Sodium in PDB 6ytz: Crystal Structure of Malus Domestica Double Bond Reductase (Mddbr) in Complex with Nadph

The structure of Crystal Structure of Malus Domestica Double Bond Reductase (Mddbr) in Complex with Nadph, PDB code: 6ytz was solved by R.Caliandro, I.Polsinelli, N.Demitri, S.Benini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.44 / 1.40
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.545, 68.645, 145.398, 90, 90, 90
R / Rfree (%)	12.2 / 16.6

The binding sites of Sodium atom in the Crystal Structure of Malus Domestica Double Bond Reductase (Mddbr) in Complex with Nadph (pdb code 6ytz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Malus Domestica Double Bond Reductase (Mddbr) in Complex with Nadph, PDB code: 6ytz:

Sodium binding site 1 out of 1 in the Crystal Structure of Malus Domestica Double Bond Reductase (Mddbr) in Complex with Nadph


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Malus Domestica Double Bond Reductase (Mddbr) in Complex with Nadph within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:54.4 occ:1.00 OD2 A:ASP231 2.6 20.1 1.0 O A:HOH754 2.7 49.7 1.0 NE A:ARG250 3.5 21.7 1.0 O A:GLY160 3.6 22.0 1.0 CG A:ASP231 3.6 19.6 1.0 NH2 A:ARG250 3.7 27.6 1.0 CZ A:ARG250 3.7 23.4 1.0 CA A:GLU161 4.0 18.6 1.0 N A:THR162 4.0 16.7 1.0 OD1 A:ASP231 4.0 20.6 1.0 CG2 A:THR162 4.1 18.8 1.0 O A:HOH628 4.1 33.2 1.0 CD A:ARG250 4.2 21.6 1.0 C A:GLU161 4.3 18.5 1.0 OG1 A:THR162 4.4 18.0 1.0 NH1 A:ARG250 4.4 26.7 1.0 C A:GLY160 4.4 21.4 1.0 N A:GLU161 4.6 18.7 1.0 CB A:THR162 4.7 16.8 1.0 CB A:GLU161 4.8 18.8 1.0 CG A:GLU161 4.9 20.3 1.0 CB A:ASP231 4.9 17.0 1.0 CA A:THR162 5.0 16.9 1.0

R.Caliandro, I.Polsinelli, N.Demitri, F.Musiani, S.Martens, S.Benini. The Structural and Functional Characterization of Malus Domestica Double Bond Reductase Mddbr Provides Insights Towards the Identification of Its Substrates. Int.J.Biol.Macromol. V. 171 89 2021.
ISSN: ISSN 0141-8130
PubMed: 33412202
DOI: 10.1016/J.IJBIOMAC.2020.12.190