Sodium in PDB 6qrr: X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 Mgy

All present enzymatic activity of X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 Mgy:
5.3.1.5;

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 Mgy, PDB code: 6qrr was solved by H.Taberman, C.S.Bury, M.J.Van Der Woerd, E.H.Snell, E.F.Garman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.69 / 1.10
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.478, 97.459, 102.485, 90.00, 90.00, 90.00
R / Rfree (%)	12.1 / 14.7

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 Mgy also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Manganese	(Mn)	4 atoms

The binding sites of Sodium atom in the X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 Mgy (pdb code 6qrr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 Mgy, PDB code: 6qrr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 Mgy


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Na418 b:19.5 occ:1.00 O A:HOH651 2.7 17.9 1.0 O A:HOH564 2.9 35.9 0.9 O A:HOH903 3.0 42.9 1.0 N A:LEU241 3.0 10.7 1.0 C A:GLY239 3.4 11.4 1.0 N A:LYS240 3.4 11.0 1.0 CA A:GLY239 3.6 12.1 1.0 CB A:LEU241 3.7 10.5 1.0 CA A:LEU241 3.8 10.2 1.0 O A:GLY239 3.8 13.4 1.0 CD2 A:LEU236 3.9 11.4 1.0 O A:LEU241 3.9 12.8 1.0 C A:LYS240 4.0 10.3 1.0 CA A:LEU236 4.1 9.4 1.0 C A:LEU241 4.1 10.9 1.0 O A:HOH973 4.2 69.9 0.8 CA A:LYS240 4.2 10.7 1.0 O A:ALA235 4.2 10.1 1.0 O A:LEU236 4.3 11.2 1.0 N A:GLY239 4.4 11.4 1.0 C A:LEU236 4.7 10.0 1.0 C1 A:EDO411 4.7 24.6 0.3 C1 A:EDO411 4.8 26.6 0.7 N A:LEU236 4.8 9.3 1.0 CG A:LEU236 4.8 10.3 1.0 C A:ALA235 4.9 9.0 1.0 CB A:LEU236 4.9 10.6 1.0

Sodium binding site 2 out of 2 in the X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 Mgy


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Na419 b:21.2 occ:1.00 O A:HOH979 2.6 41.5 1.0 OD2 A:ASP156 2.7 14.6 1.0 OD1 A:ASP153 2.8 14.4 1.0 NH1 A:ARG157 3.0 14.7 1.0 O A:HOH814 3.2 44.5 1.0 CG A:ASP156 3.6 12.4 1.0 CB A:ASP156 3.6 12.2 1.0 CG A:ASP153 3.7 11.9 1.0 CA A:ASP153 3.7 10.6 1.0 O A:HOH772 3.7 68.1 1.0 CZ A:ARG157 3.8 14.9 1.0 NH2 A:ARG157 3.8 16.5 1.0 CB A:ASP153 3.9 11.2 1.0 C2 A:EDO406 3.9 29.1 1.0 O A:HOH954 4.0 77.9 1.0 O A:HOH630 4.1 23.1 0.9 O A:ASP153 4.2 10.5 1.0 O2 A:EDO406 4.4 29.1 1.0 C A:ASP153 4.5 9.9 1.0 O A:HOH1007 4.5 53.7 1.0 N A:ASP153 4.7 9.4 1.0 OD1 A:ASP156 4.8 13.2 1.0 OD2 A:ASP153 4.8 12.1 1.0 O A:ARG152 4.9 10.6 1.0 O A:HOH906 5.0 0.5 1.0

H.Taberman, C.S.Bury, M.J.Van Der Woerd, E.H.Snell, E.F.Garman. Structural Knowledge or X-Ray Damage? A Case Study on Xylose Isomerase Illustrating Both. J.Synchrotron Radiat. V. 26 931 2019.
ISSN: ESSN 1600-5775
PubMed: 31274415
DOI: 10.1107/S1600577519005599