Sodium in PDB 6yux: Crystal Structure of Malus Domestica Double Bond Reductase (Mddbr) Ternary Complex

The structure of Crystal Structure of Malus Domestica Double Bond Reductase (Mddbr) Ternary Complex, PDB code: 6yux 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)	48.52 / 1.36
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.491, 68.611, 145.969, 90, 90, 90
R / Rfree (%)	14.3 / 17.9

The binding sites of Sodium atom in the Crystal Structure of Malus Domestica Double Bond Reductase (Mddbr) Ternary Complex (pdb code 6yux). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Malus Domestica Double Bond Reductase (Mddbr) Ternary Complex, PDB code: 6yux:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Malus Domestica Double Bond Reductase (Mddbr) Ternary Complex


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) Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:42.8 occ:1.00 O A:HOH677 2.1 56.6 1.0 OD2 A:ASP231 2.8 14.8 1.0 O A:GLY160 3.4 18.4 1.0 NH2 A:ARG250 3.6 20.7 1.0 NE A:ARG250 3.6 18.2 1.0 CZ A:ARG250 3.8 22.5 1.0 CG A:ASP231 3.8 14.4 1.0 CA A:GLU161 3.9 15.1 1.0 N A:THR162 4.1 13.4 1.0 O A:HOH574 4.1 25.5 1.0 OD1 A:ASP231 4.1 15.6 1.0 C A:GLY160 4.2 17.5 1.0 CG2 A:THR162 4.2 14.9 1.0 C A:GLU161 4.4 15.5 1.0 CD A:ARG250 4.5 18.3 1.0 N A:GLU161 4.5 14.3 1.0 NH1 A:ARG250 4.6 22.0 1.0 OG1 A:THR162 4.7 14.6 1.0 CG A:GLU161 4.8 16.1 1.0 CB A:GLU161 4.8 14.5 1.0 CB A:THR162 4.9 14.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Malus Domestica Double Bond Reductase (Mddbr) Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Malus Domestica Double Bond Reductase (Mddbr) Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:30.7 occ:1.00 O A:HOH611 2.7 18.0 1.0 O A:ILE261 2.8 14.8 1.0 ND2 A:ASN265 3.0 19.4 1.0 CE2 A:PHE23 3.9 25.4 1.0 CG A:ASN265 4.0 18.3 1.0 C A:ILE261 4.0 13.8 1.0 CB A:ASN265 4.0 18.6 1.0 O A:SER262 4.0 16.4 1.0 CB A:TYR334 4.1 14.0 1.0 C A:SER262 4.1 17.1 1.0 N A:TYR264 4.2 17.2 1.0 N A:ASN265 4.2 18.6 1.0 CZ A:PHE23 4.2 29.4 1.0 CA A:SER262 4.2 14.8 1.0 CD1 A:TYR334 4.2 15.2 1.0 N6A A:NAP401 4.4 15.9 1.0 N7A A:NAP401 4.4 13.5 1.0 CG A:TYR334 4.6 14.2 1.0 N A:SER262 4.6 14.0 1.0 CB A:TYR264 4.6 16.7 1.0 O A:TYR334 4.6 16.1 1.0 N A:GLN263 4.7 16.1 1.0 CG1 A:ILE261 4.7 14.3 1.0 CA A:TYR334 4.7 15.8 1.0 CA A:TYR264 4.8 17.1 1.0 CA A:ASN265 4.8 18.5 1.0 C A:TYR264 4.8 17.2 1.0 CD2 A:PHE23 4.8 22.4 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