Magnesium in PDB 6qry: X-Ray Radiation Dose Series on Xylose Isomerase - Merged Data

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

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - Merged Data, PDB code: 6qry 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)	39.67 / 1.17
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.350, 97.280, 102.290, 90.00, 90.00, 90.00
R / Rfree (%)	9.3 / 11

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - Merged Data 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 - Merged Data (pdb code 6qry). 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 - Merged Data, PDB code: 6qry:
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 - Merged Data


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 - Merged Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg416 b:6.0 occ:0.50 MN A:MN415 0.2 15.6 0.5 HO2 A:EDO401 1.4 14.7 1.0 OE1 A:GLU217 1.7 6.7 0.1 OD2 A:ASP245 2.0 11.4 1.0 OE2 A:GLU181 2.0 11.0 1.0 OE1 A:GLU217 2.1 9.8 0.9 OD2 A:ASP287 2.1 10.9 1.0 O2 A:EDO401 2.2 12.3 1.0 O A:HOH633 2.3 15.4 0.7 CD A:GLU217 2.9 6.5 0.1 CD A:GLU181 3.0 10.4 1.0 CG A:ASP287 3.2 9.0 1.0 CG A:ASP245 3.2 9.9 1.0 C2 A:EDO401 3.3 13.0 1.0 CD A:GLU217 3.3 8.2 0.9 OE1 A:GLU181 3.3 11.6 1.0 HB2 A:GLU217 3.4 8.9 0.9 H22 A:EDO401 3.4 15.6 1.0 HB3 A:ASP287 3.4 10.1 1.0 HB2 A:GLU217 3.5 8.0 0.1 HB2 A:ASP287 3.5 10.1 1.0 H21 A:EDO401 3.5 15.6 1.0 OE2 A:GLU217 3.6 6.3 0.1 CB A:ASP287 3.6 8.4 1.0 HE1 A:HIS220 3.6 10.3 0.7 HB3 A:ASP245 3.6 10.8 1.0 MN A:MN414 3.8 5.4 0.0 HB2 A:ASP245 3.8 10.8 1.0 CB A:ASP245 3.8 9.0 1.0 CG A:GLU217 3.9 6.6 0.1 O A:HOH724 4.0 14.4 0.9 O A:HOH568 4.0 13.8 1.0 HE1 A:HIS220 4.0 8.9 0.3 CG A:GLU217 4.1 8.0 0.9 CB A:GLU217 4.1 7.4 0.9 CE1 A:HIS220 4.1 8.6 0.7 HG3 A:GLU217 4.1 7.9 0.1 CB A:GLU217 4.2 6.6 0.1 HG3 A:GLU217 4.2 9.6 0.9 OD1 A:ASP245 4.2 11.1 1.0 OE2 A:GLU217 4.2 8.5 0.9 OD1 A:ASP287 4.3 9.3 1.0 CG A:GLU181 4.3 10.0 1.0 CE1 A:HIS220 4.3 7.4 0.3 HD21 A:ASN215 4.4 12.6 1.0 O A:HOH546 4.4 76.8 1.0 HB3 A:GLU217 4.4 8.9 0.9 NE2 A:HIS220 4.5 7.5 0.3 HG3 A:GLU181 4.5 12.0 1.0 HG2 A:GLU181 4.5 12.0 1.0 HB3 A:GLU217 4.6 8.0 0.1 HZ2 A:TRP16 4.6 11.5 1.0 HD22 A:ASN215 4.6 12.6 1.0 C1 A:EDO401 4.6 13.1 1.0 NE2 A:HIS220 4.7 9.1 0.7 HG2 A:GLU217 4.8 7.9 0.1 HO1 A:EDO409 4.8 70.5 1.0 H12 A:EDO401 4.8 15.7 1.0 ND2 A:ASN215 4.8 10.5 1.0 MN A:MN414 4.8 8.6 0.4 ND1 A:HIS220 4.8 8.4 0.7 MN A:MN414 4.8 9.4 0.6 HD1 A:HIS220 4.9 10.1 0.7 H11 A:EDO401 5.0 15.7 1.0 HG2 A:GLU217 5.0 9.6 0.9

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


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 - Merged Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg417 b:16.1 occ:0.51 O A:HOH625 2.0 19.5 0.9 O A:HOH968 2.0 32.1 1.0 O A:HOH986 2.1 35.8 0.7 O A:HOH634 2.1 20.8 0.9 O A:HOH897 3.6 99.1 1.0 O A:HOH1010 3.9 61.3 0.8 O A:HOH776 4.0 22.3 0.9 H11 A:EDO406 4.0 68.8 1.0 OD2 A:ASP153 4.3 11.8 1.0 OD1 A:ASP153 4.3 12.8 1.0 O A:HOH955 4.3 77.2 1.0 CG A:ASP153 4.7 10.9 1.0 O A:HOH520 4.8 54.6 1.0 O A:HOH867 4.8 55.2 1.0 H21 A:EDO406 4.9 68.4 1.0 C1 A:EDO406 4.9 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