Magnesium in PDB 4fp1: P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid

Enzymatic activity of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid

All present enzymatic activity of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid:
5.1.2.2;

Protein crystallography data

The structure of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid, PDB code: 4fp1 was solved by A.D.Lietzan, M.St.Maurice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	50.00 / 1.68
*Space group*	I 4 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	148.870, 148.870, 169.640, 90.00, 90.00, 90.00
*R / R_free (%)*	16.9 / 19.3

Other elements in 4fp1:

The structure of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid (pdb code 4fp1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid, PDB code: 4fp1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4fp1

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Magnesium Binding Sites List in 4fp1

Magnesium binding site 1 out of 2 in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg401 b:13.0 occ:1.00	O	A:HOH732	1.8	24.9	1.0
	O	A:HOH733	2.1	20.1	1.0
	OE2	A:GLU247	2.1	9.1	0.5
	OE2	A:GLU221	2.2	9.6	1.0
	OD2	A:ASP195	2.2	11.1	1.0
	O	A:HOH730	2.3	15.0	1.0
	OE1	A:GLU247	2.3	13.8	0.5
	OE2	A:GLU247	2.8	13.9	0.5
	CD	A:GLU247	2.9	12.9	0.5
	CD	A:GLU247	3.0	10.1	0.5
	CG	A:ASP195	3.1	10.5	1.0
	CD	A:GLU221	3.2	9.6	1.0
	O05	A:BFM402	3.3	25.5	0.5
	OE1	A:GLU247	3.3	10.9	0.5
	OD1	A:ASP195	3.4	9.9	1.0
	O	A:HOH750	3.6	21.0	1.0
	O04	A:BFM402	3.8	26.4	0.5
	C03	A:BFM402	3.8	26.0	0.5
	NZ	A:LYS166	3.9	14.9	1.0
	NZ	A:LYS164	4.0	8.5	1.0
	CG	A:GLU221	4.0	8.7	1.0
	ND2	A:ASN197	4.1	15.2	1.0
	OE1	A:GLU221	4.1	9.6	1.0
	OE1	A:GLU222	4.3	13.1	1.0
	CG	A:GLU247	4.3	11.4	0.5
	NE2	A:HIS297	4.4	11.0	1.0
	CD2	A:HIS297	4.4	9.8	1.0
	CG	A:GLU247	4.4	9.5	0.5
	CB	A:ASP195	4.4	9.1	1.0
	O	A:HOH731	4.4	14.8	1.0
	CE	A:MET268	4.6	7.7	1.0
	CE	A:LYS164	4.7	8.2	1.0
	CG	A:ASN197	4.9	14.8	1.0
	O	A:HOH729	5.0	19.0	1.0

Magnesium binding site 2 out of 2 in 4fp1

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Magnesium Binding Sites List in 4fp1

Magnesium binding site 2 out of 2 in the P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of P. Putida Mandelate Racemase Co-Crystallized with 3,3,3-Trifluoro-2- Hydroxy-2-(Trifluoromethyl) Propionic Acid within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg401 b:17.7 occ:1.00	O	B:HOH682	1.7	29.8	1.0
	O	B:HOH687	2.0	29.3	1.0
	OE2	B:GLU221	2.2	14.4	1.0
	OE1	B:GLU247	2.2	12.3	0.5
	O	B:HOH681	2.3	19.5	1.0
	OD2	B:ASP195	2.3	16.1	1.0
	OE1	B:GLU247	2.4	16.8	0.5
	OE2	B:GLU247	2.8	18.1	0.5
	CD	B:GLU247	2.9	16.6	0.5
	CD	B:GLU247	3.1	13.5	0.5
	CG	B:ASP195	3.2	16.0	1.0
	O04	B:BFM402	3.3	39.0	1.0
	CD	B:GLU221	3.3	14.2	1.0
	OE2	B:GLU247	3.3	13.9	0.5
	OD1	B:ASP195	3.5	14.8	1.0
	O	B:HOH689	3.7	31.5	1.0
	C03	B:BFM402	3.8	38.2	1.0
	O05	B:BFM402	3.8	43.0	1.0
	NZ	B:LYS166	4.0	21.1	1.0
	NZ	B:LYS164	4.0	14.2	1.0
	CG	B:GLU221	4.0	13.8	1.0
	ND2	B:ASN197	4.1	20.7	1.0
	OE1	B:GLU221	4.1	14.5	1.0
	OE1	B:GLU222	4.3	17.8	1.0
	CG	B:GLU247	4.4	14.6	0.5
	CB	B:ASP195	4.5	14.7	1.0
	O	B:HOH526	4.5	21.4	1.0
	CG	B:GLU247	4.5	12.7	0.5
	NE2	B:HIS297	4.5	15.6	1.0
	CD2	B:HIS297	4.5	15.6	1.0
	CE	B:MET268	4.6	11.5	1.0
	CE	B:LYS164	4.7	14.6	1.0
	CG	B:ASN197	4.9	19.8	1.0
	O	B:HOH548	5.0	22.7	1.0

Reference:

M.Nagar, A.D.Lietzan, M.St Maurice, S.L.Bearne. Potent Inhibition of Mandelate Racemase By A Fluorinated Substrate-Product Analogue with A Novel Binding Mode. Biochemistry V. 53 1169 2014.
ISSN: ISSN 0006-2960
PubMed: 24472022
DOI: 10.1021/BI401703H

Page generated: Fri Aug 16 15:13:50 2024

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