Magnesium in PDB 6qrw: X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy

All present enzymatic activity of X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy:
5.3.1.5;

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy, PDB code: 6qrw 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)	39.79 / 1.17
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.592, 97.609, 102.583, 90.00, 90.00, 90.00
R / Rfree (%)	10.6 / 12.4

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy also contains other interesting chemical elements:

Manganese	(Mn)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy (pdb code 6qrw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy, PDB code: 6qrw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg416 b:10.9 occ:0.51 MN A:MN415 0.3 16.8 0.6 HO2 A:EDO401 1.5 20.1 1.0 OE1 A:GLU217 1.6 8.0 0.1 OE2 A:GLU181 2.0 14.1 1.0 OE1 A:GLU217 2.0 12.5 0.9 OD2 A:ASP245 2.1 14.5 1.0 OD2 A:ASP287 2.1 14.2 1.0 O A:HOH655 2.3 20.8 0.7 O2 A:EDO401 2.3 16.8 1.0 CD A:GLU217 2.8 8.0 0.1 CD A:GLU181 3.0 13.6 1.0 CG A:ASP287 3.2 11.9 1.0 CD A:GLU217 3.2 10.7 0.9 CG A:ASP245 3.3 12.6 1.0 C2 A:EDO401 3.3 18.1 1.0 OE1 A:GLU181 3.3 14.8 1.0 HB2 A:GLU217 3.4 10.9 0.9 H22 A:EDO401 3.4 21.7 1.0 HB3 A:ASP287 3.4 13.5 1.0 HB2 A:GLU217 3.4 9.7 0.1 OE2 A:GLU217 3.5 7.9 0.1 HE1 A:HIS220 3.6 12.8 0.7 HB2 A:ASP287 3.6 13.5 1.0 H21 A:EDO401 3.6 21.7 1.0 CB A:ASP287 3.6 11.3 1.0 HB3 A:ASP245 3.7 13.7 1.0 MN A:MN414 3.7 10.8 0.1 HB2 A:ASP245 3.9 13.7 1.0 CB A:ASP245 3.9 11.4 1.0 CG A:GLU217 3.9 8.0 0.1 HE1 A:HIS220 3.9 10.6 0.3 O A:HOH569 4.0 18.2 1.0 O A:HOH702 4.0 18.1 0.9 CG A:GLU217 4.0 9.7 0.9 CE1 A:HIS220 4.1 10.7 0.7 CB A:GLU217 4.1 9.1 0.9 HG3 A:GLU217 4.1 9.6 0.1 CB A:GLU217 4.1 8.1 0.1 HG3 A:GLU217 4.1 11.6 0.9 OE2 A:GLU217 4.2 11.0 0.9 CE1 A:HIS220 4.2 8.9 0.3 OD1 A:ASP287 4.2 11.9 1.0 OD1 A:ASP245 4.3 14.1 1.0 CG A:GLU181 4.3 12.5 1.0 O A:HOH629 4.3 81.2 1.0 NE2 A:HIS220 4.4 8.9 0.3 HB3 A:GLU217 4.4 10.9 0.9 HG3 A:GLU181 4.5 15.0 1.0 HD21 A:ASN215 4.5 16.0 1.0 HB3 A:GLU217 4.5 9.7 0.1 HG2 A:GLU181 4.5 15.0 1.0 C1 A:EDO401 4.7 18.5 1.0 HZ2 A:TRP16 4.7 14.2 1.0 NE2 A:HIS220 4.7 10.9 0.7 HD22 A:ASN215 4.7 16.0 1.0 HG2 A:GLU217 4.7 9.6 0.1 MN A:MN414 4.7 12.3 0.4 MN A:MN414 4.8 12.0 0.5 ND1 A:HIS220 4.8 10.6 0.7 H12 A:EDO401 4.8 22.3 1.0 HO1 A:EDO409 4.8 78.4 1.0 ND2 A:ASN215 4.9 13.3 1.0 HD1 A:HIS220 4.9 12.7 0.7 HG2 A:GLU217 4.9 11.6 0.9

Magnesium binding site 2 out of 2 in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg417 b:18.9 occ:0.53 O A:HOH610 2.0 22.7 0.9 O A:HOH970 2.0 34.1 1.0 O A:HOH994 2.1 37.9 0.8 O A:HOH617 2.2 23.7 0.9 O A:HOH901 3.5 100.0 1.0 O A:HOH997 3.9 63.8 0.9 O A:HOH771 4.0 27.5 0.9 H11 A:EDO406 4.1 72.5 1.0 OD2 A:ASP153 4.2 14.2 1.0 OD1 A:ASP153 4.3 15.0 1.0 O A:HOH940 4.4 80.9 1.0 CG A:ASP153 4.7 13.2 1.0 O A:HOH520 4.8 59.0 1.0 H21 A:EDO406 4.9 72.1 1.0 O A:HOH853 4.9 58.5 1.0 C1 A:EDO406 5.0 60.4 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