Sodium in PDB 6qrs: 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: 6qrs 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)	35.32 / 1.17
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.501, 97.489, 102.503, 90.00, 90.00, 90.00
R / Rfree (%)	9.9 / 11.7

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 6qrs). 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: 6qrs:
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:17.1 occ:1.00 H A:LEU241 2.3 11.4 1.0 O A:HOH673 2.7 16.2 1.0 O A:HOH585 2.8 41.0 0.9 O A:HOH912 2.9 44.7 1.0 HD23 A:LEU236 3.0 12.7 1.0 HA2 A:GLY239 3.0 12.7 1.0 HB3 A:LEU241 3.0 11.3 1.0 N A:LEU241 3.1 9.5 1.0 HA A:LEU236 3.1 10.2 1.0 H A:LYS240 3.4 11.8 1.0 C A:GLY239 3.4 10.6 1.0 N A:LYS240 3.4 9.8 1.0 CA A:GLY239 3.6 10.6 1.0 CB A:LEU241 3.7 9.4 1.0 CA A:LEU241 3.8 9.4 1.0 HB2 A:LEU241 3.8 11.3 1.0 O A:GLY239 3.8 11.8 1.0 CD2 A:LEU236 3.9 10.6 1.0 O A:LEU241 3.9 12.0 1.0 H11 A:EDO411 3.9 35.0 0.3 C A:LYS240 4.0 9.6 1.0 H12 A:EDO411 4.1 21.3 0.7 CA A:LEU236 4.1 8.5 1.0 C A:LEU241 4.1 10.0 1.0 HD22 A:LEU236 4.2 12.7 1.0 O A:HOH978 4.2 66.9 0.7 H A:GLY239 4.2 12.4 1.0 CA A:LYS240 4.2 10.1 1.0 O A:ALA235 4.3 9.4 1.0 O A:LEU236 4.3 10.2 1.0 HD21 A:LEU236 4.3 12.7 1.0 HA3 A:GLY239 4.4 12.7 1.0 N A:GLY239 4.4 10.3 1.0 HO1 A:EDO411 4.5 18.6 0.7 HA A:LYS240 4.5 12.1 1.0 HO1 A:EDO411 4.5 35.3 0.3 H12 A:EDO411 4.6 35.0 0.3 HD1 A:PHE242 4.6 13.9 1.0 HA A:LEU241 4.7 11.2 1.0 C A:LEU236 4.7 9.3 1.0 C1 A:EDO411 4.7 29.2 0.3 H11 A:EDO411 4.7 21.3 0.7 C1 A:EDO411 4.8 17.8 0.7 N A:LEU236 4.8 8.5 1.0 CG A:LEU236 4.8 9.7 1.0 HG A:LEU236 4.8 11.7 1.0 CB A:LEU236 4.9 9.4 1.0 C A:ALA235 4.9 8.5 1.0 HB3 A:LEU236 4.9 11.3 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:20.2 occ:1.00 HH12 A:ARG157 2.2 15.9 1.0 O A:HOH982 2.6 47.0 1.0 OD2 A:ASP156 2.7 12.9 1.0 OD1 A:ASP153 2.8 12.8 1.0 HA A:ASP153 2.9 11.5 1.0 NH1 A:ARG157 3.0 13.2 1.0 O A:HOH789 3.1 38.8 1.0 HB2 A:ASP156 3.1 12.7 1.0 H21 A:EDO406 3.2 56.4 1.0 HH22 A:ARG157 3.3 17.6 1.0 HH11 A:ARG157 3.4 15.9 1.0 HB3 A:ASP156 3.6 12.7 1.0 CG A:ASP156 3.6 11.2 1.0 CB A:ASP156 3.6 10.6 1.0 CG A:ASP153 3.7 11.1 1.0 HB3 A:ASP153 3.7 12.2 1.0 CA A:ASP153 3.7 9.6 1.0 H22 A:EDO406 3.8 56.4 1.0 CZ A:ARG157 3.8 13.3 1.0 O A:HOH797 3.8 58.4 1.0 NH2 A:ARG157 3.9 14.7 1.0 CB A:ASP153 3.9 10.2 1.0 C2 A:EDO406 3.9 47.0 1.0 HO2 A:EDO406 3.9 55.5 1.0 O A:HOH923 4.0 71.0 1.0 O A:HOH634 4.1 20.7 0.9 O A:ASP153 4.2 9.9 1.0 O A:HOH1003 4.4 56.2 1.0 O2 A:EDO406 4.5 46.2 1.0 C A:ASP153 4.5 9.3 1.0 HH21 A:ARG157 4.7 17.6 1.0 OD2 A:ASP153 4.7 11.7 1.0 N A:ASP153 4.7 8.8 1.0 OD1 A:ASP156 4.8 11.8 1.0 HB2 A:ASP153 4.9 12.2 1.0 O A:HOH897 4.9 98.7 1.0 HG2 A:ARG157 4.9 12.3 1.0 O A:ARG152 4.9 9.6 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