Magnesium in PDB 2y59: Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein

Enzymatic activity of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein

All present enzymatic activity of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein:
3.4.16.4;

Protein crystallography data

The structure of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein, PDB code: 2y59 was solved by E.Sauvage, A.Zervosen, R.Herman, F.Kerff, M.Rocaboy, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	42.00 / 2.50
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	103.880, 91.353, 106.919, 90.00, 94.27, 90.00
*R / R_free (%)*	19.5 / 25.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein (pdb code 2y59). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein, PDB code: 2y59:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2y59

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Magnesium Binding Sites List in 2y59

Magnesium binding site 1 out of 4 in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg507 b:27.1 occ:1.00	NE2	A:HIS247	2.1	34.7	1.0
	O	A:GLU188	2.2	31.8	1.0
	OE2	A:GLU251	2.3	41.1	1.0
	CD	A:GLU251	2.9	40.0	1.0
	CE1	A:HIS247	3.0	36.2	1.0
	CD2	A:HIS247	3.0	34.1	1.0
	OE1	A:GLU251	3.1	39.4	1.0
	C	A:GLU188	3.4	32.3	1.0
	O	A:ALA186	3.8	29.1	1.0
	ND1	A:HIS247	4.1	35.6	1.0
	CG	A:HIS247	4.1	33.8	1.0
	CG	A:GLU251	4.3	38.8	1.0
	N	A:GLY189	4.3	32.5	1.0
	CA	A:GLU188	4.3	32.3	1.0
	CA	A:GLY189	4.4	33.2	1.0
	CB	A:GLU188	4.4	32.8	1.0
	N	A:GLU188	4.6	31.2	1.0
	C	A:GLY189	4.7	33.4	1.0
	C	A:ALA186	4.8	28.9	1.0
	C	A:ALA187	4.9	30.6	1.0
	N	A:TYR190	5.0	33.1	1.0
	CD2	A:LEU248	5.0	25.9	1.0

Magnesium binding site 2 out of 4 in 2y59

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Magnesium Binding Sites List in 2y59

Magnesium binding site 2 out of 4 in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg508 b:61.0 occ:1.00	ND1	A:HIS462	2.9	55.5	1.0
	O	A:ALA402	3.4	38.7	1.0
	CG2	A:VAL406	3.5	37.3	1.0
	CG	A:HIS462	3.6	53.8	1.0
	CE1	A:HIS462	3.6	56.7	1.0
	CB	A:HIS462	3.8	52.8	1.0
	O	A:GLN463	3.9	51.6	1.0
	O	A:GLU404	4.0	37.9	1.0
	CB	A:VAL406	4.3	37.2	1.0
	C	A:ALA402	4.4	38.3	1.0
	N	A:GLN463	4.5	53.6	1.0
	CD2	A:HIS462	4.5	54.2	1.0
	NE2	A:HIS462	4.5	56.2	1.0
	CA	A:HIS462	4.7	54.0	1.0
	CA	A:ALA402	4.8	39.3	1.0
	C	A:GLN463	4.9	52.1	1.0

Magnesium binding site 3 out of 4 in 2y59

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Magnesium Binding Sites List in 2y59

Magnesium binding site 3 out of 4 in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Mg508 b:47.8 occ:1.00	O	D:GLU188	2.1	39.4	1.0
	OE2	D:GLU251	2.4	49.9	1.0
	NE2	D:HIS247	2.5	43.2	1.0
	OE1	D:GLU251	2.8	50.3	1.0
	CD	D:GLU251	2.9	50.8	1.0
	CD2	D:HIS247	3.1	41.9	1.0
	C	D:GLU188	3.3	38.9	1.0
	O	D:ALA186	3.5	39.0	1.0
	CE1	D:HIS247	3.6	43.6	1.0
	CA	D:GLU188	4.0	38.6	1.0
	N	D:GLU188	4.1	37.4	1.0
	CB	D:GLU188	4.1	39.5	1.0
	N	D:GLY189	4.3	38.4	1.0
	CG	D:HIS247	4.4	40.9	1.0
	CG	D:GLU251	4.4	51.5	1.0
	ND1	D:HIS247	4.6	41.5	1.0
	C	D:ALA186	4.6	37.9	1.0
	CA	D:GLY189	4.6	39.4	1.0
	C	D:ALA187	4.7	36.8	1.0
	C	D:GLY189	4.8	39.3	1.0
	CD2	D:LEU248	4.8	33.7	1.0

Magnesium binding site 4 out of 4 in 2y59

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Magnesium Binding Sites List in 2y59

Magnesium binding site 4 out of 4 in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Mg509 b:48.7 occ:1.00	ND1	D:HIS462	2.8	72.1	1.0
	CG2	D:VAL406	3.4	54.1	1.0
	CG	D:HIS462	3.7	71.4	1.0
	CB	D:HIS462	3.7	70.2	1.0
	CE1	D:HIS462	3.9	72.6	1.0
	O	D:HOH2045	4.3	48.9	1.0
	O	D:ALA402	4.4	57.0	1.0
	CA	D:HIS462	4.5	71.8	1.0
	CB	D:VAL406	4.8	52.9	1.0
	CD2	D:HIS462	4.9	71.5	1.0
	O	D:GLU404	4.9	52.7	1.0
	O	D:GLN463	4.9	71.5	1.0
	N	D:GLN463	5.0	71.8	1.0
	NE2	D:HIS462	5.0	72.2	1.0

Reference:

A.Zervosen, R.Herman, F.Kerff, A.Herman, A.Bouillez, F.Prati, R.F.Pratt, J.M.Frere, B.Joris, A.Luxen, P.Charlier, E.Sauvage. Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin- Binding Protein. J.Am.Chem.Soc. V. 133 10839 2011.
ISSN: ISSN 0002-7863
PubMed: 21574608
DOI: 10.1021/JA200696Y

Page generated: Wed Aug 14 07:25:59 2024

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