Sodium in PDB 5nuf: Cytosolic Malate Dehydrogenase 1

All present enzymatic activity of Cytosolic Malate Dehydrogenase 1:
1.1.1.37;

The structure of Cytosolic Malate Dehydrogenase 1, PDB code: 5nuf was solved by D.Young, J.Messens, J.Huang, J.-P.Reichheld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.67 / 1.80
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.592, 118.545, 148.219, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 31.4

The binding sites of Sodium atom in the Cytosolic Malate Dehydrogenase 1 (pdb code 5nuf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Cytosolic Malate Dehydrogenase 1, PDB code: 5nuf:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Cytosolic Malate Dehydrogenase 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cytosolic Malate Dehydrogenase 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:44.1 occ:1.00 O A:HOH688 2.4 50.0 1.0 OD2 A:ASP221 2.6 28.6 1.0 CG A:ASP221 3.5 27.9 1.0 O A:ASP217 3.6 24.5 1.0 CB A:ASP221 3.7 26.8 1.0 C A:ASP217 3.8 25.0 1.0 N A:ALA218 4.0 27.8 1.0 CB A:ASP217 4.0 23.8 1.0 CA A:ALA218 4.1 29.8 1.0 CA A:ASP217 4.5 21.3 1.0 OD1 A:ASP221 4.7 24.9 1.0 CB A:ALA218 5.0 32.7 1.0

Sodium binding site 2 out of 3 in the Cytosolic Malate Dehydrogenase 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cytosolic Malate Dehydrogenase 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:37.0 occ:0.85 OD2 A:ASP275 2.4 27.1 1.0 O A:HOH680 2.7 42.4 1.0 O A:HOH650 2.7 18.6 1.0 NE2 A:GLN301 3.1 26.2 1.0 OG A:SER277 3.3 23.4 1.0 O A:HOH533 3.4 25.6 0.9 CG A:ASP275 3.5 24.2 1.0 OD1 A:ASP275 3.8 21.9 1.0 O A:HOH639 3.8 29.2 0.8 CD1 A:ILE299 4.3 16.6 1.0 CD A:GLN301 4.4 24.0 1.0 O A:HOH673 4.4 23.7 1.0 CB A:ILE299 4.5 17.1 1.0 CB A:SER277 4.6 23.3 1.0 CB A:ASP275 4.8 23.1 1.0 CG1 A:ILE299 4.8 16.6 1.0

Sodium binding site 3 out of 3 in the Cytosolic Malate Dehydrogenase 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cytosolic Malate Dehydrogenase 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na408 b:37.9 occ:0.87 OE1 B:GLU170 2.3 23.4 1.0 O C:HOH660 2.4 27.6 0.9 O B:HOH652 2.5 31.4 0.8 CD B:GLU170 3.3 22.7 1.0 CG B:GLU170 3.6 18.2 1.0 O B:HOH509 3.6 19.0 1.0 CB B:GLU170 3.6 15.6 1.0 O4 A:SO4402 3.8 26.9 1.0 C3 B:GOL406 3.8 29.8 0.8 NH2 A:ARG7 3.9 16.0 1.0 C1 B:GOL406 3.9 24.9 0.8 CZ A:ARG7 4.2 17.2 1.0 NE A:ARG7 4.4 16.3 1.0 C2 B:GOL406 4.4 28.8 0.8 OE2 B:GLU170 4.5 22.6 1.0 O3 B:GOL406 4.5 31.3 0.8 CA B:GLU170 4.6 15.6 1.0 S A:SO4402 4.8 22.6 1.0 CD1 C:ILE59 4.8 16.8 1.0 O1 B:GOL406 4.9 23.2 0.8 NH1 A:ARG7 5.0 17.4 1.0 O B:HOH576 5.0 20.5 0.9 O B:GLU170 5.0 14.9 1.0

J.Huang, A.K.Niazi, D.Young, L.A.Rosado, D.Vertommen, N.Bodra, M.R.Abdelgawwad, F.Vignols, B.Wei, K.Wahni, T.Bashandy, L.Bariat, F.Van Breusegem, J.Messens, J.P.Reichheld. Self-Protection of Cytosolic Malate Dehydrogenase Against Oxidative Stress in Arabidopsis. J. Exp. Bot. V. 69 3491 2018.
ISSN: ESSN 1460-2431
PubMed: 29194485
DOI: 10.1093/JXB/ERX396