Sodium in PDB 1lk7: Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid

All present enzymatic activity of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid:
5.3.1.6;

The structure of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid, PDB code: 1lk7 was solved by K.Ishikawa, I.Matsui, F.Payan, C.Cambillau, H.Ishida, Y.Kawarabayasi, H.Kikuchi, A.Roussel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.689, 114.923, 119.578, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.7

The structure of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid also contains other interesting chemical elements:

Chlorine

(Cl)

10 atoms

The binding sites of Sodium atom in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid (pdb code 1lk7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid, PDB code: 1lk7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2011 b:25.1 occ:1.00 O A:ASN175 2.2 25.0 1.0 O A:HOH2049 2.3 32.4 1.0 O A:HOH2019 2.3 28.0 1.0 O B:ASN175 2.4 26.1 1.0 O B:HOH2026 2.4 24.0 1.0 O A:HOH2050 2.4 31.2 1.0 C A:ASN175 3.4 25.2 1.0 C B:ASN175 3.6 26.0 1.0 O A:HOH2020 4.1 57.3 1.0 O B:HOH2020 4.1 40.4 1.0 O A:HOH2075 4.2 45.9 1.0 CA A:ASN175 4.3 24.6 1.0 O D:HOH2050 4.3 34.5 1.0 O D:HOH2053 4.3 35.2 1.0 CB A:ASN175 4.3 25.3 1.0 N A:GLY176 4.4 25.6 1.0 CA A:GLY176 4.4 25.4 1.0 CA B:ASN175 4.5 26.6 1.0 OD1 B:ASN177 4.5 25.6 1.0 OD1 A:ASN177 4.5 23.9 1.0 CB B:ASN175 4.5 27.6 1.0 N B:GLY176 4.5 24.9 1.0 O B:HOH2048 4.6 37.7 1.0 O B:HOH2050 4.7 46.9 1.0 CA B:GLY176 4.7 24.4 1.0 OD1 A:ASN175 4.8 34.8 1.0 ND2 A:ASN177 4.8 23.3 1.0 OD1 B:ASN175 4.8 41.1 1.0 ND2 B:ASN177 4.8 22.8 1.0 C A:GLY176 4.9 25.5 1.0 CG A:ASN177 5.0 25.1 1.0 CG B:ASN177 5.0 24.8 1.0

Sodium binding site 2 out of 2 in the Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of D-Ribose-5-Phosphate Isomerase From in Complex with Phospho-Erythronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Na2012 b:25.6 occ:1.00 O D:HOH2039 2.3 24.2 1.0 O C:ASN175 2.4 25.5 1.0 O D:ASN175 2.4 26.2 1.0 O D:HOH2040 2.5 26.3 1.0 O C:HOH2051 2.5 23.6 1.0 O C:HOH2052 2.6 28.4 1.0 C C:ASN175 3.5 24.9 1.0 C D:ASN175 3.6 26.5 1.0 O D:HOH2046 4.0 31.0 1.0 O C:HOH2033 4.0 32.5 1.0 O D:HOH2053 4.2 35.2 1.0 CB D:ASN175 4.3 26.8 1.0 O D:HOH2050 4.3 34.5 1.0 CB C:ASN175 4.3 26.3 1.0 CA C:ASN175 4.4 25.9 1.0 CA D:ASN175 4.4 26.7 1.0 O D:HOH2068 4.5 39.0 1.0 OD1 C:ASN177 4.5 26.4 1.0 N C:GLY176 4.5 24.9 1.0 O C:HOH2090 4.5 41.0 1.0 N D:GLY176 4.6 26.1 1.0 O D:HOH2018 4.6 47.0 1.0 OD1 D:ASN177 4.6 24.5 1.0 CA C:GLY176 4.6 25.1 1.0 OD1 D:ASN175 4.6 29.7 1.0 CA D:GLY176 4.6 25.5 1.0 ND2 C:ASN177 4.7 24.8 1.0 ND2 D:ASN177 4.8 27.6 1.0 CG C:ASN177 5.0 25.5 1.0 C C:GLY176 5.0 25.5 1.0

K.Ishikawa, I.Matsui, F.Payan, C.Cambillau, H.Ishida, Y.Kawarabayasi, H.Kikuchi, A.Roussel. A Hyperthermostable D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii Characterization and Three-Dimensional Structure Structure V. 10 877 2002.
ISSN: ISSN 0969-2126
PubMed: 12057201
DOI: 10.1016/S0969-2126(02)00779-7