystallography data

The structure of X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue, Manganese and Nadph., PDB code: 2y1f was solved by L.M.Henriksson, A.M.S.Larsson, T.Bergfors, C.Bjorkelid, T.Unge, S.L.Mowbray, T.A.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	45.00 / 1.96
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	67.439, 65.019, 86.169, 90.00, 102.05, 90.00
*R / R_free (%)*	17.2 / 21

Other elements in 2y1f:

Chlorine

(Cl)

2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue, Manganese and Nadph. (pdb code 2y1f). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue, Manganese and Nadph., PDB code: 2y1f:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 2y1f

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Manganese Binding Sites List in 2y1f

Manganese binding site 1 out of 2 in the X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue, Manganese and Nadph.

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue, Manganese and Nadph. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn1392 b:13.8 occ:1.00	OD1	A:ASP151	2.2	14.1	1.0
	OE1	A:GLU153	2.2	13.1	1.0
	OE2	A:GLU222	2.2	13.2	1.0
	O2	A:34F1390	2.2	18.0	1.0
	O1	A:34F1390	2.2	16.6	1.0
	C1	A:34F1390	2.8	19.0	1.0
	N1	A:34F1390	2.8	19.0	1.0
	CD	A:GLU153	2.9	11.5	1.0
	OE2	A:GLU153	3.0	12.6	1.0
	CD	A:GLU222	3.1	11.7	1.0
	CG	A:ASP151	3.1	13.1	1.0
	OE1	A:GLU222	3.6	12.4	1.0
	OD2	A:ASP151	3.6	13.2	1.0
	NZ	A:LYS128	3.6	15.7	1.0
	OG	A:SER152	4.0	13.5	1.0
	C5N	A:NDP1391	4.0	38.4	1.0
	N	A:SER152	4.1	12.0	1.0
	ND2	A:ASN218	4.1	12.3	1.0
	C2	A:34F1390	4.2	20.5	1.0
	CG	A:GLU222	4.3	11.1	1.0
	CB	A:ASP151	4.3	13.5	1.0
	CG	A:GLU153	4.4	11.4	1.0
	N	A:GLU153	4.5	11.0	1.0
	C3	A:34F1390	4.5	20.6	1.0
	CA	A:ASP151	4.6	12.8	1.0
	C	A:ASP151	4.6	12.9	1.0
	C4	A:34F1390	4.7	21.7	1.0
	C6N	A:NDP1391	4.8	38.7	1.0
	CB	A:GLU153	4.9	10.3	1.0
	C4N	A:NDP1391	4.9	38.5	1.0
	OD1	A:ASN218	4.9	13.8	1.0
	CB	A:SER152	4.9	11.9	1.0
	CA	A:SER152	4.9	12.0	1.0
	NZ	A:LYS219	5.0	12.3	1.0
	CG	A:ASN218	5.0	11.8	1.0
	CE	A:LYS128	5.0	16.4	1.0

Manganese binding site 2 out of 2 in 2y1f

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Manganese Binding Sites List in 2y1f

Manganese binding site 2 out of 2 in the X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue, Manganese and Nadph.

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase, Dxr, RV2870C, From Mycobacterium Tuberculosis, in Complex with A 3,4- Dichlorophenyl-Substituted Fosmidomycin Analogue, Manganese and Nadph. within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn1390 b:16.9 occ:1.00	OD2	B:ASP151	2.2	19.5	1.0
	OE2	B:GLU222	2.2	14.9	1.0
	O	B:HOH2247	2.2	18.0	1.0
	OE1	B:GLU153	2.2	15.6	1.0
	O	B:HOH2248	2.2	19.3	1.0
	O	B:HOH2246	2.2	16.0	1.0
	CG	B:ASP151	2.9	17.3	1.0
	OD1	B:ASP151	2.9	20.0	1.0
	CD	B:GLU153	3.1	13.0	1.0
	CD	B:GLU222	3.2	13.3	1.0
	OE2	B:GLU153	3.4	14.2	1.0
	OE1	B:GLU222	3.6	11.5	1.0
	OG	B:SER152	4.0	15.5	1.0
	ND2	B:ASN218	4.1	12.7	1.0
	C5N	B:NDP1392	4.3	58.5	1.0
	CB	B:ASP151	4.3	14.2	1.0
	CG	B:GLU222	4.3	10.9	1.0
	CG	B:GLU153	4.5	11.5	1.0
	O	B:HOH2251	4.6	27.1	1.0
	NZ	B:LYS128	4.6	25.1	1.0
	N	B:GLU153	4.7	11.3	1.0
	N	B:SER152	4.7	12.2	1.0
	NZ	B:LYS219	4.8	11.5	1.0
	C4N	B:NDP1392	4.9	58.2	1.0
	CB	B:GLU153	4.9	10.6	1.0
	O4	B:SO41391	5.0	18.4	1.0

Reference:

M.Andaloussi, L.M.Henriksson, A.Wieckowska, M.Lindh, C.Bjorkelid, A.M.S.Larsson, H.Iyer, B.R.Srinivasa, T.Bergfors, T.Unge, S.L.Mowbray, M.Larhed, T.A.Jones, A.Karlen. Design, Synthesis and X-Ray Crystallographic Studies of Alpha-Aryl Substituted Fosmidomycin Analogues As Inhibitors of Mycobacterium Tuberculosis 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase J.Med.Chem V. 54 4964 2011.
ISSN: ISSN 0022-2623
PubMed: 21678907
DOI: 10.1021/JM2000085

Page generated: Sat Oct 5 15:29:36 2024

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