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Sodium in PDB 6qrt: X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 Mgy

Enzymatic activity of X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 Mgy

All present enzymatic activity of X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 Mgy:
5.3.1.5;

Protein crystallography data

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 Mgy, PDB code: 6qrt 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) 35.33 / 1.17
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.523, 97.518, 102.522, 90.00, 90.00, 90.00
R / Rfree (%) n/a / 11.8

Other elements in 6qrt:

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 Mgy also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 Mgy (pdb code 6qrt). 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 - 1.38 Mgy, PDB code: 6qrt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6qrt

Go back to Sodium Binding Sites List in 6qrt
Sodium binding site 1 out of 2 in the X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 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 - 1.38 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na418

b:17.6
occ:1.00
H A:LEU241 2.3 11.8 1.0
O A:HOH690 2.6 17.3 1.0
O A:HOH569 2.8 39.6 0.9
O A:HOH911 2.9 44.1 1.0
HD23 A:LEU236 3.0 13.6 1.0
HA2 A:GLY239 3.0 13.5 1.0
HB3 A:LEU241 3.0 12.0 1.0
N A:LEU241 3.1 9.9 1.0
HA A:LEU236 3.1 10.9 1.0
H A:LYS240 3.4 12.2 1.0
C A:GLY239 3.4 11.0 1.0
N A:LYS240 3.4 10.2 1.0
CA A:GLY239 3.6 11.3 1.0
CB A:LEU241 3.7 10.0 1.0
CA A:LEU241 3.8 9.9 1.0
HB2 A:LEU241 3.8 12.0 1.0
O A:GLY239 3.8 12.4 1.0
CD2 A:LEU236 3.9 11.3 1.0
H11 A:EDO411 3.9 35.8 0.3
O A:LEU241 3.9 12.7 1.0
C A:LYS240 4.0 10.1 1.0
H12 A:EDO411 4.1 22.2 0.7
CA A:LEU236 4.1 9.1 1.0
C A:LEU241 4.1 10.7 1.0
H A:GLY239 4.2 13.0 1.0
HD22 A:LEU236 4.2 13.6 1.0
CA A:LYS240 4.2 10.2 1.0
O A:ALA235 4.2 9.8 1.0
O A:HOH979 4.2 62.8 0.7
O A:LEU236 4.3 10.8 1.0
HD21 A:LEU236 4.4 13.6 1.0
HA3 A:GLY239 4.4 13.5 1.0
N A:GLY239 4.4 10.8 1.0
HO1 A:EDO411 4.5 19.6 0.7
HO1 A:EDO411 4.5 36.0 0.3
HA A:LYS240 4.5 12.2 1.0
H12 A:EDO411 4.6 35.8 0.3
HD1 A:PHE242 4.6 14.4 1.0
C A:LEU236 4.7 9.7 1.0
HA A:LEU241 4.7 11.9 1.0
C1 A:EDO411 4.7 29.8 0.3
H11 A:EDO411 4.7 22.2 0.7
N A:LEU236 4.8 8.9 1.0
C1 A:EDO411 4.8 18.5 0.7
CG A:LEU236 4.8 10.3 1.0
HG A:LEU236 4.8 12.3 1.0
CB A:LEU236 4.9 9.9 1.0
C A:ALA235 4.9 9.0 1.0
HB3 A:LEU236 4.9 11.8 1.0

Sodium binding site 2 out of 2 in 6qrt

Go back to Sodium Binding Sites List in 6qrt
Sodium binding site 2 out of 2 in the X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 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 - 1.38 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na419

b:21.0
occ:1.00
HH12 A:ARG157 2.2 16.2 1.0
O A:HOH988 2.6 45.8 1.0
OD2 A:ASP156 2.7 13.4 1.0
OD1 A:ASP153 2.8 13.4 1.0
HA A:ASP153 2.9 11.8 1.0
NH1 A:ARG157 3.0 13.5 1.0
HB2 A:ASP156 3.1 13.1 1.0
O A:HOH791 3.2 40.7 1.0
H21 A:EDO406 3.2 58.5 1.0
HH22 A:ARG157 3.3 18.1 1.0
HH11 A:ARG157 3.4 16.2 1.0
HB3 A:ASP156 3.6 13.1 1.0
CG A:ASP156 3.6 11.6 1.0
CB A:ASP156 3.6 10.9 1.0
CG A:ASP153 3.6 11.6 1.0
HB3 A:ASP153 3.7 12.7 1.0
CA A:ASP153 3.7 9.8 1.0
H22 A:EDO406 3.8 58.5 1.0
O A:HOH802 3.8 61.5 1.0
CZ A:ARG157 3.8 13.7 1.0
NH2 A:ARG157 3.8 15.1 1.0
CB A:ASP153 3.9 10.5 1.0
C2 A:EDO406 3.9 48.8 1.0
HO2 A:EDO406 3.9 57.9 1.0
O A:HOH931 4.0 71.0 1.0
O A:HOH637 4.1 22.5 0.9
O A:ASP153 4.2 10.1 1.0
O A:HOH1003 4.4 59.0 0.9
O2 A:EDO406 4.5 48.2 1.0
C A:ASP153 4.5 9.5 1.0
HH21 A:ARG157 4.6 18.1 1.0
OD2 A:ASP153 4.7 12.6 1.0
N A:ASP153 4.7 9.4 1.0
OD1 A:ASP156 4.8 12.4 1.0
HB2 A:ASP153 4.8 12.7 1.0
O A:HOH896 4.9 97.4 1.0
HG2 A:ARG157 4.9 12.8 1.0
O A:ARG152 4.9 10.3 1.0

Reference:

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
Page generated: Tue Oct 8 12:56:30 2024

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