Magnesium in PDB 6qrt: 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;

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

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 1.38 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 - 1.38 Mgy (pdb code 6qrt). 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 - 1.38 Mgy, PDB code: 6qrt:
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 - 1.38 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 - 1.38 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg416 b:6.8 occ:0.55 MN A:MN415 0.2 16.2 0.5 HO2 A:EDO401 1.5 15.3 1.0 OE1 A:GLU217 1.7 7.2 0.1 OE2 A:GLU181 2.0 11.4 1.0 OD2 A:ASP245 2.0 11.7 1.0 OE1 A:GLU217 2.1 10.1 0.9 OD2 A:ASP287 2.1 11.2 1.0 O2 A:EDO401 2.3 12.7 1.0 O A:HOH661 2.4 15.5 0.7 CD A:GLU217 2.9 7.1 0.1 CD A:GLU181 3.0 10.9 1.0 CG A:ASP287 3.2 9.5 1.0 CG A:ASP245 3.2 10.3 1.0 CD A:GLU217 3.3 8.7 0.9 C2 A:EDO401 3.3 13.3 1.0 OE1 A:GLU181 3.3 12.0 1.0 HB2 A:GLU217 3.4 9.7 0.9 HB3 A:ASP287 3.4 10.9 1.0 H22 A:EDO401 3.4 16.0 1.0 HB2 A:GLU217 3.5 8.8 0.1 HB2 A:ASP287 3.5 10.9 1.0 H21 A:EDO401 3.5 16.0 1.0 HE1 A:HIS220 3.6 10.9 0.7 CB A:ASP287 3.6 9.1 1.0 OE2 A:GLU217 3.6 6.8 0.1 HB3 A:ASP245 3.6 11.3 1.0 MN A:MN414 3.8 6.5 0.0 HB2 A:ASP245 3.8 11.3 1.0 CB A:ASP245 3.8 9.4 1.0 CG A:GLU217 3.9 7.1 0.1 O A:HOH719 4.0 15.6 0.9 O A:HOH583 4.0 14.2 1.0 HE1 A:HIS220 4.0 9.1 0.3 CG A:GLU217 4.1 8.5 0.9 CE1 A:HIS220 4.1 9.1 0.7 CB A:GLU217 4.1 8.1 0.9 HG3 A:GLU217 4.1 8.6 0.1 CB A:GLU217 4.1 7.3 0.1 OD1 A:ASP245 4.2 11.4 1.0 HG3 A:GLU217 4.2 10.2 0.9 OE2 A:GLU217 4.2 9.2 0.9 OD1 A:ASP287 4.3 9.7 1.0 CE1 A:HIS220 4.3 7.6 0.3 CG A:GLU181 4.3 10.4 1.0 HD21 A:ASN215 4.4 13.3 1.0 HB3 A:GLU217 4.4 9.7 0.9 O A:HOH566 4.4 73.8 1.0 NE2 A:HIS220 4.5 7.5 0.3 HG3 A:GLU181 4.5 12.4 1.0 HB3 A:GLU217 4.5 8.8 0.1 HG2 A:GLU181 4.6 12.4 1.0 HZ2 A:TRP16 4.6 12.6 1.0 HD22 A:ASN215 4.6 13.3 1.0 C1 A:EDO401 4.6 13.7 1.0 NE2 A:HIS220 4.7 9.5 0.7 HG2 A:GLU217 4.8 8.6 0.1 H12 A:EDO401 4.8 16.5 1.0 MN A:MN414 4.8 9.0 0.4 HO1 A:EDO409 4.8 65.2 1.0 ND2 A:ASN215 4.8 11.1 1.0 ND1 A:HIS220 4.8 9.2 0.7 MN A:MN414 4.8 9.4 0.6 HD1 A:HIS220 4.9 11.0 0.7 HG2 A:GLU217 5.0 10.2 0.9 H11 A:EDO401 5.0 16.5 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg417 b:17.9 occ:0.57 O A:HOH621 2.0 20.6 0.9 O A:HOH971 2.0 31.2 1.0 O A:HOH991 2.1 35.3 0.8 O A:HOH637 2.2 22.5 0.9 O A:HOH896 3.5 97.4 1.0 O A:HOH1003 4.0 59.0 0.9 O A:HOH766 4.0 23.3 0.9 H11 A:EDO406 4.1 59.3 1.0 OD2 A:ASP153 4.3 12.6 1.0 OD1 A:ASP153 4.3 13.4 1.0 O A:HOH947 4.3 80.0 1.0 CG A:ASP153 4.7 11.6 1.0 O A:HOH521 4.8 54.5 1.0 O A:HOH867 4.8 55.6 1.0 C1 A:EDO406 4.9 49.4 1.0 H21 A:EDO406 5.0 58.5 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