Magnesium 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:

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 6qrs). 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: 6qrs:
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:7.8 occ:0.52 MN A:MN415 0.1 12.8 0.5 HO2 A:EDO401 1.5 14.0 1.0 OE1 A:GLU217 1.7 7.0 0.1 OE2 A:GLU181 2.0 10.8 1.0 OD2 A:ASP245 2.0 10.9 1.0 OE1 A:GLU217 2.1 9.3 0.9 OD2 A:ASP287 2.1 10.3 1.0 O2 A:EDO401 2.3 11.7 1.0 O A:HOH649 2.4 14.1 0.6 CD A:GLU217 2.9 7.0 0.1 CD A:GLU181 3.0 10.1 1.0 CG A:ASP287 3.2 8.8 1.0 CG A:ASP245 3.2 9.7 1.0 C2 A:EDO401 3.3 12.0 1.0 OE1 A:GLU181 3.3 11.0 1.0 CD A:GLU217 3.3 8.0 0.9 H22 A:EDO401 3.4 14.4 1.0 HB3 A:ASP287 3.4 9.8 1.0 HB2 A:GLU217 3.4 8.9 0.9 HB2 A:GLU217 3.5 8.5 0.1 HB2 A:ASP287 3.5 9.8 1.0 H21 A:EDO401 3.5 14.4 1.0 CB A:ASP287 3.6 8.2 1.0 HE1 A:HIS220 3.6 9.8 0.6 OE2 A:GLU217 3.6 6.8 0.1 HB3 A:ASP245 3.6 10.6 1.0 MN A:MN414 3.8 5.4 0.0 HB2 A:ASP245 3.8 10.6 1.0 CB A:ASP245 3.8 8.8 1.0 CG A:GLU217 3.9 7.1 0.1 O A:HOH729 4.0 13.5 0.9 O A:HOH572 4.0 13.3 1.0 HE1 A:HIS220 4.1 9.4 0.4 CE1 A:HIS220 4.1 8.1 0.6 CG A:GLU217 4.1 7.8 0.9 CB A:GLU217 4.1 7.4 0.9 HG3 A:GLU217 4.1 8.5 0.1 CB A:GLU217 4.2 7.1 0.1 OD1 A:ASP245 4.2 10.7 1.0 HG3 A:GLU217 4.2 9.4 0.9 OE2 A:GLU217 4.2 8.1 0.9 OD1 A:ASP287 4.3 9.0 1.0 CG A:GLU181 4.3 9.9 1.0 CE1 A:HIS220 4.3 7.8 0.4 HD21 A:ASN215 4.4 12.4 1.0 HB3 A:GLU217 4.4 8.9 0.9 NE2 A:HIS220 4.5 8.0 0.4 HG3 A:GLU181 4.5 11.9 1.0 O A:HOH546 4.5 70.1 1.0 HG2 A:GLU181 4.6 11.9 1.0 HB3 A:GLU217 4.6 8.5 0.1 HZ2 A:TRP16 4.6 11.3 1.0 C1 A:EDO401 4.6 12.2 1.0 HD22 A:ASN215 4.6 12.4 1.0 NE2 A:HIS220 4.7 8.8 0.6 H12 A:EDO401 4.7 14.6 1.0 HO1 A:EDO409 4.8 62.5 1.0 HG2 A:GLU217 4.8 8.5 0.1 ND2 A:ASN215 4.8 10.3 1.0 MN A:MN414 4.8 8.2 0.4 MN A:MN414 4.8 8.3 0.5 ND1 A:HIS220 4.8 8.2 0.6 HD1 A:HIS220 4.9 9.8 0.6 H11 A:EDO401 4.9 14.6 1.0

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:16.9 occ:0.55 O A:HOH646 2.0 18.3 0.8 O A:HOH969 2.0 29.4 1.0 O A:HOH985 2.1 34.1 0.8 O A:HOH634 2.1 20.7 0.9 O A:HOH897 3.5 98.7 1.0 O A:HOH1003 3.9 56.2 1.0 O A:HOH774 4.0 22.3 0.9 H11 A:EDO406 4.1 57.3 1.0 O A:HOH954 4.2 77.9 1.0 OD2 A:ASP153 4.3 11.7 1.0 OD1 A:ASP153 4.3 12.8 1.0 CG A:ASP153 4.7 11.1 1.0 O A:HOH523 4.8 49.2 1.0 O A:HOH872 4.9 55.9 1.0 C1 A:EDO406 4.9 47.7 1.0 H21 A:EDO406 5.0 56.4 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