Sodium in PDB 6qry: X-Ray Radiation Dose Series on Xylose Isomerase - Merged Data

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

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - Merged Data, PDB code: 6qry 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)	39.67 / 1.17
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.350, 97.280, 102.290, 90.00, 90.00, 90.00
R / Rfree (%)	9.3 / 11

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - Merged Data 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 - Merged Data (pdb code 6qry). 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 - Merged Data, PDB code: 6qry:
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 - Merged Data


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 - Merged Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Na418 b:16.8 occ:1.00 H A:LEU241 2.3 11.1 1.0 O A:HOH671 2.6 16.0 1.0 O A:HOH569 2.8 40.7 0.9 O A:HOH907 2.9 43.6 1.0 HD23 A:LEU236 3.0 12.5 1.0 HA2 A:GLY239 3.0 12.8 1.0 HB3 A:LEU241 3.0 11.2 1.0 N A:LEU241 3.1 9.3 1.0 HA A:LEU236 3.1 10.2 1.0 H A:LYS240 3.4 11.7 1.0 C A:GLY239 3.4 10.5 1.0 N A:LYS240 3.4 9.7 1.0 CA A:GLY239 3.6 10.7 1.0 CB A:LEU241 3.7 9.4 1.0 CA A:LEU241 3.8 9.3 1.0 HB2 A:LEU241 3.8 11.2 1.0 O A:GLY239 3.8 11.8 1.0 H11 A:EDO411 3.9 36.5 0.3 O A:LEU241 3.9 12.2 1.0 CD2 A:LEU236 3.9 10.4 1.0 C A:LYS240 4.0 9.4 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 9.9 1.0 HD22 A:LEU236 4.2 12.5 1.0 H A:GLY239 4.2 12.3 1.0 CA A:LYS240 4.2 9.7 1.0 O A:ALA235 4.2 9.1 1.0 O A:LEU236 4.3 10.0 1.0 O A:HOH980 4.3 61.0 0.8 HA3 A:GLY239 4.4 12.8 1.0 HD21 A:LEU236 4.4 12.5 1.0 N A:GLY239 4.4 10.3 1.0 HO1 A:EDO411 4.4 36.7 0.3 HO1 A:EDO411 4.4 18.6 0.7 HA A:LYS240 4.5 11.7 1.0 H12 A:EDO411 4.5 36.5 0.3 HD1 A:PHE242 4.6 13.6 1.0 C1 A:EDO411 4.6 30.4 0.3 HA A:LEU241 4.6 11.1 1.0 C A:LEU236 4.7 9.2 1.0 H11 A:EDO411 4.7 21.3 0.7 C1 A:EDO411 4.8 17.7 0.7 N A:LEU236 4.8 8.4 1.0 CG A:LEU236 4.8 9.6 1.0 HG A:LEU236 4.8 11.5 1.0 CB A:LEU236 4.9 9.0 1.0 C A:ALA235 4.9 8.3 1.0 HB3 A:LEU236 4.9 10.8 1.0 O A:HOH765 5.0 47.2 1.0

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


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 - Merged Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Na419 b:19.9 occ:1.00 HH12 A:ARG157 2.2 15.7 1.0 O A:HOH984 2.6 44.6 1.0 OD2 A:ASP156 2.7 12.8 1.0 OD1 A:ASP153 2.8 12.8 1.0 HA A:ASP153 2.9 11.2 1.0 NH1 A:ARG157 3.0 13.1 1.0 HB2 A:ASP156 3.1 12.4 1.0 O A:HOH799 3.1 39.9 1.0 HH22 A:ARG157 3.3 17.3 1.0 H21 A:EDO406 3.3 68.4 1.0 HH11 A:ARG157 3.4 15.7 1.0 HB3 A:ASP156 3.6 12.4 1.0 CG A:ASP156 3.6 11.2 1.0 CB A:ASP156 3.6 10.4 1.0 HB3 A:ASP153 3.6 11.7 1.0 CG A:ASP153 3.6 10.9 1.0 CA A:ASP153 3.7 9.3 1.0 H22 A:EDO406 3.8 68.4 1.0 O A:HOH780 3.8 58.3 1.0 CZ A:ARG157 3.8 13.2 1.0 NH2 A:ARG157 3.9 14.4 1.0 CB A:ASP153 3.9 9.8 1.0 HO2 A:EDO406 3.9 68.0 1.0 C2 A:EDO406 4.0 57.0 1.0 O A:HOH932 4.0 70.6 1.0 O A:HOH634 4.1 20.8 0.9 O A:ASP153 4.2 9.5 1.0 O2 A:EDO406 4.4 56.7 1.0 C A:ASP153 4.5 9.0 1.0 O A:HOH1010 4.6 61.3 0.8 HH21 A:ARG157 4.7 17.3 1.0 OD2 A:ASP153 4.7 11.8 1.0 N A:ASP153 4.7 8.9 1.0 OD1 A:ASP156 4.8 11.9 1.0 HB2 A:ASP153 4.8 11.7 1.0 HG2 A:ARG157 4.9 12.1 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