Sodium in PDB 5c6m: Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis

All present enzymatic activity of Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis:
4.1.2.4;

The structure of Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis, PDB code: 5c6m was solved by O.H.Weiergraeber, M.Dick, J.Bramski, J.Pietruszka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.70 / 1.76
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	154.030, 52.510, 143.210, 90.00, 122.34, 90.00
R / Rfree (%)	16.8 / 19.8

The structure of Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis (pdb code 5c6m). 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 Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis, PDB code: 5c6m:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis


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 Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:35.7 occ:1.00 O A:HOH634 2.3 54.5 1.0 O A:HOH553 2.4 20.2 1.0 O A:PHE76 2.4 21.0 1.0 O A:HOH610 2.5 33.5 1.0 O B:HOH674 2.6 28.2 1.0 O A:HOH484 2.7 31.3 1.0 C A:PHE76 3.6 18.9 1.0 O A:HOH627 3.8 33.1 1.0 N A:PHE76 4.0 16.2 1.0 NE2 A:HIS78 4.1 23.3 1.0 OE2 A:GLU89 4.2 27.5 1.0 O A:HOH472 4.2 27.6 1.0 O B:HOH428 4.2 42.5 1.0 CA A:PHE76 4.2 14.7 1.0 O A:HOH423 4.3 19.8 1.0 O A:HOH688 4.5 15.9 1.0 CD2 A:HIS78 4.5 26.8 1.0 OE1 A:GLU89 4.6 27.0 1.0 CB A:PHE76 4.6 15.8 1.0 N A:PRO77 4.7 17.6 1.0 CD A:GLU89 4.7 24.8 1.0 CD A:PRO77 4.9 20.7 1.0 O B:HOH559 5.0 40.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis


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 Deoxyribose-Phosphate Aldolase From Shewanella Halifaxensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:35.3 occ:1.00 O B:HOH623 2.3 47.6 1.0 O B:PHE76 2.4 18.1 1.0 O B:HOH581 2.4 31.4 1.0 O B:HOH525 2.4 18.0 1.0 O A:HOH689 2.6 25.9 1.0 O B:HOH523 2.7 27.5 1.0 C B:PHE76 3.5 16.8 1.0 O B:HOH609 3.9 34.2 1.0 O A:HOH600 3.9 51.4 1.0 N B:PHE76 3.9 18.6 1.0 CA B:PHE76 4.2 15.9 1.0 NE2 B:HIS78 4.2 25.0 1.0 O B:HOH476 4.3 22.4 1.0 OE2 B:GLU89 4.4 26.5 1.0 O B:HOH449 4.4 18.0 1.0 O B:HOH668 4.5 13.2 1.0 CD2 B:HIS78 4.6 25.9 1.0 CB B:PHE76 4.6 16.6 1.0 N B:PRO77 4.6 17.2 1.0 OE1 B:GLU89 4.7 28.5 1.0 CD B:PRO77 4.8 21.6 1.0 CD B:GLU89 4.9 23.4 1.0 O A:HOH624 5.0 41.7 1.0

M.Dick, O.H.Weiergraber, T.Classen, C.Bisterfeld, J.Bramski, H.Gohlke, J.Pietruszka. Trading Off Stability Against Activity in Extremophilic Aldolases. Sci Rep V. 6 17908 2016.
ISSN: ESSN 2045-2322
PubMed: 26783049
DOI: 10.1038/SREP17908