Magnesium in PDB 6qrx: X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy

All present enzymatic activity of X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy:
5.3.1.5;

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 Mgy, PDB code: 6qrx 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)	38.74 / 1.17
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.612, 97.636, 102.598, 90.00, 90.00, 90.00
R / Rfree (%)	10.9 / 12.8

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 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 - 3.88 Mgy (pdb code 6qrx). 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 - 3.88 Mgy, PDB code: 6qrx:
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 - 3.88 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 - 3.88 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg416 b:13.4 occ:0.52 MN A:MN415 0.3 16.3 0.6 OE1 A:GLU217 1.5 8.5 0.1 HO2 A:EDO401 1.6 22.2 1.0 OE1 A:GLU217 2.0 13.2 0.9 OE2 A:GLU181 2.0 15.1 1.0 OD2 A:ASP245 2.1 15.2 1.0 OD2 A:ASP287 2.1 15.1 1.0 O A:HOH618 2.2 25.1 0.9 O2 A:EDO401 2.4 18.5 1.0 CD A:GLU217 2.7 8.8 0.1 CD A:GLU181 3.0 14.7 1.0 CG A:ASP287 3.2 12.3 1.0 CD A:GLU217 3.2 10.9 0.9 CG A:ASP245 3.3 13.0 1.0 HB2 A:GLU217 3.3 11.4 0.9 OE1 A:GLU181 3.3 16.2 1.0 C2 A:EDO401 3.4 20.2 1.0 HB3 A:ASP287 3.4 13.9 1.0 OE2 A:GLU217 3.4 9.0 0.1 HB2 A:GLU217 3.4 10.4 0.1 H22 A:EDO401 3.4 24.3 1.0 HE1 A:HIS220 3.5 13.4 0.7 HB2 A:ASP287 3.6 13.9 1.0 H21 A:EDO401 3.6 24.3 1.0 CB A:ASP287 3.6 11.6 1.0 HB3 A:ASP245 3.6 13.9 1.0 MN A:MN414 3.7 7.7 0.0 CG A:GLU217 3.8 8.7 0.1 CB A:ASP245 3.9 11.6 1.0 HB2 A:ASP245 3.9 13.9 1.0 HE1 A:HIS220 3.9 11.3 0.3 O A:HOH566 4.0 18.8 1.0 CG A:GLU217 4.0 10.2 0.9 CE1 A:HIS220 4.0 11.2 0.7 CB A:GLU217 4.1 9.5 0.9 HG3 A:GLU217 4.1 10.5 0.1 O A:HOH706 4.1 22.1 0.9 CB A:GLU217 4.1 8.7 0.1 HG3 A:GLU217 4.1 12.2 0.9 OE2 A:GLU217 4.1 11.4 0.9 CE1 A:HIS220 4.2 9.4 0.3 OD1 A:ASP287 4.2 12.4 1.0 OD1 A:ASP245 4.3 14.6 1.0 CG A:GLU181 4.3 13.3 1.0 O A:HOH614 4.3 83.9 1.0 HB3 A:GLU217 4.4 11.4 0.9 NE2 A:HIS220 4.4 9.5 0.3 HG3 A:GLU181 4.5 16.0 1.0 HB3 A:GLU217 4.5 10.4 0.1 HD21 A:ASN215 4.5 16.7 1.0 HG2 A:GLU181 4.5 16.0 1.0 HG2 A:GLU217 4.6 10.5 0.1 NE2 A:HIS220 4.7 11.4 0.7 HZ2 A:TRP16 4.7 14.6 1.0 MN A:MN414 4.7 14.6 0.5 C1 A:EDO401 4.7 20.7 1.0 HD22 A:ASN215 4.7 16.7 1.0 ND1 A:HIS220 4.8 10.8 0.7 MN A:MN414 4.8 12.1 0.5 H12 A:EDO401 4.8 24.9 1.0 HO1 A:EDO409 4.8 82.0 1.0 HD1 A:HIS220 4.9 13.0 0.7 ND2 A:ASN215 4.9 13.9 1.0 HG2 A:GLU217 4.9 12.2 0.9

Magnesium binding site 2 out of 2 in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.88 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 - 3.88 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg417 b:20.2 occ:0.57 O A:HOH608 2.0 24.6 1.0 O A:HOH994 2.0 38.6 0.8 O A:HOH970 2.1 36.2 1.0 O A:HOH659 2.1 25.1 1.0 O A:HOH903 3.5 0.2 1.0 O A:HOH1001 3.9 64.6 0.9 O A:HOH776 4.0 29.4 1.0 H11 A:EDO406 4.1 75.3 1.0 OD2 A:ASP153 4.2 14.6 1.0 OD1 A:ASP153 4.3 15.7 1.0 O A:HOH946 4.3 80.8 1.0 CG A:ASP153 4.7 13.7 1.0 O A:HOH521 4.8 62.2 1.0 H21 A:EDO406 4.9 74.8 1.0 C1 A:EDO406 4.9 62.7 1.0 O A:HOH859 5.0 57.4 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