Magnesium in PDB 4c7y: Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide

Enzymatic activity of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide

All present enzymatic activity of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide:
1.2.99.7;

Protein crystallography data

The structure of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide, PDB code: 4c7y was solved by H.D.Correia, M.J.Romao, T.Santos-Silva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	124.06 / 1.57
*Space group*	P 6₁ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	143.250, 143.250, 162.300, 90.00, 90.00, 120.00
*R / R_free (%)*	13.44 / 15.792

Other elements in 4c7y:

The structure of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide also contains other interesting chemical elements:

Molybdenum	(Mo)	1 atom
Iron	(Fe)	4 atoms
Chlorine	(Cl)	2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide (pdb code 4c7y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide, PDB code: 4c7y:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4c7y

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Magnesium Binding Sites List in 4c7y

Magnesium binding site 1 out of 3 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg916 b:26.6 occ:1.00	O	A:HOH3226	2.0	36.8	1.0
	O	A:HOH2210	2.0	29.3	1.0
	O	A:HOH2214	2.1	20.1	1.0
	O	A:HOH3225	2.1	40.4	1.0
	O	A:HOH2377	2.1	29.0	1.0
	O	A:HOH3224	2.2	35.5	1.0
	O	A:LEU85	4.2	13.2	1.0
	OE2	A:GLU162	4.2	23.9	1.0
	O	A:HOH2213	4.2	33.7	1.0
	O	A:HOH2083	4.3	35.5	1.0
	OE1	A:GLU162	4.4	23.7	1.0
	O	A:HOH2708	4.5	33.5	1.0
	O	A:HOH2190	4.5	17.2	1.0
	CD	A:PRO87	4.6	13.4	1.0
	CD	A:GLU162	4.8	24.9	1.0
	OD1	A:ASN84	4.8	22.1	1.0

Magnesium binding site 2 out of 3 in 4c7y

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Magnesium Binding Sites List in 4c7y

Magnesium binding site 2 out of 3 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg917 b:23.5 occ:1.00	O	A:HOH3228	2.0	24.4	1.0
	O	A:HOH3230	2.1	23.2	1.0
	O	A:HOH3231	2.1	22.3	1.0
	O	A:HOH3229	2.1	26.9	1.0
	O	A:HOH2871	2.1	15.1	1.0
	O	A:HOH3227	2.3	26.6	1.0
	O	A:HOH2869	4.0	22.8	1.0
	O	A:HOH2872	4.2	15.2	1.0
	O	A:HOH2394	4.2	15.0	1.0
	O	A:HOH2912	4.2	21.5	1.0
	O	A:HOH2397	4.3	21.1	1.0
	OD1	A:ASP572	4.4	13.3	1.0
	OD1	A:ASN511	4.7	14.1	1.0
	O	A:HOH2904	4.8	25.8	1.0
	O	A:HOH2443	4.9	26.1	1.0

Magnesium binding site 3 out of 3 in 4c7y

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Magnesium Binding Sites List in 4c7y

Magnesium binding site 3 out of 3 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Sodium Dithionite and Sodium Sulfide within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg919 b:10.3 occ:1.00	OE2	A:GLU903	2.0	13.8	1.0
	O	A:HOH3218	2.0	10.5	1.0
	OE2	A:GLU899	2.1	11.2	1.0
	O	A:HOH3208	2.1	14.4	1.0
	O	A:HOH3210	2.1	11.6	1.0
	CD	A:GLU903	3.1	17.4	1.0
	CD	A:GLU899	3.1	11.2	1.0
	CG	A:GLU899	3.5	11.0	1.0
	CG	A:GLU903	3.6	14.2	1.0
	O	A:HOH3209	3.7	15.4	1.0
	O	A:HOH3206	4.0	25.6	1.0
	OE1	A:GLU903	4.1	22.8	1.0
	O	A:HOH3207	4.2	33.9	1.0
	OE1	A:GLU899	4.3	12.2	1.0
	O	A:HOH3217	4.8	31.2	1.0
	O	A:HOH3205	4.9	22.5	1.0

Reference:

J.Marangon, H.D.Correia, C.D.Brondino, J.J.G.Moura, M.J.Romao, P.J.Gonzalez, T.Santos-Silva. Kinetic and Structural Studies of Aldehyde Oxidoreductase From Desulfovibrio Gigas Reveal A Dithiolene-Based Chemistry For Enzyme Activation and Inhibition By H2O2. Plos One V. 8 83234 2013.
ISSN: ISSN 1932-6203
PubMed: 24391748
DOI: 10.1371/JOURNAL.PONE.0083234

Page generated: Thu Aug 15 16:44:34 2024

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