Manganese in PDB 6qrr: 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: 6qrr 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)	38.69 / 1.10
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.478, 97.459, 102.485, 90.00, 90.00, 90.00
R / Rfree (%)	12.1 / 14.7

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 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 - 0.13 Mgy (pdb code 6qrr). 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 - 0.13 Mgy, PDB code: 6qrr:
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 - 0.13 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 - 0.13 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn414 b:8.1 occ:0.41 MN A:MN414 0.0 8.1 0.4 MN A:MN414 0.8 8.8 0.6 OD1 A:ASP257 1.6 10.7 0.6 MN A:MN414 1.8 10.7 0.0 OD1 A:ASP257 1.9 13.2 0.4 O A:HOH586 1.9 12.6 1.0 OD2 A:ASP255 2.0 11.9 0.4 OE2 A:GLU217 2.0 8.6 0.9 OE2 A:GLU217 2.1 9.6 0.1 CG A:ASP257 2.5 10.8 0.6 OD1 A:ASP255 2.6 9.5 0.6 OD2 A:ASP255 2.6 12.3 0.6 CG A:ASP257 2.7 10.4 0.4 CG A:ASP255 2.8 10.1 0.4 OD1 A:ASP255 2.8 11.8 0.4 OD2 A:ASP257 2.9 14.7 0.6 OD2 A:ASP257 2.9 13.1 0.4 CG A:ASP255 3.0 10.6 0.6 CD A:GLU217 3.0 8.5 0.9 NE2 A:HIS220 3.1 9.7 0.7 CD A:GLU217 3.3 9.3 0.1 OE1 A:GLU217 3.3 9.9 0.9 ND2 A:ASN247 3.6 8.8 1.0 NE2 A:HIS220 3.7 7.3 0.3 CD2 A:HIS220 3.8 8.5 0.7 O A:HOH538 3.8 25.3 1.0 O A:HOH535 3.9 63.9 0.5 OE1 A:GLU217 3.9 11.3 0.1 CB A:ASP257 3.9 9.3 0.6 O A:HOH638 4.0 13.6 0.6 CD2 A:HIS220 4.0 8.2 0.3 CE1 A:HIS220 4.0 9.1 0.7 O A:HOH540 4.1 11.6 1.0 CB A:ASP257 4.1 11.8 0.4 CB A:ASP255 4.2 9.5 0.4 OD2 A:ASP287 4.3 11.0 1.0 O A:HOH528 4.3 26.6 0.9 CG A:GLU217 4.4 8.4 0.9 CG A:GLU217 4.4 7.8 0.1 O A:ASP287 4.5 9.2 1.0 O A:HOH536 4.5 72.3 1.0 CB A:ASP255 4.5 9.9 0.6 CA A:ASP257 4.5 10.0 0.6 CA A:ASP257 4.5 9.6 0.4 CG A:ASP287 4.5 9.3 1.0 N A:ASP257 4.7 9.0 1.0 OD1 A:ASP287 4.7 9.8 1.0 MG A:MG416 4.8 9.9 0.5 MN A:MN415 4.9 13.3 0.5 CE1 A:HIS220 4.9 7.6 0.3 CG A:ASN247 4.9 8.1 1.0 CG A:HIS220 4.9 8.3 0.7

Manganese binding site 2 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 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 - 0.13 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn414 b:8.8 occ:0.55 MN A:MN414 0.0 8.8 0.6 MN A:MN414 0.8 8.1 0.4 MN A:MN414 1.4 10.7 0.0 OD2 A:ASP255 1.7 11.9 0.4 OE2 A:GLU217 2.0 8.6 0.9 OE2 A:GLU217 2.1 9.6 0.1 O A:HOH586 2.2 12.6 1.0 OD2 A:ASP255 2.2 12.3 0.6 OD1 A:ASP255 2.3 9.5 0.6 NE2 A:HIS220 2.3 9.7 0.7 OD1 A:ASP257 2.3 10.7 0.6 CG A:ASP255 2.4 10.1 0.4 OD1 A:ASP255 2.6 11.8 0.4 OD1 A:ASP257 2.6 13.2 0.4 CG A:ASP255 2.6 10.6 0.6 CD A:GLU217 3.0 8.5 0.9 NE2 A:HIS220 3.0 7.3 0.3 CD2 A:HIS220 3.1 8.5 0.7 CD2 A:HIS220 3.3 8.2 0.3 OE1 A:GLU217 3.3 9.9 0.9 CG A:ASP257 3.3 10.8 0.6 CD A:GLU217 3.3 9.3 0.1 CE1 A:HIS220 3.3 9.1 0.7 O A:HOH538 3.3 25.3 1.0 CG A:ASP257 3.4 10.4 0.4 OD2 A:ASP257 3.5 13.1 0.4 OD2 A:ASP257 3.6 14.7 0.6 O A:HOH638 3.7 13.6 0.6 O A:HOH535 3.9 63.9 0.5 CB A:ASP255 3.9 9.5 0.4 OE1 A:GLU217 3.9 11.3 0.1 ND2 A:ASN247 4.1 8.8 1.0 CB A:ASP255 4.1 9.9 0.6 O A:HOH536 4.2 72.3 1.0 CE1 A:HIS220 4.2 7.6 0.3 O A:HOH540 4.2 11.6 1.0 CG A:HIS220 4.2 8.3 0.7 CG A:GLU217 4.3 8.4 0.9 ND1 A:HIS220 4.3 9.6 0.7 CG A:GLU217 4.4 7.8 0.1 CG A:HIS220 4.5 6.8 0.3 O A:HOH528 4.5 26.6 0.9 OD2 A:ASP287 4.6 11.0 1.0 CE A:LYS183 4.6 9.6 0.3 CB A:ASP257 4.7 9.3 0.6 NZ A:LYS183 4.7 14.4 0.3 MG A:MG416 4.7 9.9 0.5 MN A:MN415 4.8 13.3 0.5 CB A:ASP257 4.9 11.8 0.4 ND1 A:HIS220 5.0 6.8 0.3

Manganese binding site 3 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 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 - 0.13 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn414 b:10.7 occ:0.04 MN A:MN414 0.0 10.7 0.0 MN A:MN414 1.4 8.8 0.6 NE2 A:HIS220 1.8 9.7 0.7 MN A:MN414 1.8 8.1 0.4 O A:HOH586 2.0 12.6 1.0 OE2 A:GLU217 2.2 9.6 0.1 NE2 A:HIS220 2.2 7.3 0.3 OE2 A:GLU217 2.3 8.6 0.9 CE1 A:HIS220 2.4 9.1 0.7 O A:HOH638 2.4 13.6 0.6 OE1 A:GLU217 2.5 9.9 0.9 OD2 A:ASP255 2.6 11.9 0.4 CD A:GLU217 2.7 8.5 0.9 O A:HOH538 2.9 25.3 1.0 OD2 A:ASP255 2.9 12.3 0.6 CD A:GLU217 3.0 9.3 0.1 CD2 A:HIS220 3.0 8.2 0.3 CD2 A:HIS220 3.1 8.5 0.7 CE1 A:HIS220 3.2 7.6 0.3 OE1 A:GLU217 3.2 11.3 0.1 O A:HOH536 3.3 72.3 1.0 OD1 A:ASP255 3.4 9.5 0.6 OD1 A:ASP257 3.4 10.7 0.6 CG A:ASP255 3.5 10.1 0.4 CG A:ASP255 3.6 10.6 0.6 ND1 A:HIS220 3.6 9.6 0.7 MG A:MG416 3.7 9.9 0.5 O A:HOH535 3.7 63.9 0.5 OD1 A:ASP257 3.7 13.2 0.4 MN A:MN415 3.8 13.3 0.5 OD1 A:ASP255 3.8 11.8 0.4 OD2 A:ASP287 3.8 11.0 1.0 CG A:HIS220 3.9 8.3 0.7 CG A:HIS220 4.1 6.8 0.3 CG A:GLU217 4.1 8.4 0.9 ND1 A:HIS220 4.2 6.8 0.3 OE2 A:GLU181 4.2 11.1 1.0 OD2 A:ASP257 4.2 14.7 0.6 CG A:GLU217 4.2 7.8 0.1 CG A:ASP257 4.3 10.8 0.6 OD2 A:ASP257 4.3 13.1 0.4 CG A:ASP257 4.5 10.4 0.4 CG A:ASP287 4.6 9.3 1.0 CE A:LYS183 4.6 9.6 0.3 NZ A:LYS183 4.7 14.4 0.3 CB A:GLU217 4.8 6.3 0.1 CB A:GLU217 4.8 8.7 0.9 CD A:LYS183 4.8 8.5 0.3 ND2 A:ASN247 4.8 8.8 1.0 CB A:ASP255 4.8 9.5 0.4 CE A:LYS183 5.0 10.1 0.7

Manganese binding site 4 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 0.13 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 - 0.13 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn415 b:13.3 occ:0.54 MG A:MG416 0.1 9.9 0.5 OE1 A:GLU217 1.7 11.3 0.1 OD2 A:ASP245 1.9 11.8 1.0 OD2 A:ASP287 2.0 11.0 1.0 OE2 A:GLU181 2.1 11.1 1.0 OE1 A:GLU217 2.1 9.9 0.9 O2 A:EDO401 2.2 12.0 1.0 O A:HOH638 2.4 13.6 0.6 CD A:GLU217 2.9 9.3 0.1 CD A:GLU181 3.0 10.3 1.0 CG A:ASP287 3.1 9.3 1.0 CG A:ASP245 3.1 10.2 1.0 C2 A:EDO401 3.2 12.1 1.0 OE1 A:GLU181 3.3 11.8 1.0 CD A:GLU217 3.4 8.5 0.9 CB A:ASP287 3.5 9.0 1.0 OE2 A:GLU217 3.6 9.6 0.1 MN A:MN414 3.8 10.7 0.0 CB A:ASP245 3.8 10.3 1.0 O A:HOH732 3.9 13.6 0.9 CG A:GLU217 4.0 7.8 0.1 O A:HOH586 4.1 12.6 1.0 OD1 A:ASP245 4.1 11.7 1.0 OD1 A:ASP287 4.2 9.8 1.0 CE1 A:HIS220 4.2 9.1 0.7 CG A:GLU217 4.2 8.4 0.9 CB A:GLU217 4.2 8.7 0.9 CB A:GLU217 4.3 6.3 0.1 OE2 A:GLU217 4.3 8.6 0.9 CG A:GLU181 4.4 10.5 1.0 CE1 A:HIS220 4.5 7.6 0.3 C1 A:EDO401 4.5 12.5 1.0 NE2 A:HIS220 4.6 7.3 0.3 O A:HOH536 4.7 72.3 1.0 ND2 A:ASN215 4.7 11.2 1.0 NE2 A:HIS220 4.8 9.7 0.7 MN A:MN414 4.8 8.8 0.6 MN A:MN414 4.9 8.1 0.4 ND1 A:HIS220 4.9 9.6 0.7

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