Magnesium in PDB 4ume: Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule

Enzymatic activity of Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule

All present enzymatic activity of Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule:
3.1.3.45;

Protein crystallography data

The structure of Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule, PDB code: 4ume was solved by S.Dhindwal, S.Tomar, P.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	37.38 / 2.09
*Space group*	I 4
*Cell size a, b, c (Å), α, β, γ (°)*	86.610, 86.610, 41.400, 90.00, 90.00, 90.00
*R / R_free (%)*	19.015 / 25.844

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule (pdb code 4ume). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule, PDB code: 4ume:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4ume

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Magnesium Binding Sites List in 4ume

Magnesium binding site 1 out of 4 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule

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 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1175 b:17.6 occ:1.00	OD2	A:ASP17	2.0	15.2	1.0
	OD1	A:ASP110	2.0	14.8	1.0
	O	A:HOH2007	2.1	14.9	1.0
	O	A:HOH2009	2.1	12.8	1.0
	O	A:HOH2006	2.1	17.1	1.0
	O	A:ASP19	2.2	13.1	1.0
	CG	A:ASP17	3.0	14.5	1.0
	CG	A:ASP110	3.1	15.2	1.0
	C	A:ASP19	3.3	13.3	1.0
	OD1	A:ASP17	3.4	14.2	1.0
	OD2	A:ASP110	3.5	14.6	1.0
	OD2	A:ASP114	4.0	12.4	1.0
	CA	A:ASP19	4.1	14.0	1.0
	N	A:ASP19	4.2	13.5	1.0
	CB	A:ASP19	4.2	14.6	1.0
	O	A:HOH2082	4.3	23.6	1.0
	CB	A:ASP17	4.3	14.0	1.0
	CB	A:ASP110	4.4	14.9	1.0
	N	A:GLY20	4.4	13.0	1.0
	O	A:HOH2048	4.5	12.9	1.0
	N	A:ASP110	4.5	14.3	1.0
	O8	A:KDO1174	4.5	33.0	1.0
	O	A:HOH2008	4.6	6.2	1.0
	C8	A:KDO1174	4.6	33.2	1.0
	CA	A:GLY20	4.6	12.7	1.0
	N	A:ASP111	4.8	15.6	1.0
	CB	A:ASP111	4.8	15.3	1.0
	CA	A:ASP110	4.9	15.1	1.0
	C	A:VAL18	4.9	13.4	1.0
	CG1	A:ILE21	5.0	12.2	1.0

Magnesium binding site 2 out of 4 in 4ume

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Magnesium Binding Sites List in 4ume

Magnesium binding site 2 out of 4 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule

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 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1176 b:16.2 occ:0.25	O	A:HOH2085	2.3	18.9	1.0
	O	A:HOH2086	2.5	42.9	1.0
	O	A:HOH2084	3.3	30.6	1.0
	OE1	A:GLN26	4.6	17.4	1.0
	NE2	A:GLN26	4.9	17.7	1.0

Magnesium binding site 3 out of 4 in 4ume

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Magnesium Binding Sites List in 4ume

Magnesium binding site 3 out of 4 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule

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 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1177 b:85.3 occ:0.25	O	A:HOH2084	2.8	30.6	1.0
	MG	A:MG1178	3.1	25.8	0.2
	CG2	A:THR36	5.0	12.3	1.0

Magnesium binding site 4 out of 4 in 4ume

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Magnesium Binding Sites List in 4ume

Magnesium binding site 4 out of 4 in the Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of 3-Deoxy-D-Manno-Octulosonate 8- Phosphate Phosphatase From Moraxella Catarrhalis in Complex with Magnesium Ion and Kdo Molecule within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1178 b:25.8 occ:0.25	MG	A:MG1177	3.1	85.3	0.2
	O	A:HOH2021	3.2	11.7	1.0
	OG1	A:THR36	4.5	12.1	1.0
	CG2	A:THR36	4.8	12.3	1.0

Reference:

S.Dhindwal, P.Priyadarshini, D.N.Patil, S.Tapas, P.Kumar, S.Tomar, P.Kumar. Ligand-Bound Structures of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase From Moraxella Catarrhalis Reveal A Water Channel Connecting to the Active Site For the Second Step of Catalysis Acta Crystallogr.,Sect.D V. 71 239 2015.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004714025218

Page generated: Tue Aug 20 04:50:59 2024

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