Manganese in PDB 4ytr: Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose

The structure of Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, PDB code: 4ytr was solved by H.Yoshida, A.Yoshihara, T.Ishii, K.Izumori, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.71 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.380, 126.330, 92.920, 90.00, 98.70, 90.00
R / Rfree (%)	18.8 / 23.5

The binding sites of Manganese atom in the Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose (pdb code 4ytr). 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 C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose, PDB code: 4ytr:
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 C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-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 C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:20.6 occ:1.00 OE2 A:GLU152 2.0 18.0 1.0 O A:HOH669 2.0 23.4 1.0 OD2 A:ASP185 2.0 19.5 1.0 ND1 A:HIS211 2.1 15.0 1.0 OE1 A:GLU246 2.8 24.8 1.0 CE1 A:HIS211 2.9 17.1 1.0 CD A:GLU152 3.0 17.9 1.0 CG A:HIS211 3.1 15.2 1.0 CG A:ASP185 3.2 17.8 1.0 OE1 A:GLU152 3.4 18.8 1.0 CB A:HIS211 3.6 14.3 1.0 CB A:ASP185 3.7 14.5 1.0 CD A:GLU246 3.8 24.6 1.0 CD2 A:HIS188 4.0 13.9 1.0 NE2 A:HIS188 4.1 13.0 1.0 NE2 A:HIS211 4.1 16.7 1.0 OE2 A:GLU246 4.1 24.0 1.0 NH2 A:ARG217 4.1 20.4 1.0 CD2 A:HIS211 4.2 15.9 1.0 NE2 A:GLN183 4.2 15.3 1.0 OD1 A:ASP185 4.2 19.0 1.0 CG A:GLU152 4.3 14.6 1.0 O A:HOH604 4.4 15.2 1.0 O A:HOH613 4.7 18.8 1.0 O A:HOH695 4.9 40.7 1.0 CA A:ASP185 5.0 13.5 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-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 C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:27.7 occ:1.00 OD2 B:ASP185 2.0 14.2 1.0 OE2 B:GLU152 2.1 22.5 1.0 ND1 B:HIS211 2.1 11.6 1.0 O B:HOH702 2.3 23.4 1.0 OE1 B:GLU246 2.8 21.0 1.0 CE1 B:HIS211 3.0 14.1 1.0 CG B:ASP185 3.1 18.0 1.0 CG B:HIS211 3.2 12.1 1.0 CD B:GLU152 3.2 20.7 1.0 CB B:ASP185 3.6 15.2 1.0 CB B:HIS211 3.6 13.8 1.0 CD B:GLU246 3.7 19.2 1.0 OE1 B:GLU152 3.7 20.8 1.0 OE2 B:GLU246 3.9 24.2 1.0 NE2 B:GLN183 4.0 23.4 1.0 O B:HOH641 4.1 16.0 1.0 OD1 B:ASP185 4.1 18.9 1.0 CD2 B:HIS188 4.2 16.9 1.0 NH2 B:ARG217 4.2 22.4 1.0 NE2 B:HIS211 4.2 13.0 1.0 CD2 B:HIS211 4.3 13.2 1.0 NE2 B:HIS188 4.3 16.9 1.0 CG B:GLU152 4.4 18.5 1.0 O B:HOH592 4.8 19.4 1.0 O B:HOH637 4.9 16.4 1.0 CA B:ASP185 4.9 15.1 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-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 C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:25.2 occ:1.00 OD2 C:ASP185 2.0 8.5 1.0 OE2 C:GLU152 2.1 15.6 1.0 ND1 C:HIS211 2.2 17.1 1.0 O5 C:TGJ402 2.3 40.3 1.0 OE1 C:GLU246 2.8 16.6 1.0 CE1 C:HIS211 3.1 15.2 1.0 CG C:ASP185 3.1 12.5 1.0 CD C:GLU152 3.1 16.8 1.0 C5 C:TGJ402 3.2 44.7 1.0 CG C:HIS211 3.3 15.2 1.0 OE1 C:GLU152 3.5 16.6 1.0 CB C:ASP185 3.6 13.0 1.0 CB C:HIS211 3.6 14.0 1.0 O4 C:TGJ402 3.7 45.6 1.0 CD C:GLU246 3.8 19.4 1.0 C4 C:TGJ402 4.0 46.2 1.0 OE2 C:GLU246 4.0 20.2 1.0 CD2 C:HIS188 4.1 11.2 1.0 NE2 C:HIS188 4.1 11.6 1.0 O C:HOH632 4.1 31.9 1.0 OD1 C:ASP185 4.2 13.4 1.0 NH2 C:ARG217 4.2 22.0 1.0 NE2 C:HIS211 4.2 14.4 1.0 NE2 C:GLN183 4.3 16.2 1.0 CD2 C:HIS211 4.3 15.3 1.0 C6 C:TGJ402 4.4 43.4 1.0 C1 C:TGJ402 4.4 47.4 1.0 CG C:GLU152 4.5 12.4 1.0 C3 C:TGJ402 4.9 47.3 1.0 CA C:ASP185 4.9 13.4 1.0 O6 C:TGJ402 5.0 40.9 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-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 C66S From Pseudomonas Cichorii in Complex with 1-Deoxy L-Tagatose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:21.6 occ:1.00 OD2 D:ASP185 2.0 15.5 1.0 OE2 D:GLU152 2.0 19.6 1.0 O D:HOH721 2.2 25.6 1.0 ND1 D:HIS211 2.2 15.1 1.0 OE1 D:GLU246 2.8 17.9 1.0 CD D:GLU152 3.1 20.4 1.0 CG D:ASP185 3.1 17.0 1.0 CE1 D:HIS211 3.1 15.4 1.0 CG D:HIS211 3.3 15.2 1.0 OE1 D:GLU152 3.5 19.8 1.0 CB D:ASP185 3.6 16.6 1.0 CD D:GLU246 3.7 19.4 1.0 CB D:HIS211 3.7 16.1 1.0 OE2 D:GLU246 3.8 20.6 1.0 NH2 D:ARG217 4.0 19.2 1.0 CD2 D:HIS188 4.1 10.5 1.0 NE2 D:HIS188 4.1 10.0 1.0 O D:HOH588 4.1 22.4 1.0 OD1 D:ASP185 4.1 16.9 1.0 NE2 D:GLN183 4.3 19.4 1.0 NE2 D:HIS211 4.3 17.5 1.0 CG D:GLU152 4.4 17.2 1.0 CD2 D:HIS211 4.4 14.9 1.0 O D:HOH700 4.6 30.1 1.0 O D:HOH589 4.8 23.6 1.0 CA D:ASP185 4.9 16.0 1.0

H.Yoshida, A.Yoshihara, T.Ishii, K.Izumori, S.Kamitori. X-Ray Structures of the Pseudomonas Cichorii D-Tagatose 3-Epimerase Mutant Form C66S Recognizing Deoxy Sugars As Substrates Appl. Microbiol. Biotechnol. V. 100 10403 2016.
ISSN: ESSN 1432-0614
PubMed: 27368739
DOI: 10.1007/S00253-016-7673-7