Sodium in PDB 6mvt: Structure of A Bacterial ALDH16 Complexed with Nadh

The structure of Structure of A Bacterial ALDH16 Complexed with Nadh, PDB code: 6mvt was solved by J.J.Tanner, L.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.27 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.719, 159.109, 62.664, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.4

The binding sites of Sodium atom in the Structure of A Bacterial ALDH16 Complexed with Nadh (pdb code 6mvt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of A Bacterial ALDH16 Complexed with Nadh, PDB code: 6mvt:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of A Bacterial ALDH16 Complexed with Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Bacterial ALDH16 Complexed with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:14.5 occ:1.00 O A:LEU732 2.4 16.8 1.0 O A:GLY460 2.7 17.6 1.0 O A:ARG457 2.7 28.4 1.0 O A:HOH1219 2.8 22.0 1.0 N A:ARG457 3.4 20.9 1.0 C A:LEU732 3.5 20.0 1.0 O A:HOH1142 3.6 32.2 1.0 C A:ARG457 3.6 23.8 1.0 O A:HOH1128 3.7 28.1 1.0 C A:GLY460 3.7 22.1 1.0 CA A:ARG457 3.8 20.9 1.0 O A:HOH1095 3.9 22.7 1.0 C A:VAL456 3.9 23.5 1.0 CA A:LYS733 4.0 19.7 1.0 N A:LYS733 4.1 18.7 1.0 CD2 A:PHE461 4.2 15.6 1.0 CA A:VAL456 4.3 23.2 1.0 C A:LYS733 4.3 17.7 1.0 N A:ARG734 4.3 15.7 1.0 CB A:PHE461 4.3 16.8 1.0 CA A:GLY460 4.4 15.7 1.0 CB A:LEU732 4.4 12.0 1.0 N A:GLY460 4.5 11.4 1.0 CA A:LEU732 4.6 16.9 1.0 O A:VAL456 4.6 25.9 1.0 O A:ASN731 4.6 18.9 1.0 N A:PHE461 4.6 21.3 1.0 CG A:PHE461 4.8 17.2 1.0 CA A:PHE461 4.8 19.3 1.0 N A:GLU458 4.8 17.1 1.0 CG A:ARG734 4.8 13.5 1.0 O A:LYS733 5.0 18.4 1.0

Sodium binding site 2 out of 3 in the Structure of A Bacterial ALDH16 Complexed with Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Bacterial ALDH16 Complexed with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Na803 b:6.4 occ:1.00 O A:TRP192 2.6 17.6 1.0 O A:ASP115 2.6 25.0 1.0 O A:VAL50 2.8 20.7 1.0 OG1 A:THR49 2.8 26.9 1.0 O A:HOH1206 2.8 22.1 1.0 OD1 A:ASP115 2.8 20.4 1.0 N A:VAL50 3.5 28.1 1.0 C A:ASP115 3.7 20.6 1.0 C A:VAL50 3.7 18.4 1.0 C A:TRP192 3.8 18.1 1.0 CG A:ASP115 3.8 21.6 1.0 CA A:ASP115 4.1 15.8 1.0 CB A:THR49 4.1 27.4 1.0 CA A:VAL50 4.2 20.0 1.0 C A:THR49 4.3 23.6 1.0 CA A:THR49 4.4 22.3 1.0 CA A:TRP192 4.5 17.4 1.0 CB A:ASP115 4.5 18.3 1.0 CD A:PRO52 4.6 20.8 1.0 OD2 A:ASP115 4.6 22.5 1.0 N A:THR193 4.8 14.2 1.0 N A:ASN51 4.8 20.5 1.0 CB A:TRP192 4.9 21.4 1.0 N A:ASN116 4.9 23.8 1.0 CA A:THR193 4.9 22.8 1.0 O A:HOH1078 4.9 17.1 1.0 CG2 A:THR193 5.0 13.9 1.0

Sodium binding site 3 out of 3 in the Structure of A Bacterial ALDH16 Complexed with Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Bacterial ALDH16 Complexed with Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Na804 b:9.2 occ:1.00 O A:LEU621 2.5 26.2 1.0 O A:VAL619 2.6 18.7 1.0 O A:HOH1195 2.7 38.8 1.0 O A:GLY623 2.9 20.5 1.0 O A:HOH1291 2.9 33.4 1.0 O A:HOH1150 3.0 25.8 1.0 C A:LEU621 3.7 25.5 1.0 N A:GLY623 3.7 14.8 1.0 C A:VAL619 3.8 16.4 1.0 C A:GLY623 3.9 16.0 1.0 CG2 A:VAL619 4.1 11.7 1.0 O A:HOH1222 4.1 20.9 1.0 C A:ARG622 4.2 22.5 1.0 CA A:GLY623 4.3 19.6 1.0 N A:LEU621 4.4 25.0 1.0 N A:VAL619 4.4 17.0 1.0 C A:PRO620 4.4 25.5 1.0 CA A:ARG622 4.6 22.6 1.0 N A:ARG622 4.6 25.6 1.0 CA A:VAL619 4.6 14.6 1.0 CA A:LEU621 4.7 24.0 1.0 O A:PRO620 4.7 35.3 1.0 N A:PRO620 4.8 17.9 1.0 CA A:PRO620 4.8 18.3 1.0 O A:ARG622 4.9 23.5 1.0 O A:HOH1320 5.0 37.9 1.0

L.K.Liu, J.J.Tanner. Crystal Structure of Aldehyde Dehydrogenase 16 Reveals Trans-Hierarchical Structural Similarity and A New Dimer. J. Mol. Biol. V. 431 524 2019.
ISSN: ESSN 1089-8638
PubMed: 30529746
DOI: 10.1016/J.JMB.2018.11.030