Magnesium in PDB 2iyy: Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4

Enzymatic activity of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4

All present enzymatic activity of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4:
2.7.1.71;

Protein crystallography data

The structure of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4, PDB code: 2iyy was solved by M.D.Hartmann, G.P.Bourenkov, A.Oberschall, N.Strizhov, H.D.Bartunik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	19.16 / 1.62
*Space group*	P 3₁ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	59.349, 59.349, 102.867, 90.00, 90.00, 120.00
*R / R_free (%)*	17.5 / 23.3

Other elements in 2iyy:

The structure of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4 (pdb code 2iyy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4, PDB code: 2iyy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2iyy

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Magnesium Binding Sites List in 2iyy

Magnesium binding site 1 out of 3 in the Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg211 b:59.8 occ:1.00	OE2	A:GLU38	2.2	38.8	1.0
	O	A:HOH2088	2.2	21.9	1.0
	O	A:HOH2063	3.1	51.5	1.0
	N	A:ILE45	3.3	20.5	1.0
	CD	A:GLU38	3.3	43.8	1.0
	OG	A:SER44	3.6	26.6	0.3
	CB	A:SER44	3.7	23.8	0.7
	CB	A:SER44	3.7	21.8	0.3
	CA	A:SER44	3.8	23.9	1.0
	OE1	A:GLU38	3.9	42.1	1.0
	CG1	A:ILE45	3.9	24.5	0.5
	CB	A:ILE45	3.9	19.9	0.5
	C	A:SER44	4.0	17.6	1.0
	O	A:HOH2085	4.1	28.7	1.0
	CB	A:ILE45	4.2	25.3	0.5
	CA	A:ILE45	4.2	19.6	0.5
	CA	A:ILE45	4.2	22.4	0.5
	O	A:HOH2164	4.2	37.0	1.0
	N	A:ALA46	4.3	20.3	1.0
	CG	A:GLU38	4.5	23.0	1.0
	CG1	A:ILE45	4.6	32.8	0.5
	OG	A:SER44	4.7	20.0	0.7
	C	A:ILE45	4.8	20.9	1.0

Magnesium binding site 2 out of 3 in 2iyy

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Magnesium Binding Sites List in 2iyy

Magnesium binding site 2 out of 3 in the Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg212 b:36.3 occ:0.70	OE2	A:GLU56	2.2	46.2	1.0
	CD	A:GLU56	3.1	31.3	1.0
	OE1	A:GLU56	3.2	42.0	1.0
	O	A:HOH2112	3.7	51.3	1.0
	CG1	A:ILE60	4.2	28.1	1.0
	O	A:HOH2099	4.4	24.4	0.5
	CG	A:GLU56	4.5	30.3	1.0
	CD1	A:ILE60	4.5	35.8	1.0

Magnesium binding site 3 out of 3 in 2iyy

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Magnesium Binding Sites List in 2iyy

Magnesium binding site 3 out of 3 in the Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Shikimate Kinase From Mycobacterium Tuberculosis in Complex with Shikimate-3-Phosphate and SO4 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg213 b:40.9 occ:0.25	O	A:HOH2236	2.0	51.1	1.0
	O3	A:SO4205	2.2	17.8	0.2
	O1	A:SO4205	2.4	28.6	0.2
	S	A:SO4205	2.8	29.6	0.2
	NH1	A:ARG20	3.6	39.8	1.0
	CG2	A:THR17	3.8	47.3	1.0
	O4	A:SO4205	3.9	34.2	0.2
	O2	A:SO4205	3.9	36.5	0.2
	CB	A:THR17	4.0	34.3	1.0
	NE	A:ARG21	4.5	27.6	0.5
	NE	A:ARG21	4.5	66.2	0.5
	CD	A:ARG20	4.6	26.5	0.5
	CA	A:THR17	4.6	35.6	1.0
	CZ	A:ARG20	4.7	55.0	1.0
	CD	A:ARG20	4.8	53.4	0.5
	O	A:THR17	4.9	32.2	1.0
	CG	A:ARG21	5.0	24.6	0.5

Reference:

M.D.Hartmann, G.P.Bourenkov, A.Oberschall, N.Strizhov, H.D.Bartunik. Mechanism of Phosphoryl Transfer Catalyzed By Shikimate Kinase From Mycobacterium Tuberculosis. J.Mol.Biol. V. 364 411 2006.
ISSN: ISSN 0022-2836
PubMed: 17020768
DOI: 10.1016/J.JMB.2006.09.001

Page generated: Wed Aug 14 00:20:26 2024

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