Magnesium 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:

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

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 Mgy, PDB code: 6qrr:
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 - 0.13 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 - 0.13 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg416 b:9.9 occ:0.46 MN A:MN415 0.1 13.3 0.5 OE1 A:GLU217 1.7 11.3 0.1 OE2 A:GLU181 2.0 11.1 1.0 OD2 A:ASP287 2.0 11.0 1.0 OE1 A:GLU217 2.0 9.9 0.9 OD2 A:ASP245 2.1 11.8 1.0 O2 A:EDO401 2.2 12.0 1.0 O A:HOH638 2.3 13.6 0.6 CD A:GLU217 2.9 9.3 0.1 CD A:GLU181 3.0 10.3 1.0 CG A:ASP287 3.1 9.3 1.0 C2 A:EDO401 3.2 12.1 1.0 CG A:ASP245 3.2 10.2 1.0 CD A:GLU217 3.3 8.5 0.9 OE1 A:GLU181 3.3 11.8 1.0 OE2 A:GLU217 3.6 9.6 0.1 CB A:ASP287 3.6 9.0 1.0 MN A:MN414 3.7 10.7 0.0 CB A:ASP245 3.9 10.3 1.0 CG A:GLU217 4.0 7.8 0.1 O A:HOH586 4.0 12.6 1.0 O A:HOH732 4.0 13.6 0.9 CE1 A:HIS220 4.1 9.1 0.7 CG A:GLU217 4.1 8.4 0.9 CB A:GLU217 4.1 8.7 0.9 CB A:GLU217 4.2 6.3 0.1 OE2 A:GLU217 4.2 8.6 0.9 OD1 A:ASP245 4.2 11.7 1.0 OD1 A:ASP287 4.2 9.8 1.0 CG A:GLU181 4.3 10.5 1.0 CE1 A:HIS220 4.4 7.6 0.3 NE2 A:HIS220 4.5 7.3 0.3 C1 A:EDO401 4.6 12.5 1.0 O A:HOH536 4.6 72.3 1.0 NE2 A:HIS220 4.6 9.7 0.7 MN A:MN414 4.7 8.8 0.6 MN A:MN414 4.8 8.1 0.4 ND2 A:ASN215 4.8 11.2 1.0 ND1 A:HIS220 4.8 9.6 0.7

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg417 b:18.6 occ:0.53 O A:HOH628 2.0 22.6 0.9 O A:HOH980 2.1 31.7 0.8 O A:HOH951 2.1 28.1 1.0 O A:HOH630 2.2 23.1 0.9 O A:HOH906 3.4 0.5 1.0 O A:HOH1007 4.0 53.7 1.0 O A:HOH775 4.0 22.4 0.9 OD2 A:ASP153 4.2 12.1 1.0 OD1 A:ASP153 4.3 14.4 1.0 O A:HOH915 4.4 92.4 1.0 O A:HOH541 4.6 60.2 1.0 CG A:ASP153 4.7 11.9 1.0 O A:HOH843 4.9 64.1 1.0 O1 A:EDO406 4.9 58.2 1.0 C1 A:EDO406 5.0 39.8 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