Manganese in PDB 6qrw: X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy

All present enzymatic activity of X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy:
5.3.1.5;

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy, PDB code: 6qrw 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)	39.79 / 1.17
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.592, 97.609, 102.583, 90.00, 90.00, 90.00
R / Rfree (%)	10.6 / 12.4

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Manganese atom in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy (pdb code 6qrw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy, PDB code: 6qrw:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn414 b:12.3 occ:0.42 MN A:MN414 0.0 12.3 0.4 MN A:MN414 0.7 12.0 0.5 MN A:MN414 1.7 10.8 0.1 OD1 A:ASP257 1.8 14.4 0.7 OD2 A:ASP255 1.8 13.7 0.4 OD1 A:ASP257 1.9 11.3 0.3 O A:HOH569 1.9 18.2 1.0 OE2 A:GLU217 2.0 11.0 0.9 OE2 A:GLU217 2.1 7.9 0.1 OD1 A:ASP255 2.6 11.1 0.6 OD2 A:ASP255 2.6 13.1 0.6 CG A:ASP257 2.7 14.1 0.7 CG A:ASP255 2.7 13.7 0.4 CG A:ASP257 2.8 11.3 0.3 NE2 A:HIS220 2.9 10.9 0.7 OD2 A:ASP257 2.9 16.2 0.7 CG A:ASP255 2.9 11.4 0.6 OD1 A:ASP255 3.0 15.5 0.4 CD A:GLU217 3.0 10.7 0.9 OD2 A:ASP257 3.0 11.9 0.3 HD21 A:ASN247 3.2 12.5 1.0 OE1 A:GLU217 3.3 12.5 0.9 CD A:GLU217 3.3 8.0 0.1 NE2 A:HIS220 3.5 8.9 0.3 HD2 A:HIS220 3.6 9.9 0.3 HD22 A:ASN247 3.6 12.5 1.0 O A:HOH547 3.7 60.0 0.5 CD2 A:HIS220 3.7 10.2 0.7 HD2 A:HIS220 3.7 12.2 0.7 ND2 A:ASN247 3.7 10.4 1.0 O A:HOH543 3.7 36.4 1.0 CE1 A:HIS220 3.8 10.7 0.7 CD2 A:HIS220 3.8 8.2 0.3 OE1 A:GLU217 3.9 8.0 0.1 O A:HOH655 4.0 20.8 0.7 HE1 A:HIS220 4.0 12.8 0.7 CB A:ASP257 4.1 12.9 0.7 O A:HOH522 4.2 13.4 1.0 CB A:ASP255 4.2 12.3 0.4 CB A:ASP257 4.2 11.1 0.3 HA A:ASP257 4.2 12.4 0.3 HA A:ASP257 4.3 13.0 0.7 HG2 A:GLU217 4.3 9.6 0.1 O A:HOH629 4.3 81.2 1.0 HB3 A:ASP255 4.3 14.8 0.4 CG A:GLU217 4.4 9.7 0.9 OD2 A:ASP287 4.4 14.2 1.0 O A:HOH523 4.4 31.0 1.0 CB A:ASP255 4.4 11.4 0.6 HG2 A:GLU217 4.4 11.6 0.9 HE3 A:LYS183 4.5 14.3 0.4 CG A:GLU217 4.5 8.0 0.1 H A:ASP257 4.5 12.0 0.7 H A:ASP257 4.5 12.0 0.3 HZ2 A:LYS183 4.5 15.9 0.4 HB2 A:ASP255 4.6 14.8 0.4 HB2 A:ASP257 4.6 15.5 0.7 HB3 A:ASP257 4.6 13.3 0.3 HB3 A:ASP257 4.6 15.5 0.7 O A:ASP287 4.6 11.6 1.0 CE1 A:HIS220 4.6 8.9 0.3 CA A:ASP257 4.6 10.8 0.7 CA A:ASP257 4.7 10.3 0.3 HE3 A:LYS183 4.7 15.2 0.6 CG A:ASP287 4.7 11.9 1.0 HZ1 A:LYS183 4.7 15.9 0.4 MG A:MG416 4.7 10.9 0.5 HB3 A:ASP255 4.7 13.7 0.6 HZ2 A:LYS289 4.8 20.3 0.7 HG3 A:GLU217 4.8 11.6 0.9 CG A:HIS220 4.8 9.8 0.7 HB2 A:ASP257 4.8 13.3 0.3 N A:ASP257 4.8 10.0 1.0 HZ3 A:LYS289 4.8 20.3 0.7 ND1 A:HIS220 4.8 10.6 0.7 HB2 A:ASP255 4.9 13.7 0.6 OD1 A:ASP287 4.9 11.9 1.0 MN A:MN415 4.9 16.8 0.6 HZ2 A:LYS183 4.9 18.3 0.6 HB3 A:ASP287 5.0 13.5 1.0 NZ A:LYS183 5.0 13.2 0.4

Manganese binding site 2 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn414 b:12.0 occ:0.51 MN A:MN414 0.0 12.0 0.5 MN A:MN414 0.7 12.3 0.4 MN A:MN414 1.3 10.8 0.1 OD2 A:ASP255 1.6 13.7 0.4 OE2 A:GLU217 2.0 11.0 0.9 NE2 A:HIS220 2.2 10.9 0.7 OD1 A:ASP255 2.2 11.1 0.6 OE2 A:GLU217 2.3 7.9 0.1 OD2 A:ASP255 2.3 13.1 0.6 O A:HOH569 2.3 18.2 1.0 OD1 A:ASP257 2.4 14.4 0.7 CG A:ASP255 2.4 13.7 0.4 OD1 A:ASP257 2.6 11.3 0.3 CG A:ASP255 2.6 11.4 0.6 OD1 A:ASP255 2.7 15.5 0.4 NE2 A:HIS220 2.8 8.9 0.3 HD2 A:HIS220 2.9 9.9 0.3 CD A:GLU217 3.0 10.7 0.9 CD2 A:HIS220 3.0 10.2 0.7 HD2 A:HIS220 3.1 12.2 0.7 CD2 A:HIS220 3.2 8.2 0.3 CE1 A:HIS220 3.3 10.7 0.7 OE1 A:GLU217 3.3 12.5 0.9 CG A:ASP257 3.3 14.1 0.7 O A:HOH543 3.4 36.4 1.0 CD A:GLU217 3.4 8.0 0.1 CG A:ASP257 3.4 11.3 0.3 HD21 A:ASN247 3.5 12.5 1.0 HE1 A:HIS220 3.5 12.8 0.7 OD2 A:ASP257 3.6 16.2 0.7 OD2 A:ASP257 3.6 11.9 0.3 HE3 A:LYS183 3.8 14.3 0.4 O A:HOH547 3.8 60.0 0.5 CB A:ASP255 3.9 12.3 0.4 O A:HOH655 3.9 20.8 0.7 HE3 A:LYS183 4.0 15.2 0.6 HZ2 A:LYS183 4.0 15.9 0.4 OE1 A:GLU217 4.0 8.0 0.1 CE1 A:HIS220 4.1 8.9 0.3 CB A:ASP255 4.1 11.4 0.6 HB3 A:ASP255 4.1 14.8 0.4 HD22 A:ASN247 4.1 12.5 1.0 ND2 A:ASN247 4.1 10.4 1.0 HB2 A:ASP255 4.1 14.8 0.4 CG A:HIS220 4.2 9.8 0.7 O A:HOH629 4.2 81.2 1.0 HZ1 A:LYS183 4.2 15.9 0.4 O A:HOH522 4.2 13.4 1.0 ND1 A:HIS220 4.3 10.6 0.7 HG2 A:GLU217 4.3 9.6 0.1 CG A:GLU217 4.3 9.7 0.9 HG2 A:GLU217 4.3 11.6 0.9 NZ A:LYS183 4.4 13.2 0.4 HZ2 A:LYS183 4.4 18.3 0.6 HB2 A:ASP255 4.4 13.7 0.6 CG A:GLU217 4.5 8.0 0.1 HB3 A:ASP255 4.5 13.7 0.6 CG A:HIS220 4.5 8.3 0.3 HE1 A:HIS220 4.5 10.6 0.3 CE A:LYS183 4.5 11.9 0.4 O A:HOH523 4.6 31.0 1.0 HD2 A:LYS183 4.7 13.1 0.4 OD2 A:ASP287 4.7 14.2 1.0 CB A:ASP257 4.8 12.9 0.7 MG A:MG416 4.8 10.9 0.5 HD2 A:LYS183 4.8 13.1 0.6 H A:ASP257 4.8 12.0 0.7 H A:ASP257 4.8 12.0 0.3 HA A:ASP257 4.8 12.4 0.3 HA A:ASP257 4.8 13.0 0.7 CE A:LYS183 4.8 12.7 0.6 CB A:ASP257 4.8 11.1 0.3 HG3 A:GLU217 4.9 11.6 0.9 ND1 A:HIS220 4.9 8.4 0.3 HZ1 A:LYS183 4.9 18.3 0.6 NZ A:LYS183 4.9 15.2 0.6 HA A:ASP255 4.9 12.8 1.0 HB3 A:GLU217 4.9 9.7 0.1 MN A:MN415 5.0 16.8 0.6 H A:HIS220 5.0 10.3 0.3

Manganese binding site 3 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn414 b:10.8 occ:0.07 MN A:MN414 0.0 10.8 0.1 MN A:MN414 1.3 12.0 0.5 MN A:MN414 1.7 12.3 0.4 NE2 A:HIS220 1.8 10.9 0.7 O A:HOH569 2.0 18.2 1.0 NE2 A:HIS220 2.1 8.9 0.3 OE2 A:GLU217 2.3 7.9 0.1 OE2 A:GLU217 2.3 11.0 0.9 CE1 A:HIS220 2.4 10.7 0.7 HE1 A:HIS220 2.4 12.8 0.7 OD2 A:ASP255 2.5 13.7 0.4 OE1 A:GLU217 2.6 12.5 0.9 O A:HOH655 2.6 20.8 0.7 CD A:GLU217 2.7 10.7 0.9 O A:HOH543 2.8 36.4 1.0 OD2 A:ASP255 2.9 13.1 0.6 CD2 A:HIS220 3.0 8.2 0.3 CD2 A:HIS220 3.0 10.2 0.7 CD A:GLU217 3.0 8.0 0.1 HD2 A:HIS220 3.1 9.9 0.3 CE1 A:HIS220 3.1 8.9 0.3 O A:HOH629 3.2 81.2 1.0 OE1 A:GLU217 3.3 8.0 0.1 HE1 A:HIS220 3.4 10.6 0.3 OD1 A:ASP255 3.4 11.1 0.6 OD1 A:ASP257 3.5 14.4 0.7 HD2 A:HIS220 3.5 12.2 0.7 O A:HOH547 3.5 60.0 0.5 CG A:ASP255 3.5 13.7 0.4 CG A:ASP255 3.5 11.4 0.6 ND1 A:HIS220 3.6 10.6 0.7 OD1 A:ASP257 3.6 11.3 0.3 MG A:MG416 3.7 10.9 0.5 HZ2 A:LYS183 3.7 15.9 0.4 HE3 A:LYS183 3.8 14.3 0.4 CG A:HIS220 3.9 9.8 0.7 OD1 A:ASP255 3.9 15.5 0.4 MN A:MN415 4.0 16.8 0.6 OD2 A:ASP287 4.0 14.2 1.0 HD2 A:LYS183 4.0 13.1 0.4 HE3 A:LYS183 4.1 15.2 0.6 CG A:HIS220 4.1 8.3 0.3 OD2 A:ASP257 4.2 16.2 0.7 ND1 A:HIS220 4.2 8.4 0.3 CG A:GLU217 4.2 9.7 0.9 HD2 A:LYS183 4.2 13.1 0.6 HD21 A:ASN247 4.2 12.5 1.0 CG A:ASP257 4.2 14.1 0.7 HD1 A:HIS220 4.2 12.7 0.7 CG A:GLU217 4.3 8.0 0.1 OE2 A:GLU181 4.3 14.1 1.0 HZ2 A:LYS183 4.3 18.3 0.6 OD2 A:ASP257 4.3 11.9 0.3 NZ A:LYS183 4.3 13.2 0.4 HG2 A:GLU217 4.4 9.6 0.1 CG A:ASP257 4.4 11.3 0.3 HZ1 A:LYS183 4.4 15.9 0.4 HG2 A:GLU217 4.4 11.6 0.9 CE A:LYS183 4.4 11.9 0.4 HB3 A:GLU217 4.5 9.7 0.1 HB3 A:GLU217 4.6 10.9 0.9 HO2 A:EDO401 4.6 20.1 1.0 CG A:ASP287 4.7 11.9 1.0 CD A:LYS183 4.7 10.9 0.4 HO1 A:EDO409 4.7 78.4 1.0 HG3 A:GLU217 4.7 11.6 0.9 CE A:LYS183 4.8 12.7 0.6 HD22 A:ASN247 4.8 12.5 1.0 CB A:ASP255 4.8 12.3 0.4 HB2 A:GLU217 4.8 9.7 0.1 HB2 A:GLU217 4.8 10.9 0.9 CB A:GLU217 4.8 9.1 0.9 ND2 A:ASN247 4.8 10.4 1.0 CB A:GLU217 4.8 8.1 0.1 CD A:LYS183 4.9 10.9 0.6 HB2 A:ASP255 4.9 14.8 0.4 NZ A:LYS183 4.9 15.2 0.6 HD1 A:HIS220 4.9 10.1 0.3 HB3 A:ASP255 4.9 14.8 0.4 HG3 A:LYS183 5.0 11.8 0.6 CB A:ASP255 5.0 11.4 0.6

Manganese binding site 4 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Radiation Dose Series on Xylose Isomerase - 3.25 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn415 b:16.8 occ:0.56 MG A:MG416 0.3 10.9 0.5 HO2 A:EDO401 1.3 20.1 1.0 OE1 A:GLU217 1.8 8.0 0.1 OD2 A:ASP245 1.9 14.5 1.0 OD2 A:ASP287 2.0 14.2 1.0 OE2 A:GLU181 2.1 14.1 1.0 O2 A:EDO401 2.1 16.8 1.0 OE1 A:GLU217 2.2 12.5 0.9 O A:HOH655 2.4 20.8 0.7 CD A:GLU181 3.0 13.6 1.0 CD A:GLU217 3.0 8.0 0.1 CG A:ASP287 3.1 11.9 1.0 CG A:ASP245 3.1 12.6 1.0 C2 A:EDO401 3.2 18.1 1.0 OE1 A:GLU181 3.2 14.8 1.0 H22 A:EDO401 3.3 21.7 1.0 HB3 A:ASP287 3.4 13.5 1.0 HB2 A:ASP287 3.4 13.5 1.0 H21 A:EDO401 3.4 21.7 1.0 CD A:GLU217 3.5 10.7 0.9 HB2 A:GLU217 3.5 10.9 0.9 CB A:ASP287 3.5 11.3 1.0 HB2 A:GLU217 3.6 9.7 0.1 HB3 A:ASP245 3.7 13.7 1.0 OE2 A:GLU217 3.7 7.9 0.1 O A:HOH702 3.8 18.1 0.9 HE1 A:HIS220 3.8 12.8 0.7 CB A:ASP245 3.9 11.4 1.0 HB2 A:ASP245 3.9 13.7 1.0 MN A:MN414 4.0 10.8 0.1 CG A:GLU217 4.1 8.0 0.1 OD1 A:ASP245 4.1 14.1 1.0 O A:HOH569 4.1 18.2 1.0 HE1 A:HIS220 4.1 10.6 0.3 OD1 A:ASP287 4.2 11.9 1.0 CG A:GLU217 4.2 9.7 0.9 HG3 A:GLU217 4.2 9.6 0.1 CB A:GLU217 4.3 9.1 0.9 HG3 A:GLU217 4.3 11.6 0.9 HD21 A:ASN215 4.3 16.0 1.0 CB A:GLU217 4.3 8.1 0.1 CE1 A:HIS220 4.3 10.7 0.7 CG A:GLU181 4.3 12.5 1.0 OE2 A:GLU217 4.4 11.0 0.9 O A:HOH629 4.4 81.2 1.0 HZ2 A:TRP16 4.4 14.2 1.0 CE1 A:HIS220 4.5 8.9 0.3 C1 A:EDO401 4.5 18.5 1.0 HG3 A:GLU181 4.5 15.0 1.0 HD22 A:ASN215 4.6 16.0 1.0 HB3 A:GLU217 4.6 10.9 0.9 HG2 A:GLU181 4.6 15.0 1.0 NE2 A:HIS220 4.6 8.9 0.3 H12 A:EDO401 4.7 22.3 1.0 HB3 A:GLU217 4.7 9.7 0.1 ND2 A:ASN215 4.7 13.3 1.0 HO1 A:EDO409 4.8 78.4 1.0 H11 A:EDO401 4.8 22.3 1.0 HG2 A:GLU217 4.9 9.6 0.1 MN A:MN414 4.9 12.3 0.4 NE2 A:HIS220 4.9 10.9 0.7 MN A:MN414 5.0 12.0 0.5

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