Manganese in PDB 2qum: Crystal Structure of D-Tagatose 3-Epimerase From Pseudomonas Cichorii with D-Tagatose

The structure of Crystal Structure of D-Tagatose 3-Epimerase From Pseudomonas Cichorii with D-Tagatose, PDB code: 2qum was solved by H.Yoshida, M.Yamada, T.Nishitani, G.Takada, K.Izumori, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.31 / 2.28
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.414, 139.432, 92.860, 90.00, 104.04, 90.00
R / Rfree (%)	18.5 / 23.9

The binding sites of Manganese atom in the Crystal Structure of D-Tagatose 3-Epimerase From Pseudomonas Cichorii with D-Tagatose (pdb code 2qum). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of D-Tagatose 3-Epimerase From Pseudomonas Cichorii with D-Tagatose, PDB code: 2qum:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of D-Tagatose 3-Epimerase From Pseudomonas Cichorii with D-Tagatose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of D-Tagatose 3-Epimerase From Pseudomonas Cichorii with D-Tagatose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn292 b:26.0 occ:1.00 ND1 A:HIS211 2.3 10.4 1.0 OD2 A:ASP185 2.3 15.4 1.0 OE2 A:GLU152 2.3 23.0 1.0 O2 A:TAG291 2.3 70.5 1.0 OE1 A:GLU246 2.6 21.7 1.0 O3 A:TAG291 3.0 71.2 1.0 C2 A:TAG291 3.1 70.5 1.0 CE1 A:HIS211 3.1 11.2 1.0 C3 A:TAG291 3.3 70.8 1.0 CD A:GLU152 3.3 22.0 1.0 CD A:GLU246 3.3 19.7 1.0 CG A:HIS211 3.3 12.1 1.0 CG A:ASP185 3.4 16.5 1.0 OE2 A:GLU246 3.4 17.6 1.0 OE1 A:GLU152 3.7 25.2 1.0 CB A:HIS211 3.7 9.2 1.0 CB A:ASP185 3.9 16.0 1.0 NH2 A:ARG217 4.1 16.5 1.0 NE2 A:GLN183 4.3 12.9 1.0 NE2 A:HIS211 4.3 11.1 1.0 CD2 A:HIS188 4.4 10.1 1.0 CD2 A:HIS211 4.4 11.8 1.0 C1 A:TAG291 4.4 69.9 1.0 OD1 A:ASP185 4.5 17.1 1.0 CG A:GLU152 4.5 19.1 1.0 NE2 A:HIS188 4.6 8.8 1.0 CG A:GLU246 4.7 20.1 1.0 C4 A:TAG291 4.8 71.1 1.0 O A:HOH293 4.9 13.6 1.0 O1 A:TAG291 5.0 66.4 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of D-Tagatose 3-Epimerase From Pseudomonas Cichorii with D-Tagatose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of D-Tagatose 3-Epimerase From Pseudomonas Cichorii with D-Tagatose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn292 b:23.5 occ:1.00 ND1 B:HIS211 2.2 12.6 1.0 OE2 B:GLU152 2.3 16.3 1.0 OD2 B:ASP185 2.3 14.8 1.0 O2 B:TAG291 2.4 47.7 1.0 OE1 B:GLU246 2.4 16.4 1.0 O3 B:TAG291 2.8 49.9 1.0 C2 B:TAG291 3.0 49.8 1.0 CE1 B:HIS211 3.1 13.8 1.0 C3 B:TAG291 3.1 51.3 1.0 CG B:HIS211 3.2 14.5 1.0 CD B:GLU246 3.3 17.9 1.0 CD B:GLU152 3.4 15.7 1.0 CG B:ASP185 3.4 15.1 1.0 CB B:HIS211 3.5 12.9 1.0 OE2 B:GLU246 3.5 20.4 1.0 OE1 B:GLU152 3.8 15.9 1.0 CB B:ASP185 3.9 14.6 1.0 NE2 B:HIS211 4.2 14.6 1.0 NE2 B:GLN183 4.2 14.0 1.0 CD2 B:HIS211 4.3 15.7 1.0 NH2 B:ARG217 4.3 19.3 1.0 CD2 B:HIS188 4.4 6.8 1.0 C1 B:TAG291 4.4 50.9 1.0 NE2 B:HIS188 4.4 9.9 1.0 OD1 B:ASP185 4.5 15.7 1.0 CG B:GLU152 4.6 13.0 1.0 C4 B:TAG291 4.7 52.2 1.0 CG B:GLU246 4.7 17.2 1.0 O B:HOH308 4.9 5.3 1.0 CB B:GLU246 4.9 15.6 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of D-Tagatose 3-Epimerase From Pseudomonas Cichorii with D-Tagatose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of D-Tagatose 3-Epimerase From Pseudomonas Cichorii with D-Tagatose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn292 b:21.1 occ:1.00 OD2 C:ASP185 2.1 17.3 1.0 OE2 C:GLU152 2.2 12.4 1.0 O2 C:TAG291 2.2 40.5 1.0 ND1 C:HIS211 2.3 18.6 1.0 OE1 C:GLU246 2.5 14.7 1.0 C2 C:TAG291 2.9 42.9 1.0 O3 C:TAG291 3.1 45.0 1.0 CG C:ASP185 3.2 14.1 1.0 CE1 C:HIS211 3.2 20.5 1.0 C3 C:TAG291 3.2 45.3 1.0 CG C:HIS211 3.3 18.6 1.0 CD C:GLU152 3.3 11.1 1.0 CD C:GLU246 3.4 16.4 1.0 CB C:HIS211 3.6 15.4 1.0 OE2 C:GLU246 3.6 19.9 1.0 CB C:ASP185 3.8 14.3 1.0 OE1 C:GLU152 3.8 14.2 1.0 O C:HOH357 4.0 10.3 1.0 NH2 C:ARG217 4.0 12.8 1.0 OD1 C:ASP185 4.2 13.3 1.0 NE2 C:GLN183 4.3 13.5 1.0 CD2 C:HIS188 4.3 17.1 1.0 C1 C:TAG291 4.3 41.7 1.0 NE2 C:HIS211 4.4 21.1 1.0 CD2 C:HIS211 4.4 20.4 1.0 NE2 C:HIS188 4.4 14.3 1.0 CG C:GLU152 4.5 9.0 1.0 CG C:GLU246 4.7 17.6 1.0 C4 C:TAG291 4.8 48.0 1.0 O1 C:TAG291 4.8 38.9 1.0 CB C:GLU246 5.0 15.8 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of D-Tagatose 3-Epimerase From Pseudomonas Cichorii with D-Tagatose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of D-Tagatose 3-Epimerase From Pseudomonas Cichorii with D-Tagatose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn292 b:24.2 occ:1.00 OD2 D:ASP185 2.1 14.7 1.0 O2 D:TAG291 2.2 46.9 1.0 ND1 D:HIS211 2.3 15.3 1.0 OE2 D:GLU152 2.4 12.3 1.0 OE1 D:GLU246 2.4 14.0 1.0 O3 D:TAG291 3.0 49.9 1.0 C2 D:TAG291 3.1 48.7 1.0 CD D:GLU246 3.2 15.7 1.0 CG D:ASP185 3.3 15.3 1.0 CE1 D:HIS211 3.3 16.4 1.0 CG D:HIS211 3.3 14.4 1.0 C3 D:TAG291 3.4 50.9 1.0 CD D:GLU152 3.4 13.6 1.0 OE2 D:GLU246 3.4 15.8 1.0 CB D:HIS211 3.5 11.9 1.0 OE1 D:GLU152 3.7 15.4 1.0 CB D:ASP185 3.9 15.4 1.0 O D:HOH423 4.1 40.5 1.0 OD1 D:ASP185 4.2 16.9 1.0 CD2 D:HIS188 4.3 12.0 1.0 NE2 D:HIS188 4.4 8.7 1.0 C1 D:TAG291 4.4 45.9 1.0 NE2 D:GLN183 4.4 11.8 1.0 NE2 D:HIS211 4.4 15.8 1.0 CD2 D:HIS211 4.5 13.7 1.0 CG D:GLU246 4.6 17.9 1.0 CG D:GLU152 4.7 12.0 1.0 NH2 D:ARG217 4.7 15.9 1.0 O1 D:TAG291 4.9 40.3 1.0 CB D:GLU246 4.9 16.9 1.0 C4 D:TAG291 4.9 53.4 1.0 O D:HOH306 4.9 9.7 1.0

H.Yoshida, M.Yamada, T.Nishitani, G.Takada, K.Izumori, S.Kamitori. Crystal Structures of D-Tagatose 3-Epimerase From Pseudomonas Cichorii and Its Complexes with D-Tagatose and D-Fructose J.Mol.Biol. V. 374 443 2007.
ISSN: ISSN 0022-2836
PubMed: 17936787
DOI: 10.1016/J.JMB.2007.09.033