Manganese in PDB 4qsh: Crystal Structure of L. Monocytogenes Pyruvate Carboxylase in Complex with Cyclic-Di-Amp

Enzymatic activity of Crystal Structure of L. Monocytogenes Pyruvate Carboxylase in Complex with Cyclic-Di-Amp

All present enzymatic activity of Crystal Structure of L. Monocytogenes Pyruvate Carboxylase in Complex with Cyclic-Di-Amp:
6.4.1.1;

Protein crystallography data

The structure of Crystal Structure of L. Monocytogenes Pyruvate Carboxylase in Complex with Cyclic-Di-Amp, PDB code: 4qsh was solved by P.H.Choi, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	49.80 / 2.51
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	96.778, 153.296, 221.240, 90.00, 101.58, 90.00
*R / R_free (%)*	19.5 / 23.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of L. Monocytogenes Pyruvate Carboxylase in Complex with Cyclic-Di-Amp (pdb code 4qsh). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of L. Monocytogenes Pyruvate Carboxylase in Complex with Cyclic-Di-Amp, PDB code: 4qsh:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4qsh

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Manganese Binding Sites List in 4qsh

Manganese binding site 1 out of 4 in the Crystal Structure of L. Monocytogenes Pyruvate Carboxylase in Complex with Cyclic-Di-Amp

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of L. Monocytogenes Pyruvate Carboxylase in Complex with Cyclic-Di-Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn2002 b:72.2 occ:1.00	NE2	A:HIS739	2.5	31.6	1.0
	NE2	A:HIS741	2.5	41.3	1.0
	OD2	A:ASP541	2.6	37.6	1.0
	NZ	A:LYS710	3.1	44.1	1.0
	CE1	A:HIS739	3.1	33.6	1.0
	CE1	A:HIS741	3.3	40.9	1.0
	CD2	A:HIS739	3.5	32.1	1.0
	CG	A:ASP541	3.6	32.4	1.0
	CD2	A:HIS741	3.6	44.0	1.0
	OD1	A:ASP541	3.8	30.3	1.0
	ND1	A:HIS739	4.3	32.3	1.0
	CG	A:HIS739	4.5	33.0	1.0
	CE	A:LYS710	4.5	42.7	1.0
	ND1	A:HIS741	4.5	48.8	1.0
	NE2	A:GLN775	4.6	24.6	1.0
	CA	A:MET712	4.6	29.1	1.0
	CG	A:HIS741	4.7	45.2	1.0
	NH2	A:ARG540	4.7	21.4	1.0
	CB	A:ASP541	4.9	27.3	1.0
	CB	A:MET712	5.0	35.8	1.0

Manganese binding site 2 out of 4 in 4qsh

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Manganese Binding Sites List in 4qsh

Manganese binding site 2 out of 4 in the Crystal Structure of L. Monocytogenes Pyruvate Carboxylase in Complex with Cyclic-Di-Amp

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of L. Monocytogenes Pyruvate Carboxylase in Complex with Cyclic-Di-Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn2002 b:94.7 occ:1.00	OD2	B:ASP541	2.5	57.9	1.0
	NE2	B:HIS739	2.6	58.9	1.0
	NE2	B:HIS741	2.7	62.5	1.0
	NZ	B:LYS710	3.0	74.8	1.0
	CE1	B:HIS739	3.2	58.5	1.0
	CE1	B:HIS741	3.4	56.7	1.0
	CG	B:ASP541	3.4	49.0	1.0
	OD1	B:ASP541	3.6	51.0	1.0
	CD2	B:HIS739	3.7	58.6	1.0
	CD2	B:HIS741	3.8	57.1	1.0
	ND1	B:HIS739	4.4	63.6	1.0
	CE	B:LYS710	4.5	70.1	1.0
	NH2	B:ARG540	4.6	47.3	1.0
	ND1	B:HIS741	4.6	62.1	1.0
	CG	B:HIS739	4.6	57.9	1.0
	NE2	B:GLN775	4.6	53.1	1.0
	CA	B:MET712	4.8	50.5	1.0
	CB	B:ASP541	4.8	47.6	1.0
	CG	B:HIS741	4.8	56.2	1.0
	CB	B:MET712	4.8	60.2	1.0

Manganese binding site 3 out of 4 in 4qsh

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Manganese Binding Sites List in 4qsh

Manganese binding site 3 out of 4 in the Crystal Structure of L. Monocytogenes Pyruvate Carboxylase in Complex with Cyclic-Di-Amp

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of L. Monocytogenes Pyruvate Carboxylase in Complex with Cyclic-Di-Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mn1203 b:85.9 occ:1.00	NE2	C:HIS739	2.3	54.4	1.0
	NE2	C:HIS741	2.5	62.9	1.0
	OD2	C:ASP541	2.6	57.9	1.0
	CE1	C:HIS739	3.0	61.5	1.0
	NZ	C:LYS710	3.1	63.4	1.0
	CD2	C:HIS739	3.3	55.5	1.0
	CE1	C:HIS741	3.3	65.8	1.0
	CD2	C:HIS741	3.6	62.2	1.0
	CG	C:ASP541	3.6	51.6	1.0
	OD1	C:ASP541	3.9	46.5	1.0
	ND1	C:HIS739	4.1	59.5	1.0
	CG	C:HIS739	4.3	56.0	1.0
	NE2	C:GLN775	4.4	45.3	1.0
	ND1	C:HIS741	4.5	60.1	1.0
	CE	C:LYS710	4.5	66.7	1.0
	CG	C:HIS741	4.6	58.4	1.0
	CA	C:MET712	4.7	51.3	1.0
	NH2	C:ARG540	4.8	48.4	1.0
	CB	C:MET712	4.9	58.2	1.0
	CB	C:ASP541	4.9	51.7	1.0

Manganese binding site 4 out of 4 in 4qsh

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Manganese Binding Sites List in 4qsh

Manganese binding site 4 out of 4 in the Crystal Structure of L. Monocytogenes Pyruvate Carboxylase in Complex with Cyclic-Di-Amp

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of L. Monocytogenes Pyruvate Carboxylase in Complex with Cyclic-Di-Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Mn2002 b:75.1 occ:1.00	OD2	D:ASP541	2.4	36.1	1.0
	NE2	D:HIS739	2.4	30.3	1.0
	NE2	D:HIS741	2.5	40.4	1.0
	CE1	D:HIS739	3.1	32.0	1.0
	CE1	D:HIS741	3.2	37.6	1.0
	NZ	D:LYS710	3.2	52.0	1.0
	CG	D:ASP541	3.3	34.2	1.0
	CD2	D:HIS739	3.5	29.6	1.0
	OD1	D:ASP541	3.6	31.1	1.0
	CD2	D:HIS741	3.6	38.2	1.0
	ND1	D:HIS739	4.2	34.4	1.0
	ND1	D:HIS741	4.4	45.5	1.0
	NE2	D:GLN775	4.4	24.8	1.0
	CG	D:HIS739	4.5	30.0	1.0
	NH2	D:ARG540	4.6	26.2	1.0
	CG	D:HIS741	4.6	40.3	1.0
	CB	D:ASP541	4.7	29.5	1.0
	CE	D:LYS710	4.7	49.6	1.0
	CA	D:MET712	4.8	28.6	1.0

Reference:

K.Sureka, P.H.Choi, M.Precit, M.Delince, D.A.Pensinger, T.N.Huynh, A.R.Jurado, Y.A.Goo, M.Sadilek, A.T.Iavarone, J.D.Sauer, L.Tong, J.J.Woodward. The Cyclic Dinucleotide C-Di-Amp Is An Allosteric Regulator of Metabolic Enzyme Function. Cell(Cambridge,Mass.) V. 158 1389 2014.
ISSN: ISSN 0092-8674
PubMed: 25215494
DOI: 10.1016/J.CELL.2014.07.046

Page generated: Sat Oct 5 21:05:49 2024

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