Manganese in PDB 1muw: The 0.86 Angstrom Structure of Xylose Isomerase

All present enzymatic activity of The 0.86 Angstrom Structure of Xylose Isomerase:
5.3.1.5;

The structure of The 0.86 Angstrom Structure of Xylose Isomerase, PDB code: 1muw was solved by T.D.Fenn, D.Ringe, G.A.Petsko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 0.86
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	85.906, 92.883, 98.321, 90.00, 90.00, 90.00
R / Rfree (%)	12.5 / 14.3

The structure of The 0.86 Angstrom Structure of Xylose Isomerase also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the The 0.86 Angstrom Structure of Xylose Isomerase (pdb code 1muw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The 0.86 Angstrom Structure of Xylose Isomerase, PDB code: 1muw:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The 0.86 Angstrom Structure of Xylose Isomerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The 0.86 Angstrom Structure of Xylose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn451 b:5.6 occ:0.69 MN A:MN451 0.0 5.6 0.7 MN A:MN451 0.9 5.5 0.5 MN A:MN451 1.1 17.1 0.2 OD2 A:ASP254 1.6 13.0 0.3 OE2 A:GLU216 1.9 5.7 1.0 OD2 A:ASP254 2.0 10.1 0.7 O A:OH455 2.2 7.2 0.7 OD1 A:ASP256 2.3 9.8 0.4 OD1 A:ASP256 2.3 11.3 0.6 OD1 A:ASP254 2.3 6.6 0.7 HO A:OH455 2.3 10.9 0.7 NE2 A:HIS219 2.3 11.3 1.0 CG A:ASP254 2.4 7.7 0.3 CG A:ASP254 2.4 6.7 0.7 OD1 A:ASP254 2.5 13.8 0.3 CD A:GLU216 2.9 5.3 1.0 CD2 A:HIS219 3.0 7.9 1.0 HD2 A:HIS219 3.0 9.5 1.0 CG A:ASP256 3.2 8.3 0.6 OE1 A:GLU216 3.2 7.7 1.0 CG A:ASP256 3.3 7.3 0.4 HD21 A:ASN246 3.3 6.1 1.0 OD2 A:ASP256 3.3 15.3 0.6 CE1 A:HIS219 3.4 9.5 1.0 O A:HOH589 3.5 13.5 1.0 OD2 A:ASP256 3.5 11.6 0.4 HE1 A:HIS219 3.7 11.3 1.0 CB A:ASP254 3.8 7.4 0.3 O A:HOH879 3.9 35.8 1.0 CB A:ASP254 3.9 6.1 0.7 O A:HOH788 4.0 21.4 0.5 HD22 A:ASN246 4.0 6.1 1.0 ND2 A:ASN246 4.0 5.1 1.0 HE3 A:LYS182 4.0 8.0 1.0 HB2 A:ASP254 4.0 8.9 0.3 O A:HOH476 4.1 8.0 1.0 HB3 A:ASP254 4.1 8.9 0.3 CG A:HIS219 4.2 5.5 1.0 CG A:GLU216 4.2 5.1 1.0 HG2 A:GLU216 4.3 6.1 1.0 HB3 A:ASP254 4.3 7.4 0.7 HB2 A:ASP254 4.3 7.4 0.7 ND1 A:HIS219 4.4 6.8 1.0 HZ3 A:LYS182 4.5 15.7 1.0 CB A:ASP256 4.6 7.4 0.6 HA A:ASP256 4.6 6.8 0.6 H A:ASP256 4.6 6.4 0.4 HA A:ASP256 4.6 6.9 0.4 H A:ASP256 4.7 6.2 0.6 CB A:ASP256 4.7 8.1 0.4 HG3 A:GLU216 4.8 6.1 1.0 CE A:LYS182 4.8 6.7 1.0 HA A:ASP254 4.9 5.7 0.7 HD2 A:LYS182 4.9 6.7 1.0 HA3 A:GLY218 4.9 5.5 1.0 CA A:ASP254 4.9 4.7 0.7 H A:HIS219 4.9 5.8 1.0 CA A:ASP254 4.9 6.1 0.3 HB3 A:GLU216 4.9 5.6 1.0 HZ1 A:LYS182 4.9 15.7 1.0 NZ A:LYS182 5.0 10.5 1.0 HA A:ASP254 5.0 7.4 0.3 MN A:MN452 5.0 11.1 1.0

Manganese binding site 2 out of 4 in the The 0.86 Angstrom Structure of Xylose Isomerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The 0.86 Angstrom Structure of Xylose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn451 b:5.5 occ:0.48 MN A:MN451 0.0 5.5 0.5 MN A:MN451 0.9 5.6 0.7 MN A:MN451 1.5 17.1 0.2 OD1 A:ASP256 1.7 9.8 0.4 O A:OH455 1.7 7.2 0.7 OD1 A:ASP256 1.7 11.3 0.6 OD2 A:ASP254 2.1 13.0 0.3 OE2 A:GLU216 2.1 5.7 1.0 HO A:OH455 2.2 10.9 0.7 OD2 A:ASP254 2.3 10.1 0.7 CG A:ASP256 2.5 8.3 0.6 OD2 A:ASP256 2.6 15.3 0.6 CG A:ASP256 2.6 7.3 0.4 CG A:ASP254 2.8 7.7 0.3 OD1 A:ASP254 2.9 13.8 0.3 OD1 A:ASP254 2.9 6.6 0.7 CG A:ASP254 2.9 6.7 0.7 CD A:GLU216 3.0 5.3 1.0 OD2 A:ASP256 3.0 11.6 0.4 NE2 A:HIS219 3.1 11.3 1.0 OE1 A:GLU216 3.1 7.7 1.0 HD21 A:ASN246 3.2 6.1 1.0 HD22 A:ASN246 3.5 6.1 1.0 O A:HOH879 3.6 35.8 1.0 ND2 A:ASN246 3.7 5.1 1.0 O A:HOH589 3.8 13.5 1.0 CD2 A:HIS219 3.8 7.9 1.0 HD2 A:HIS219 3.8 9.5 1.0 O A:HOH788 3.9 21.4 0.5 CB A:ASP256 4.0 7.4 0.6 CE1 A:HIS219 4.0 9.5 1.0 CB A:ASP256 4.0 8.1 0.4 HA A:ASP256 4.2 6.8 0.6 HE1 A:HIS219 4.2 11.3 1.0 HA A:ASP256 4.2 6.9 0.4 O A:HOH476 4.2 8.0 1.0 CB A:ASP254 4.3 7.4 0.3 CG A:GLU216 4.3 5.1 1.0 HB3 A:ASP256 4.4 9.7 0.4 CB A:ASP254 4.4 6.1 0.7 HZ2 A:LYS288 4.4 58.8 1.0 O A:ASP286 4.4 6.3 1.0 HB3 A:ASP256 4.5 8.8 0.6 HB2 A:ASP256 4.5 8.8 0.6 H A:ASP256 4.5 6.4 0.4 HG2 A:GLU216 4.5 6.1 1.0 HB3 A:ASP254 4.5 8.9 0.3 H A:ASP256 4.5 6.2 0.6 CA A:ASP256 4.5 5.7 0.6 CA A:ASP256 4.6 5.8 0.4 OD2 A:ASP286 4.6 12.1 1.0 HB3 A:ASP254 4.6 7.4 0.7 HB2 A:ASP254 4.7 8.9 0.3 HB2 A:ASP256 4.7 9.7 0.4 CG A:ASP286 4.7 6.7 1.0 N A:ASP256 4.7 5.3 0.4 N A:ASP256 4.7 5.2 0.6 HE3 A:LYS182 4.8 8.0 1.0 HG3 A:GLU216 4.8 6.1 1.0 MN A:MN452 4.8 11.1 1.0 OD1 A:ASP286 4.8 7.5 1.0 HB3 A:ASP286 4.8 6.7 1.0 HB2 A:ASP254 4.9 7.4 0.7 CG A:HIS219 4.9 5.5 1.0 O A:HOH793 5.0 24.5 1.0 HZ3 A:LYS182 5.0 15.7 1.0 CG A:ASN246 5.0 4.1 1.0

Manganese binding site 3 out of 4 in the The 0.86 Angstrom Structure of Xylose Isomerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The 0.86 Angstrom Structure of Xylose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn451 b:17.1 occ:0.16 MN A:MN451 0.0 17.1 0.2 MN A:MN451 1.1 5.6 0.7 HO A:OH455 1.5 10.9 0.7 MN A:MN451 1.5 5.5 0.5 NE2 A:HIS219 1.8 11.3 1.0 O A:OH455 1.8 7.2 0.7 OD2 A:ASP254 1.9 13.0 0.3 OD2 A:ASP254 2.2 10.1 0.7 OE2 A:GLU216 2.5 5.7 1.0 CE1 A:HIS219 2.6 9.5 1.0 O A:HOH589 2.7 13.5 1.0 HE1 A:HIS219 2.8 11.3 1.0 CD2 A:HIS219 2.9 7.9 1.0 OE1 A:GLU216 3.0 7.7 1.0 CG A:ASP254 3.0 6.7 0.7 O A:HOH788 3.0 21.4 0.5 CD A:GLU216 3.0 5.3 1.0 CG A:ASP254 3.0 7.7 0.3 OD1 A:ASP254 3.1 6.6 0.7 HD2 A:HIS219 3.2 9.5 1.0 OD1 A:ASP256 3.2 9.8 0.4 OD1 A:ASP256 3.3 11.3 0.6 OD1 A:ASP254 3.5 13.8 0.3 HE3 A:LYS182 3.7 8.0 1.0 OD2 A:ASP256 3.8 15.3 0.6 ND1 A:HIS219 3.8 6.8 1.0 HZ3 A:LYS182 3.9 15.7 1.0 CG A:HIS219 3.9 5.5 1.0 CG A:ASP256 3.9 8.3 0.6 O A:HOH879 4.0 35.8 1.0 CG A:ASP256 4.0 7.3 0.4 HD2 A:LYS182 4.1 6.7 1.0 OD2 A:ASP256 4.1 11.6 0.4 O A:HOH788 4.1 26.3 0.5 O A:HOH793 4.2 24.5 1.0 HD21 A:ASN246 4.2 6.1 1.0 CB A:ASP254 4.2 7.4 0.3 HB2 A:ASP254 4.3 8.9 0.3 CB A:ASP254 4.3 6.1 0.7 CE A:LYS182 4.4 6.7 1.0 HB3 A:ASP254 4.4 8.9 0.3 CG A:GLU216 4.4 5.1 1.0 MN A:MN452 4.5 11.1 1.0 NZ A:LYS182 4.5 10.5 1.0 HB2 A:ASP254 4.5 7.4 0.7 HD1 A:HIS219 4.6 8.2 1.0 OE2 A:GLU180 4.6 17.5 0.5 HB3 A:ASP254 4.6 7.4 0.7 HZ1 A:LYS182 4.7 15.7 1.0 HG2 A:GLU216 4.7 6.1 1.0 OD2 A:ASP286 4.7 12.1 1.0 CD A:LYS182 4.7 5.6 1.0 OE2 A:GLU180 4.8 16.3 0.5 HB3 A:GLU216 4.8 5.6 1.0 HD22 A:ASN246 4.8 6.1 1.0 ND2 A:ASN246 4.9 5.1 1.0 HG3 A:LYS182 4.9 6.4 1.0

Manganese binding site 4 out of 4 in the The 0.86 Angstrom Structure of Xylose Isomerase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The 0.86 Angstrom Structure of Xylose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn452 b:11.1 occ:1.00 OE2 A:GLU180 1.9 16.3 0.5 OE1 A:GLU216 2.0 7.7 1.0 OD2 A:ASP244 2.1 9.7 1.0 OD2 A:ASP286 2.1 12.1 1.0 OE2 A:GLU180 2.2 17.5 0.5 O A:HOH788 2.8 21.4 0.5 CD A:GLU180 2.9 10.7 0.5 CD A:GLU180 2.9 10.7 0.5 HB2 A:GLU216 3.1 5.6 1.0 HB3 A:ASP286 3.1 6.7 1.0 CG A:ASP286 3.1 6.7 1.0 CG A:ASP244 3.1 6.7 1.0 OE1 A:GLU180 3.2 7.9 0.5 CD A:GLU216 3.2 5.3 1.0 HB2 A:ASP286 3.3 6.7 1.0 HB3 A:ASP244 3.4 6.8 1.0 CB A:ASP286 3.4 5.6 1.0 OE1 A:GLU180 3.4 16.8 0.5 HB2 A:ASP244 3.5 6.8 1.0 CB A:ASP244 3.6 5.7 1.0 HO A:OH455 3.7 10.9 0.7 O A:HOH528 3.7 10.1 1.0 CG A:GLU216 3.8 5.1 1.0 HE1 A:HIS219 3.8 11.3 1.0 CB A:GLU216 3.8 4.6 1.0 HG3 A:GLU216 3.8 6.1 1.0 O A:OH455 3.9 7.2 0.7 O A:HOH788 4.0 26.3 0.5 O A:HOH775 4.0 30.2 1.0 O A:HOH660 4.1 32.6 1.0 CG A:GLU180 4.1 7.8 0.5 HG3 A:GLU180 4.1 9.3 0.5 CG A:GLU180 4.2 6.8 0.5 OD1 A:ASP244 4.2 8.8 1.0 HG3 A:GLU180 4.2 8.1 0.5 OD1 A:ASP286 4.2 7.5 1.0 HB3 A:GLU216 4.2 5.6 1.0 OE2 A:GLU216 4.2 5.7 1.0 CE1 A:HIS219 4.3 9.5 1.0 HD21 A:ASN214 4.3 9.5 1.0 MN A:MN451 4.5 17.1 0.2 HG2 A:GLU180 4.5 9.3 0.5 HG2 A:GLU180 4.5 8.1 0.5 HD22 A:ASN214 4.6 9.5 1.0 ND2 A:ASN214 4.7 7.9 1.0 HZ2 A:TRP15 4.8 8.2 1.0 HG2 A:GLU216 4.8 6.1 1.0 MN A:MN451 4.8 5.5 0.5 NE2 A:HIS219 4.8 11.3 1.0 ND1 A:HIS219 4.8 6.8 1.0 CA A:ASP286 4.9 4.9 1.0 HD1 A:HIS219 4.9 8.2 1.0 MN A:MN451 5.0 5.6 0.7

T.D.Fenn, D.Ringe, G.A.Petsko. Active Site Dynamics at 0.86A: Crystallographic Analysis of A Metal-Mediated Hydride Shift To Be Published.