Sodium in PDB 9quu: Triosephosphate Isomerase of Rhodococcus Sp. Jg-3

All present enzymatic activity of Triosephosphate Isomerase of Rhodococcus Sp. Jg-3:
5.3.1.1;

The structure of Triosephosphate Isomerase of Rhodococcus Sp. Jg-3, PDB code: 9quu was solved by J.S.Nowak, S.Olesen, R.Baerentsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.62 / 1.63
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	86.102, 86.102, 152.835, 90, 90, 90
R / Rfree (%)	19.4 / 21.3

The binding sites of Sodium atom in the Triosephosphate Isomerase of Rhodococcus Sp. Jg-3 (pdb code 9quu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Triosephosphate Isomerase of Rhodococcus Sp. Jg-3, PDB code: 9quu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Triosephosphate Isomerase of Rhodococcus Sp. Jg-3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Triosephosphate Isomerase of Rhodococcus Sp. Jg-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:58.1 occ:1.00 O A:VAL228 2.3 59.4 1.0 O A:HOH469 2.3 61.3 1.0 O A:VAL233 2.3 57.9 1.0 O A:HOH527 2.4 60.2 1.0 O A:GLN230 2.4 62.3 1.0 O A:HOH461 2.5 58.5 1.0 C A:VAL228 3.5 59.4 1.0 C A:VAL233 3.5 55.4 1.0 C A:GLN230 3.5 61.6 1.0 C A:GLY229 3.8 61.9 1.0 N A:GLN230 3.9 61.1 1.0 O A:GLY229 4.0 67.6 1.0 CA A:GLY229 4.2 60.0 1.0 N A:VAL233 4.3 58.1 1.0 N A:GLY229 4.3 57.5 1.0 CA A:GLN230 4.4 62.5 1.0 CA A:VAL233 4.4 56.0 1.0 CG1 A:VAL228 4.4 60.3 1.0 N A:ASP234 4.4 51.8 1.0 N A:PRO231 4.5 65.6 1.0 CA A:VAL228 4.5 53.7 1.0 CA A:PRO231 4.5 63.4 1.0 C A:PRO231 4.5 63.6 1.0 CA A:ASP234 4.5 51.2 1.0 O A:PRO231 4.6 63.8 1.0 OD1 A:ASP234 4.7 58.1 1.0 CB A:VAL233 4.7 55.4 1.0 N A:ASP232 5.0 64.4 1.0

Sodium binding site 2 out of 2 in the Triosephosphate Isomerase of Rhodococcus Sp. Jg-3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Triosephosphate Isomerase of Rhodococcus Sp. Jg-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:41.6 occ:1.00 O B:VAL233 2.2 39.9 1.0 O B:VAL228 2.2 45.6 1.0 O B:HOH536 2.4 45.6 1.0 O B:HOH442 2.5 46.6 1.0 O B:GLN230 2.5 43.3 1.0 O B:HOH542 2.5 45.7 1.0 C B:VAL233 3.3 39.6 1.0 C B:VAL228 3.4 40.6 1.0 C B:GLN230 3.6 44.8 1.0 C B:GLY229 4.0 43.3 1.0 N B:GLN230 4.0 42.6 1.0 N B:VAL233 4.1 39.5 1.0 O B:HOH515 4.2 47.3 1.0 CA B:VAL233 4.2 39.8 1.0 CA B:GLY229 4.3 44.0 1.0 N B:ASP234 4.3 38.6 1.0 N B:GLY229 4.3 41.2 1.0 CG1 B:VAL228 4.3 45.4 1.0 CA B:VAL228 4.3 42.3 1.0 O B:GLY229 4.3 46.0 1.0 CA B:ASP234 4.4 39.9 1.0 O B:PRO231 4.4 47.4 1.0 CA B:GLN230 4.4 45.3 1.0 C B:PRO231 4.5 42.8 1.0 O B:HOH560 4.5 55.6 1.0 CA B:PRO231 4.5 48.4 1.0 N B:PRO231 4.6 46.9 1.0 CB B:VAL233 4.6 38.9 1.0 OD1 B:ASP234 4.7 43.0 1.0 CB B:VAL228 5.0 42.6 1.0

J.S.Nowak, S.Olesen, P.Tian, R.L.Baerentsen, D.E.Brodersen, D.E.Otzen. Role of Electrostatics in Cold Adaptation: A Comparative Study of Eury- and Stenopsychrophilic Triose Phosphate Isomerase. Biochim Biophys Acta V.1873 41072 2025PROTEINS Proteom.
ISSN: ISSN 1878-1454
PubMed: 40220927
DOI: 10.1016/J.BBAPAP.2025.141072