Sodium in PDB 4c80: Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide

All present enzymatic activity of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide:
1.2.99.7;

The structure of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide, PDB code: 4c80 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)	123.89 / 1.50
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	143.057, 143.057, 162.292, 90.00, 90.00, 120.00
R / Rfree (%)	10.325 / 13.362

The structure of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide also contains other interesting chemical elements:

Molybdenum	(Mo)	1 atom
Magnesium	(Mg)	3 atoms
Iron	(Fe)	4 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide (pdb code 4c80). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide, PDB code: 4c80:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na913 b:26.2 occ:0.50 O A:GLN29 2.4 16.7 1.0 O A:HOH2383 2.4 39.0 1.0 O A:HOH2072 2.5 23.1 1.0 O A:HOH2384 2.5 35.1 1.0 O A:HOH3092 2.7 18.0 0.5 O A:HOH2078 2.9 53.5 1.0 C A:GLN29 3.5 13.2 1.0 CA A:GLN29 3.9 13.2 1.0 O A:ARG28 4.4 12.7 1.0 O A:LEU201 4.4 15.0 1.0 O A:HOH2082 4.6 20.6 1.0 N A:GLN30 4.6 11.7 1.0 N A:GLY32 4.8 11.9 1.0 CA A:GLY32 4.8 12.1 1.0 CB A:GLN29 4.8 14.2 1.0 O A:HOH2037 4.9 30.1 1.0

Sodium binding site 2 out of 2 in the Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Aldehyde Oxidoreductase From Desulfovibrio Gigas (Mop), Soaked with Hydrogen Peroxide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na914 b:38.0 occ:1.00 O A:HOH2730 2.9 38.9 1.0 O A:HOH2729 2.9 35.5 1.0 O A:HOH2410 3.0 18.4 1.0 O A:HOH2732 3.0 40.1 1.0 O A:HOH2419 3.2 41.0 1.0 O A:HOH2409 3.2 28.6 1.0 OE1 A:GLN214 3.4 12.9 1.0 NZ A:LYS216 3.4 21.0 0.5 CG A:GLN452 3.6 10.9 1.0 OE1 A:GLN455 3.8 14.8 1.0 O A:HOH2414 4.0 21.2 1.0 NE2 A:GLN452 4.3 11.7 1.0 CD A:GLN452 4.3 9.8 1.0 CD A:GLN214 4.4 11.8 1.0 N A:GLN452 4.7 9.5 1.0 CB A:GLN451 4.7 13.1 1.0 NE2 A:GLN214 4.8 11.6 1.0 CB A:GLN452 4.8 9.8 1.0 CE A:LYS216 4.9 20.4 0.5 CA A:GLN452 4.9 9.3 1.0 OD1 A:ASN449 4.9 11.6 1.0 CD A:GLN455 5.0 12.9 1.0

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