Manganese in PDB 6qrv: X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 Mgy

All present enzymatic activity of X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 Mgy:
5.3.1.5;

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 Mgy, PDB code: 6qrv 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)	38.72 / 1.17
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.567, 97.577, 102.560, 90.00, 90.00, 90.00
R / Rfree (%)	10.4 / 12.4

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 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 - 2.63 Mgy (pdb code 6qrv). 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 - 2.63 Mgy, PDB code: 6qrv:
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 - 2.63 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 - 2.63 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn414 b:10.9 occ:0.40 MN A:MN414 0.0 10.9 0.4 MN A:MN414 0.8 11.1 0.6 MN A:MN414 1.7 9.3 0.1 OD1 A:ASP257 1.7 13.1 0.6 OD1 A:ASP257 1.9 10.7 0.4 OD2 A:ASP255 1.9 12.7 0.3 O A:HOH574 1.9 16.5 1.0 OE2 A:GLU217 2.0 10.3 0.9 OE2 A:GLU217 2.1 8.0 0.1 OD2 A:ASP255 2.6 12.8 0.7 OD1 A:ASP255 2.6 10.8 0.7 CG A:ASP257 2.6 13.1 0.6 CG A:ASP257 2.8 10.7 0.4 CG A:ASP255 2.8 12.5 0.3 OD2 A:ASP257 2.9 15.0 0.6 CG A:ASP255 2.9 11.3 0.7 NE2 A:HIS220 2.9 10.3 0.7 OD1 A:ASP255 3.0 13.7 0.3 OD2 A:ASP257 3.0 11.0 0.4 CD A:GLU217 3.0 10.0 0.9 HD21 A:ASN247 3.2 11.8 1.0 OE1 A:GLU217 3.3 11.8 0.9 CD A:GLU217 3.3 7.9 0.1 HD22 A:ASN247 3.5 11.8 1.0 NE2 A:HIS220 3.5 9.2 0.3 HD2 A:HIS220 3.6 10.4 0.3 O A:HOH557 3.7 60.4 0.5 ND2 A:ASN247 3.7 9.9 1.0 CD2 A:HIS220 3.7 9.7 0.7 HD2 A:HIS220 3.7 11.6 0.7 O A:HOH539 3.7 36.4 1.0 OE1 A:GLU217 3.9 8.0 0.1 CE1 A:HIS220 3.9 10.0 0.7 CD2 A:HIS220 3.9 8.7 0.3 O A:HOH671 4.0 19.5 0.7 HE1 A:HIS220 4.1 12.0 0.7 CB A:ASP257 4.1 12.2 0.6 CB A:ASP257 4.2 10.7 0.4 O A:HOH525 4.2 12.7 1.0 HA A:ASP257 4.2 11.7 0.4 HA A:ASP257 4.2 12.2 0.6 CB A:ASP255 4.2 11.2 0.3 O A:HOH727 4.3 77.7 0.9 HG2 A:GLU217 4.3 9.4 0.1 OD2 A:ASP287 4.3 13.2 1.0 O A:HOH521 4.4 29.7 1.0 CG A:GLU217 4.4 9.2 0.9 HB3 A:ASP255 4.4 13.4 0.3 HG2 A:GLU217 4.4 11.1 0.9 CB A:ASP255 4.4 10.9 0.7 H A:ASP257 4.4 11.3 0.4 H A:ASP257 4.5 11.3 0.6 CG A:GLU217 4.5 7.8 0.1 HB2 A:ASP257 4.6 14.7 0.6 HB3 A:ASP257 4.6 12.8 0.4 HE3 A:LYS183 4.6 12.8 0.3 O A:ASP287 4.6 11.0 1.0 HZ2 A:LYS183 4.6 13.9 0.3 CA A:ASP257 4.6 10.1 0.6 HB3 A:ASP257 4.6 14.7 0.6 CA A:ASP257 4.6 9.7 0.4 CG A:ASP287 4.6 11.0 1.0 HB2 A:ASP255 4.7 13.4 0.3 CE1 A:HIS220 4.7 9.1 0.3 HZ2 A:LYS289 4.7 18.2 0.6 HB2 A:ASP257 4.7 12.8 0.4 MG A:MG416 4.7 9.9 0.5 HE3 A:LYS183 4.7 14.5 0.7 HB3 A:ASP255 4.8 13.1 0.7 HZ1 A:LYS183 4.8 13.9 0.3 N A:ASP257 4.8 9.4 1.0 HG3 A:GLU217 4.8 11.1 0.9 HZ3 A:LYS289 4.8 18.2 0.6 CG A:HIS220 4.8 8.9 0.7 OD1 A:ASP287 4.9 11.1 1.0 ND1 A:HIS220 4.9 9.5 0.7 MN A:MN415 4.9 14.4 0.5 HB3 A:ASP287 4.9 12.3 1.0 HB2 A:ASP255 4.9 13.1 0.7 CG A:ASN247 5.0 8.7 1.0

Manganese binding site 2 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 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 - 2.63 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn414 b:11.1 occ:0.55 MN A:MN414 0.0 11.1 0.6 MN A:MN414 0.8 10.9 0.4 MN A:MN414 1.3 9.3 0.1 OD2 A:ASP255 1.6 12.7 0.3 OE2 A:GLU217 2.0 10.3 0.9 OE2 A:GLU217 2.2 8.0 0.1 NE2 A:HIS220 2.2 10.3 0.7 OD1 A:ASP255 2.2 10.8 0.7 O A:HOH574 2.2 16.5 1.0 OD2 A:ASP255 2.3 12.8 0.7 OD1 A:ASP257 2.3 13.1 0.6 CG A:ASP255 2.5 12.5 0.3 OD1 A:ASP257 2.6 10.7 0.4 CG A:ASP255 2.6 11.3 0.7 OD1 A:ASP255 2.7 13.7 0.3 NE2 A:HIS220 2.9 9.2 0.3 HD2 A:HIS220 2.9 10.4 0.3 CD A:GLU217 3.0 10.0 0.9 CD2 A:HIS220 3.0 9.7 0.7 HD2 A:HIS220 3.1 11.6 0.7 CD2 A:HIS220 3.2 8.7 0.3 CE1 A:HIS220 3.3 10.0 0.7 OE1 A:GLU217 3.3 11.8 0.9 CG A:ASP257 3.3 13.1 0.6 O A:HOH539 3.3 36.4 1.0 CD A:GLU217 3.3 7.9 0.1 CG A:ASP257 3.4 10.7 0.4 HD21 A:ASN247 3.5 11.8 1.0 HE1 A:HIS220 3.5 12.0 0.7 OD2 A:ASP257 3.5 11.0 0.4 OD2 A:ASP257 3.6 15.0 0.6 O A:HOH557 3.8 60.4 0.5 HE3 A:LYS183 3.8 12.8 0.3 O A:HOH671 3.9 19.5 0.7 CB A:ASP255 3.9 11.2 0.3 OE1 A:GLU217 3.9 8.0 0.1 HZ2 A:LYS183 4.0 13.9 0.3 HE3 A:LYS183 4.0 14.5 0.7 HD22 A:ASN247 4.1 11.8 1.0 CE1 A:HIS220 4.1 9.1 0.3 O A:HOH727 4.1 77.7 0.9 CB A:ASP255 4.1 10.9 0.7 ND2 A:ASN247 4.1 9.9 1.0 HB3 A:ASP255 4.1 13.4 0.3 HB2 A:ASP255 4.2 13.4 0.3 CG A:HIS220 4.2 8.9 0.7 O A:HOH525 4.2 12.7 1.0 HZ1 A:LYS183 4.2 13.9 0.3 ND1 A:HIS220 4.3 9.5 0.7 HG2 A:GLU217 4.3 9.4 0.1 CG A:GLU217 4.3 9.2 0.9 HG2 A:GLU217 4.3 11.1 0.9 HB2 A:ASP255 4.4 13.1 0.7 CG A:GLU217 4.4 7.8 0.1 NZ A:LYS183 4.4 11.6 0.3 CG A:HIS220 4.5 8.4 0.3 HZ2 A:LYS183 4.5 17.1 0.7 HE1 A:HIS220 4.5 10.9 0.3 HB3 A:ASP255 4.5 13.1 0.7 CE A:LYS183 4.6 10.7 0.3 O A:HOH521 4.6 29.7 1.0 OD2 A:ASP287 4.7 13.2 1.0 HD2 A:LYS183 4.7 12.0 0.3 CB A:ASP257 4.7 12.2 0.6 H A:ASP257 4.8 11.3 0.4 H A:ASP257 4.8 11.3 0.6 HA A:ASP257 4.8 11.7 0.4 HA A:ASP257 4.8 12.2 0.6 MG A:MG416 4.8 9.9 0.5 HD2 A:LYS183 4.8 12.7 0.7 CB A:ASP257 4.8 10.7 0.4 HG3 A:GLU217 4.8 11.1 0.9 CE A:LYS183 4.8 12.1 0.7 ND1 A:HIS220 4.9 8.7 0.3 HB3 A:GLU217 4.9 9.5 0.1 HA A:ASP255 4.9 12.1 1.0 MN A:MN415 5.0 14.4 0.5 HZ1 A:LYS183 5.0 17.1 0.7 NZ A:LYS183 5.0 14.3 0.7

Manganese binding site 3 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 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 - 2.63 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn414 b:9.3 occ:0.05 MN A:MN414 0.0 9.3 0.1 MN A:MN414 1.3 11.1 0.6 MN A:MN414 1.7 10.9 0.4 NE2 A:HIS220 1.8 10.3 0.7 O A:HOH574 2.0 16.5 1.0 NE2 A:HIS220 2.1 9.2 0.3 OE2 A:GLU217 2.2 8.0 0.1 OE2 A:GLU217 2.3 10.3 0.9 CE1 A:HIS220 2.3 10.0 0.7 HE1 A:HIS220 2.4 12.0 0.7 OE1 A:GLU217 2.5 11.8 0.9 OD2 A:ASP255 2.6 12.7 0.3 O A:HOH671 2.6 19.5 0.7 CD A:GLU217 2.7 10.0 0.9 O A:HOH539 2.8 36.4 1.0 OD2 A:ASP255 2.9 12.8 0.7 CD2 A:HIS220 3.0 8.7 0.3 CD A:GLU217 3.0 7.9 0.1 CD2 A:HIS220 3.0 9.7 0.7 CE1 A:HIS220 3.1 9.1 0.3 O A:HOH727 3.1 77.7 0.9 HD2 A:HIS220 3.1 10.4 0.3 OE1 A:GLU217 3.2 8.0 0.1 HE1 A:HIS220 3.3 10.9 0.3 OD1 A:ASP255 3.4 10.8 0.7 HD2 A:HIS220 3.5 11.6 0.7 OD1 A:ASP257 3.5 13.1 0.6 O A:HOH557 3.5 60.4 0.5 ND1 A:HIS220 3.5 9.5 0.7 CG A:ASP255 3.6 12.5 0.3 CG A:ASP255 3.6 11.3 0.7 OD1 A:ASP257 3.6 10.7 0.4 MG A:MG416 3.7 9.9 0.5 HZ2 A:LYS183 3.8 13.9 0.3 CG A:HIS220 3.9 8.9 0.7 HE3 A:LYS183 3.9 12.8 0.3 OD1 A:ASP255 3.9 13.7 0.3 MN A:MN415 3.9 14.4 0.5 OD2 A:ASP287 3.9 13.2 1.0 HD2 A:LYS183 4.0 12.0 0.3 CG A:HIS220 4.1 8.4 0.3 ND1 A:HIS220 4.1 8.7 0.3 HE3 A:LYS183 4.1 14.5 0.7 CG A:GLU217 4.1 9.2 0.9 HD2 A:LYS183 4.2 12.7 0.7 OD2 A:ASP257 4.2 15.0 0.6 HD21 A:ASN247 4.2 11.8 1.0 HD1 A:HIS220 4.2 11.4 0.7 CG A:GLU217 4.2 7.8 0.1 CG A:ASP257 4.3 13.1 0.6 OE2 A:GLU181 4.3 13.0 1.0 OD2 A:ASP257 4.3 11.0 0.4 HG2 A:GLU217 4.3 9.4 0.1 HZ2 A:LYS183 4.4 17.1 0.7 CG A:ASP257 4.4 10.7 0.4 NZ A:LYS183 4.4 11.6 0.3 HG2 A:GLU217 4.4 11.1 0.9 HZ1 A:LYS183 4.4 13.9 0.3 CE A:LYS183 4.5 10.7 0.3 HB3 A:GLU217 4.5 9.5 0.1 HB3 A:GLU217 4.6 10.1 0.9 HO2 A:EDO401 4.6 18.1 1.0 CG A:ASP287 4.7 11.0 1.0 HG3 A:GLU217 4.7 11.1 0.9 HB2 A:GLU217 4.7 9.5 0.1 HD22 A:ASN247 4.8 11.8 1.0 HO1 A:EDO409 4.8 72.5 1.0 HB2 A:GLU217 4.8 10.1 0.9 CD A:LYS183 4.8 10.0 0.3 CB A:GLU217 4.8 8.4 0.9 CB A:GLU217 4.8 7.9 0.1 CE A:LYS183 4.8 12.1 0.7 ND2 A:ASN247 4.8 9.9 1.0 CB A:ASP255 4.8 11.2 0.3 HD1 A:HIS220 4.9 10.4 0.3 CD A:LYS183 4.9 10.5 0.7 HB2 A:ASP255 4.9 13.4 0.3 HG3 A:LYS183 5.0 11.4 0.7 HB3 A:ASP255 5.0 13.4 0.3 HG3 A:GLU217 5.0 9.4 0.1 NZ A:LYS183 5.0 14.3 0.7 CB A:ASP255 5.0 10.9 0.7

Manganese binding site 4 out of 4 in the X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 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 - 2.63 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn415 b:14.4 occ:0.47 MG A:MG416 0.2 9.9 0.5 HO2 A:EDO401 1.3 18.1 1.0 OE1 A:GLU217 1.8 8.0 0.1 OD2 A:ASP245 1.9 13.3 1.0 OD2 A:ASP287 2.0 13.2 1.0 OE2 A:GLU181 2.1 13.0 1.0 O2 A:EDO401 2.1 15.1 1.0 OE1 A:GLU217 2.2 11.8 0.9 O A:HOH671 2.4 19.5 0.7 CD A:GLU181 3.0 12.4 1.0 CD A:GLU217 3.0 7.9 0.1 CG A:ASP287 3.1 11.0 1.0 CG A:ASP245 3.2 11.8 1.0 C2 A:EDO401 3.2 16.4 1.0 OE1 A:GLU181 3.2 14.0 1.0 H22 A:EDO401 3.4 19.7 1.0 HB3 A:ASP287 3.4 12.3 1.0 CD A:GLU217 3.4 10.0 0.9 HB2 A:ASP287 3.4 12.3 1.0 H21 A:EDO401 3.5 19.7 1.0 HB2 A:GLU217 3.5 10.1 0.9 CB A:ASP287 3.5 10.3 1.0 HB2 A:GLU217 3.6 9.5 0.1 HB3 A:ASP245 3.7 12.6 1.0 OE2 A:GLU217 3.7 8.0 0.1 HE1 A:HIS220 3.8 12.0 0.7 O A:HOH709 3.8 17.0 0.9 CB A:ASP245 3.9 10.5 1.0 HB2 A:ASP245 3.9 12.6 1.0 MN A:MN414 3.9 9.3 0.1 CG A:GLU217 4.1 7.8 0.1 O A:HOH574 4.1 16.5 1.0 HE1 A:HIS220 4.1 10.9 0.3 OD1 A:ASP245 4.1 13.2 1.0 OD1 A:ASP287 4.2 11.1 1.0 CG A:GLU217 4.2 9.2 0.9 HG3 A:GLU217 4.2 9.4 0.1 CB A:GLU217 4.3 8.4 0.9 HG3 A:GLU217 4.3 11.1 0.9 CE1 A:HIS220 4.3 10.0 0.7 CB A:GLU217 4.3 7.9 0.1 HD21 A:ASN215 4.3 15.2 1.0 CG A:GLU181 4.3 11.6 1.0 OE2 A:GLU217 4.4 10.3 0.9 O A:HOH727 4.4 77.7 0.9 CE1 A:HIS220 4.4 9.1 0.3 HZ2 A:TRP16 4.4 13.2 1.0 C1 A:EDO401 4.5 16.4 1.0 HG3 A:GLU181 4.5 13.9 1.0 HD22 A:ASN215 4.6 15.2 1.0 HB3 A:GLU217 4.6 10.1 0.9 HG2 A:GLU181 4.6 13.9 1.0 NE2 A:HIS220 4.7 9.2 0.3 H12 A:EDO401 4.7 19.7 1.0 HB3 A:GLU217 4.7 9.5 0.1 ND2 A:ASN215 4.7 12.7 1.0 HO1 A:EDO409 4.8 72.5 1.0 H11 A:EDO401 4.9 19.7 1.0 NE2 A:HIS220 4.9 10.3 0.7 MN A:MN414 4.9 10.9 0.4 HG2 A:GLU217 4.9 9.4 0.1 MN A:MN414 5.0 11.1 0.6 ND1 A:HIS220 5.0 9.5 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