Magnesium in PDB 5vz0: Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp

Enzymatic activity of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp

All present enzymatic activity of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp:
6.4.1.1;

Protein crystallography data

The structure of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp, PDB code: 5vz0 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)*	48.55 / 2.00
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	97.155, 130.390, 134.271, 65.99, 88.67, 70.14
*R / R_free (%)*	19.1 / 21.8

Other elements in 5vz0:

The structure of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp (pdb code 5vz0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp, PDB code: 5vz0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5vz0

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Magnesium Binding Sites List in 5vz0

Magnesium binding site 1 out of 3 in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1203 b:48.0 occ:1.00	O2B	A:ADP1202	1.8	66.1	1.0
	O2A	A:ADP1202	1.9	58.9	1.0
	OE2	A:GLU274	2.2	44.1	1.0
	OE1	A:GLU286	2.4	56.3	1.0
	CD	A:GLU274	3.1	35.4	1.0
	PB	A:ADP1202	3.1	74.5	1.0
	OE1	A:GLU274	3.3	45.8	1.0
	PA	A:ADP1202	3.3	57.4	1.0
	CD	A:GLU286	3.7	56.5	1.0
	O3A	A:ADP1202	3.7	63.1	1.0
	O1B	A:ADP1202	3.7	81.2	1.0
	O5'	A:ADP1202	4.2	55.7	1.0
	CE1	A:HIS207	4.3	38.2	1.0
	OE2	A:GLU286	4.3	60.6	1.0
	C5'	A:ADP1202	4.3	51.0	1.0
	ND2	A:ASN288	4.3	43.7	1.0
	OD1	A:ASN288	4.3	49.9	1.0
	O3B	A:ADP1202	4.4	61.6	1.0
	O1A	A:ADP1202	4.5	53.7	1.0
	CG	A:GLU274	4.6	35.4	1.0
	NZ	A:LYS236	4.6	48.6	1.0
	CG	A:ASN288	4.8	40.3	1.0
	CG	A:GLU286	4.8	52.5	1.0
	CE	A:LYS236	4.9	51.2	1.0
	NE2	A:HIS207	4.9	39.8	1.0
	CB	A:GLU286	4.9	42.4	1.0

Magnesium binding site 2 out of 3 in 5vz0

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Magnesium Binding Sites List in 5vz0

Magnesium binding site 2 out of 3 in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg1204 b:34.5 occ:1.00	O3B	B:ADP1203	1.8	62.1	1.0
	O	B:HOH1311	1.9	42.2	1.0
	O2A	B:ADP1203	2.0	65.0	1.0
	OE2	B:GLU274	2.2	49.2	1.0
	OE1	B:GLU286	2.2	54.2	1.0
	PB	B:ADP1203	3.1	58.0	1.0
	PA	B:ADP1203	3.2	58.0	1.0
	CD	B:GLU274	3.2	50.0	1.0
	CD	B:GLU286	3.5	61.8	1.0
	O3A	B:ADP1203	3.5	60.4	1.0
	OE1	B:GLU274	3.6	56.0	1.0
	O1B	B:ADP1203	3.7	59.3	1.0
	O5'	B:ADP1203	4.1	53.0	1.0
	C5'	B:ADP1203	4.1	49.3	1.0
	OE2	B:GLU286	4.2	54.6	1.0
	CE1	B:HIS207	4.3	38.8	1.0
	O2B	B:ADP1203	4.3	58.9	1.0
	O1A	B:ADP1203	4.4	53.6	1.0
	ND2	B:ASN288	4.5	34.5	1.0
	CG	B:GLU274	4.6	46.6	1.0
	CG	B:GLU286	4.6	62.3	1.0
	CB	B:GLU286	4.6	49.1	1.0
	OD1	B:ASN288	4.6	48.1	1.0
	NE2	B:HIS207	5.0	39.0	1.0

Magnesium binding site 3 out of 3 in 5vz0

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Magnesium Binding Sites List in 5vz0

Magnesium binding site 3 out of 3 in the Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Lactococcus Lactis Pyruvate Carboxylase G746A Mutant in Complex with Cyclic-Di-Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Mg1203 b:36.5 occ:1.00	O	D:HOH1301	1.8	37.8	1.0
	O1B	D:ADP1202	1.9	56.2	1.0
	OE1	D:GLU286	2.0	56.2	1.0
	OE2	D:GLU274	2.1	40.4	1.0
	O1A	D:ADP1202	2.3	54.7	1.0
	O2B	D:ADP1202	2.7	60.8	1.0
	PB	D:ADP1202	2.8	63.8	1.0
	CD	D:GLU274	3.2	39.2	1.0
	CD	D:GLU286	3.3	53.2	1.0
	PA	D:ADP1202	3.4	55.3	1.0
	OE1	D:GLU274	3.5	48.2	1.0
	O3A	D:ADP1202	3.6	56.2	1.0
	OE2	D:GLU286	3.9	63.4	1.0
	O3B	D:ADP1202	4.2	47.9	1.0
	ND2	D:ASN288	4.2	41.7	1.0
	OD1	D:ASN288	4.3	46.0	1.0
	O5'	D:ADP1202	4.4	51.4	1.0
	CG	D:GLU286	4.4	52.9	1.0
	O2A	D:ADP1202	4.5	59.6	1.0
	CG	D:GLU274	4.5	35.9	1.0
	CB	D:GLU286	4.6	46.9	1.0
	CE1	D:HIS207	4.6	43.8	1.0
	C5'	D:ADP1202	4.7	46.3	1.0
	CG	D:ASN288	4.7	39.8	1.0
	NZ	D:LYS236	4.9	51.6	1.0

Reference:

P.H.Choi, T.M.N.Vu, H.T.Pham, J.J.Woodward, M.S.Turner, L.Tong. Structural and Functional Studies of Pyruvate Carboxylase Regulation By Cyclic Di-Amp in Lactic Acid Bacteria. Proc. Natl. Acad. Sci. V. 114 E7226 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28808024
DOI: 10.1073/PNAS.1704756114

Page generated: Mon Sep 30 06:22:52 2024

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