Manganese 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:

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

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Radiation Dose Series on Xylose Isomerase - Merged Data, PDB code: 6qry:
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 - Merged Data


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 - Merged Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn414 b:8.6 occ:0.41 MN A:MN414 0.0 8.6 0.4 MN A:MN414 0.8 9.4 0.6 OD1 A:ASP257 1.7 11.6 0.6 MN A:MN414 1.8 5.4 0.0 OD1 A:ASP257 1.8 9.6 0.4 OD2 A:ASP255 1.9 11.4 0.4 O A:HOH568 1.9 13.8 1.0 OE2 A:GLU217 2.0 8.5 0.9 OE2 A:GLU217 2.1 6.3 0.1 OD2 A:ASP255 2.6 10.8 0.6 CG A:ASP257 2.6 11.4 0.6 OD1 A:ASP255 2.6 8.9 0.6 CG A:ASP257 2.7 9.6 0.4 CG A:ASP255 2.7 10.9 0.4 OD2 A:ASP257 2.9 13.0 0.6 OD1 A:ASP255 2.9 12.0 0.4 CG A:ASP255 2.9 9.2 0.6 OD2 A:ASP257 2.9 10.0 0.4 NE2 A:HIS220 3.0 9.1 0.7 CD A:GLU217 3.0 8.2 0.9 HD21 A:ASN247 3.2 10.1 1.0 OE1 A:GLU217 3.3 9.8 0.9 CD A:GLU217 3.3 6.5 0.1 HD22 A:ASN247 3.5 10.1 1.0 O A:HOH541 3.5 61.1 0.6 NE2 A:HIS220 3.6 7.5 0.3 HD2 A:HIS220 3.6 8.5 0.3 ND2 A:ASN247 3.6 8.4 1.0 CD2 A:HIS220 3.7 8.5 0.7 HD2 A:HIS220 3.7 10.2 0.7 O A:HOH542 3.8 29.8 0.9 OE1 A:GLU217 3.9 6.7 0.1 CD2 A:HIS220 3.9 7.1 0.3 CE1 A:HIS220 3.9 8.6 0.7 O A:HOH633 4.0 15.4 0.7 CB A:ASP257 4.1 10.4 0.6 CB A:ASP257 4.1 9.2 0.4 O A:HOH526 4.1 11.2 1.0 HE1 A:HIS220 4.1 10.3 0.7 HA A:ASP257 4.2 10.0 0.4 HA A:ASP257 4.2 10.5 0.6 CB A:ASP255 4.2 9.7 0.4 HG2 A:GLU217 4.3 7.9 0.1 O A:HOH546 4.3 76.8 1.0 OD2 A:ASP287 4.3 10.9 1.0 O A:HOH523 4.3 26.3 0.9 CG A:GLU217 4.3 8.0 0.9 HB3 A:ASP255 4.4 11.6 0.4 H A:ASP257 4.4 9.7 0.6 H A:ASP257 4.4 9.7 0.4 HG2 A:GLU217 4.4 9.6 0.9 CG A:GLU217 4.4 6.6 0.1 CB A:ASP255 4.4 9.0 0.6 HB2 A:ASP257 4.5 12.5 0.6 HB3 A:ASP257 4.5 11.1 0.4 O A:ASP287 4.5 9.1 1.0 CA A:ASP257 4.6 8.7 0.6 CA A:ASP257 4.6 8.3 0.4 HB3 A:ASP257 4.6 12.5 0.6 CG A:ASP287 4.6 9.0 1.0 HB2 A:ASP255 4.6 11.6 0.4 HE3 A:LYS183 4.7 12.3 0.4 HZ2 A:LYS289 4.7 15.7 0.6 HB2 A:ASP257 4.7 11.1 0.4 N A:ASP257 4.7 8.1 1.0 HE3 A:LYS183 4.7 12.1 0.6 CE1 A:HIS220 4.7 7.4 0.3 HZ2 A:LYS183 4.7 13.5 0.4 HB3 A:ASP255 4.7 10.8 0.6 HG3 A:GLU217 4.8 9.6 0.9 MG A:MG416 4.8 6.0 0.5 HZ3 A:LYS289 4.8 15.7 0.6 OD1 A:ASP287 4.8 9.3 1.0 HB3 A:ASP287 4.9 10.1 1.0 MN A:MN415 4.9 15.6 0.5 CG A:HIS220 4.9 7.6 0.7 HB2 A:ASP255 4.9 10.8 0.6 ND1 A:HIS220 4.9 8.4 0.7 CG A:ASN247 4.9 7.4 1.0 HZ1 A:LYS183 5.0 13.5 0.4

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


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 - Merged Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn414 b:9.4 occ:0.55 MN A:MN414 0.0 9.4 0.6 MN A:MN414 0.8 8.6 0.4 MN A:MN414 1.3 5.4 0.0 OD2 A:ASP255 1.6 11.4 0.4 OE2 A:GLU217 2.0 8.5 0.9 OE2 A:GLU217 2.2 6.3 0.1 OD2 A:ASP255 2.2 10.8 0.6 NE2 A:HIS220 2.2 9.1 0.7 OD1 A:ASP255 2.3 8.9 0.6 O A:HOH568 2.3 13.8 1.0 OD1 A:ASP257 2.3 11.6 0.6 CG A:ASP255 2.4 10.9 0.4 OD1 A:ASP257 2.5 9.6 0.4 CG A:ASP255 2.6 9.2 0.6 OD1 A:ASP255 2.6 12.0 0.4 NE2 A:HIS220 2.9 7.5 0.3 HD2 A:HIS220 2.9 8.5 0.3 CD A:GLU217 2.9 8.2 0.9 CD2 A:HIS220 3.0 8.5 0.7 HD2 A:HIS220 3.1 10.2 0.7 CD2 A:HIS220 3.2 7.1 0.3 OE1 A:GLU217 3.3 9.8 0.9 CE1 A:HIS220 3.3 8.6 0.7 CD A:GLU217 3.3 6.5 0.1 O A:HOH542 3.3 29.8 0.9 CG A:ASP257 3.3 11.4 0.6 CG A:ASP257 3.4 9.6 0.4 HD21 A:ASN247 3.5 10.1 1.0 OD2 A:ASP257 3.5 10.0 0.4 HE1 A:HIS220 3.6 10.3 0.7 OD2 A:ASP257 3.6 13.0 0.6 O A:HOH541 3.6 61.1 0.6 O A:HOH633 3.8 15.4 0.7 CB A:ASP255 3.9 9.7 0.4 HE3 A:LYS183 3.9 12.3 0.4 OE1 A:GLU217 3.9 6.7 0.1 HE3 A:LYS183 4.0 12.1 0.6 HD22 A:ASN247 4.0 10.1 1.0 CB A:ASP255 4.1 9.0 0.6 ND2 A:ASN247 4.1 8.4 1.0 O A:HOH546 4.1 76.8 1.0 CE1 A:HIS220 4.1 7.4 0.3 HB3 A:ASP255 4.1 11.6 0.4 HB2 A:ASP255 4.1 11.6 0.4 HZ2 A:LYS183 4.2 13.5 0.4 CG A:HIS220 4.2 7.6 0.7 HG2 A:GLU217 4.2 7.9 0.1 O A:HOH526 4.2 11.2 1.0 CG A:GLU217 4.3 8.0 0.9 ND1 A:HIS220 4.3 8.4 0.7 HG2 A:GLU217 4.3 9.6 0.9 CG A:GLU217 4.4 6.6 0.1 HB2 A:ASP255 4.4 10.8 0.6 HZ1 A:LYS183 4.4 13.5 0.4 HB3 A:ASP255 4.5 10.8 0.6 CG A:HIS220 4.5 6.8 0.3 HE1 A:HIS220 4.6 8.9 0.3 HZ2 A:LYS183 4.6 14.2 0.6 O A:HOH523 4.6 26.3 0.9 NZ A:LYS183 4.6 11.2 0.4 OD2 A:ASP287 4.6 10.9 1.0 CE A:LYS183 4.7 10.2 0.4 HD2 A:LYS183 4.7 11.4 0.4 CB A:ASP257 4.7 10.4 0.6 H A:ASP257 4.7 9.7 0.6 H A:ASP257 4.8 9.7 0.4 HD2 A:LYS183 4.8 10.6 0.6 HA A:ASP257 4.8 10.0 0.4 HA A:ASP257 4.8 10.5 0.6 CB A:ASP257 4.8 9.2 0.4 MG A:MG416 4.8 6.0 0.5 HG3 A:GLU217 4.8 9.6 0.9 CE A:LYS183 4.8 10.1 0.6 ND1 A:HIS220 4.9 7.0 0.3 MN A:MN415 4.9 15.6 0.5 HA A:ASP255 4.9 10.1 1.0 HB3 A:GLU217 4.9 8.0 0.1 H A:HIS220 5.0 8.2 0.3 CA A:ASP255 5.0 8.4 1.0

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


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 - Merged Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn414 b:5.4 occ:0.04 MN A:MN414 0.0 5.4 0.0 MN A:MN414 1.3 9.4 0.6 MN A:MN414 1.8 8.6 0.4 NE2 A:HIS220 1.8 9.1 0.7 O A:HOH568 2.0 13.8 1.0 NE2 A:HIS220 2.1 7.5 0.3 OE2 A:GLU217 2.2 6.3 0.1 OE2 A:GLU217 2.3 8.5 0.9 CE1 A:HIS220 2.3 8.6 0.7 HE1 A:HIS220 2.4 10.3 0.7 O A:HOH633 2.5 15.4 0.7 OE1 A:GLU217 2.5 9.8 0.9 OD2 A:ASP255 2.6 11.4 0.4 CD A:GLU217 2.7 8.2 0.9 O A:HOH542 2.8 29.8 0.9 OD2 A:ASP255 2.9 10.8 0.6 CD A:GLU217 2.9 6.5 0.1 CD2 A:HIS220 2.9 7.1 0.3 CD2 A:HIS220 3.0 8.5 0.7 HD2 A:HIS220 3.1 8.5 0.3 CE1 A:HIS220 3.1 7.4 0.3 O A:HOH546 3.1 76.8 1.0 OE1 A:GLU217 3.2 6.7 0.1 O A:HOH541 3.4 61.1 0.6 HE1 A:HIS220 3.4 8.9 0.3 OD1 A:ASP255 3.4 8.9 0.6 HD2 A:HIS220 3.4 10.2 0.7 OD1 A:ASP257 3.5 11.6 0.6 CG A:ASP255 3.5 10.9 0.4 ND1 A:HIS220 3.5 8.4 0.7 CG A:ASP255 3.5 9.2 0.6 OD1 A:ASP257 3.6 9.6 0.4 MG A:MG416 3.8 6.0 0.5 OD1 A:ASP255 3.8 12.0 0.4 CG A:HIS220 3.9 7.6 0.7 MN A:MN415 3.9 15.6 0.5 OD2 A:ASP287 3.9 10.9 1.0 HZ2 A:LYS183 3.9 13.5 0.4 HE3 A:LYS183 4.0 12.3 0.4 HD2 A:LYS183 4.1 11.4 0.4 CG A:HIS220 4.1 6.8 0.3 HE3 A:LYS183 4.1 12.1 0.6 CG A:GLU217 4.1 8.0 0.9 ND1 A:HIS220 4.1 7.0 0.3 HD2 A:LYS183 4.2 10.6 0.6 CG A:GLU217 4.2 6.6 0.1 OD2 A:ASP257 4.2 13.0 0.6 HD21 A:ASN247 4.2 10.1 1.0 OE2 A:GLU181 4.2 11.0 1.0 HD1 A:HIS220 4.2 10.1 0.7 CG A:ASP257 4.3 11.4 0.6 HG2 A:GLU217 4.3 7.9 0.1 OD2 A:ASP257 4.3 10.0 0.4 CG A:ASP257 4.4 9.6 0.4 HG2 A:GLU217 4.4 9.6 0.9 HZ2 A:LYS183 4.5 14.2 0.6 HB3 A:GLU217 4.5 8.0 0.1 HB3 A:GLU217 4.5 8.9 0.9 NZ A:LYS183 4.6 11.2 0.4 HO2 A:EDO401 4.6 14.7 1.0 CE A:LYS183 4.6 10.2 0.4 HO1 A:EDO409 4.6 70.5 1.0 HZ1 A:LYS183 4.6 13.5 0.4 CG A:ASP287 4.7 9.0 1.0 HB2 A:GLU217 4.7 8.0 0.1 HG3 A:GLU217 4.7 9.6 0.9 HB2 A:GLU217 4.7 8.9 0.9 HD22 A:ASN247 4.7 10.1 1.0 CB A:GLU217 4.8 7.4 0.9 CB A:GLU217 4.8 6.6 0.1 CE A:LYS183 4.8 10.1 0.6 CB A:ASP255 4.8 9.7 0.4 CD A:LYS183 4.8 9.5 0.4 ND2 A:ASN247 4.8 8.4 1.0 HB2 A:ASP255 4.9 11.6 0.4 CD A:LYS183 4.9 8.8 0.6 HD1 A:HIS220 4.9 8.4 0.3 HG3 A:GLU217 4.9 7.9 0.1 HG3 A:LYS183 4.9 9.4 0.6 HB3 A:ASP255 5.0 11.6 0.4 CB A:ASP255 5.0 9.0 0.6

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


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 - Merged Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn415 b:15.6 occ:0.48 MG A:MG416 0.2 6.0 0.5 HO2 A:EDO401 1.3 14.7 1.0 OE1 A:GLU217 1.8 6.7 0.1 OD2 A:ASP245 2.0 11.4 1.0 OD2 A:ASP287 2.0 10.9 1.0 OE2 A:GLU181 2.1 11.0 1.0 O2 A:EDO401 2.1 12.3 1.0 OE1 A:GLU217 2.2 9.8 0.9 O A:HOH633 2.4 15.4 0.7 CD A:GLU217 3.0 6.5 0.1 CD A:GLU181 3.0 10.4 1.0 CG A:ASP287 3.1 9.0 1.0 C2 A:EDO401 3.2 13.0 1.0 CG A:ASP245 3.2 9.9 1.0 OE1 A:GLU181 3.3 11.6 1.0 H22 A:EDO401 3.3 15.6 1.0 HB3 A:ASP287 3.3 10.1 1.0 HB2 A:ASP287 3.4 10.1 1.0 H21 A:EDO401 3.4 15.6 1.0 CD A:GLU217 3.4 8.2 0.9 CB A:ASP287 3.5 8.4 1.0 HB2 A:GLU217 3.5 8.9 0.9 HB2 A:GLU217 3.6 8.0 0.1 HB3 A:ASP245 3.7 10.8 1.0 OE2 A:GLU217 3.7 6.3 0.1 HE1 A:HIS220 3.7 10.3 0.7 O A:HOH724 3.8 14.4 0.9 CB A:ASP245 3.9 9.0 1.0 MN A:MN414 3.9 5.4 0.0 HB2 A:ASP245 3.9 10.8 1.0 O A:HOH568 4.0 13.8 1.0 CG A:GLU217 4.1 6.6 0.1 OD1 A:ASP245 4.1 11.1 1.0 HE1 A:HIS220 4.1 8.9 0.3 OD1 A:ASP287 4.2 9.3 1.0 CG A:GLU217 4.2 8.0 0.9 CE1 A:HIS220 4.2 8.6 0.7 HG3 A:GLU217 4.3 7.9 0.1 CB A:GLU217 4.3 7.4 0.9 HG3 A:GLU217 4.3 9.6 0.9 CB A:GLU217 4.3 6.6 0.1 HD21 A:ASN215 4.3 12.6 1.0 OE2 A:GLU217 4.3 8.5 0.9 CG A:GLU181 4.4 10.0 1.0 O A:HOH546 4.4 76.8 1.0 HZ2 A:TRP16 4.4 11.5 1.0 CE1 A:HIS220 4.4 7.4 0.3 C1 A:EDO401 4.5 13.1 1.0 HG3 A:GLU181 4.6 12.0 1.0 HD22 A:ASN215 4.6 12.6 1.0 HB3 A:GLU217 4.6 8.9 0.9 NE2 A:HIS220 4.6 7.5 0.3 HG2 A:GLU181 4.6 12.0 1.0 H12 A:EDO401 4.6 15.7 1.0 HO1 A:EDO409 4.7 70.5 1.0 ND2 A:ASN215 4.7 10.5 1.0 HB3 A:GLU217 4.8 8.0 0.1 H11 A:EDO401 4.8 15.7 1.0 NE2 A:HIS220 4.8 9.1 0.7 MN A:MN414 4.9 8.6 0.4 HG2 A:GLU217 4.9 7.9 0.1 MN A:MN414 4.9 9.4 0.6 ND1 A:HIS220 5.0 8.4 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