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

The structure of Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy D-Tagatose, PDB code: 4ytq 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)	19.32 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.327, 126.308, 99.498, 90.00, 101.77, 90.00
R / Rfree (%)	17.4 / 21.3

The binding sites of Manganese atom in the Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy D-Tagatose (pdb code 4ytq). 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 D-Tagatose, PDB code: 4ytq:
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 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 C66S From Pseudomonas Cichorii in Complex with 1-Deoxy D-Tagatose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:16.8 occ:1.00 OD2 A:ASP185 1.9 11.7 1.0 O5 A:TGD402 2.0 55.1 0.5 OE2 A:GLU152 2.0 15.9 1.0 O2 A:TGD402 2.1 41.2 0.5 ND1 A:HIS211 2.1 13.1 1.0 O3 A:TGD402 2.6 43.6 0.5 OE1 A:GLU246 2.7 19.2 1.0 O4 A:TGD402 2.8 56.6 0.5 CD A:GLU152 3.0 17.4 1.0 CG A:ASP185 3.0 12.6 1.0 C2 A:TGD402 3.1 42.9 0.5 CE1 A:HIS211 3.1 13.6 1.0 C5 A:TGD402 3.1 55.9 0.5 CG A:HIS211 3.2 13.2 1.0 OE1 A:GLU152 3.3 16.8 1.0 C3 A:TGD402 3.4 44.3 0.5 C4 A:TGD402 3.5 56.8 0.5 CB A:HIS211 3.5 11.0 1.0 CB A:ASP185 3.6 13.6 1.0 CD A:GLU246 3.6 21.4 1.0 OE2 A:GLU246 3.8 23.4 1.0 NH2 A:ARG217 4.0 15.8 1.0 CD2 A:HIS188 4.1 10.3 1.0 OD1 A:ASP185 4.1 15.6 1.0 O A:HOH546 4.1 16.6 1.0 NE2 A:HIS188 4.1 7.8 1.0 NE2 A:HIS211 4.2 14.5 1.0 NE2 A:GLN183 4.3 13.2 1.0 CD2 A:HIS211 4.3 14.7 1.0 C6 A:TGD402 4.4 55.4 0.5 CG A:GLU152 4.4 13.7 1.0 C1 A:TGD402 4.4 41.7 0.5 C4 A:TGD402 4.6 45.5 0.5 C3 A:TGD402 4.9 57.1 0.5 CA A:ASP185 4.9 12.7 1.0 C6 A:TGD402 4.9 45.9 0.5 O6 A:TGD402 4.9 53.9 0.5 CG A:GLU246 5.0 20.0 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 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 C66S From Pseudomonas Cichorii in Complex with 1-Deoxy D-Tagatose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:23.6 occ:1.00 OD2 B:ASP185 2.0 13.5 1.0 OE2 B:GLU152 2.0 18.5 1.0 O B:HOH691 2.1 20.2 1.0 ND1 B:HIS211 2.1 12.5 1.0 OE1 B:GLU246 2.7 18.8 1.0 CE1 B:HIS211 3.0 15.0 1.0 CD B:GLU152 3.1 19.0 1.0 CG B:ASP185 3.1 15.0 1.0 CG B:HIS211 3.2 14.3 1.0 OE1 B:GLU152 3.4 17.2 1.0 CB B:ASP185 3.6 13.8 1.0 CB B:HIS211 3.6 11.2 1.0 CD B:GLU246 3.7 18.6 1.0 OE2 B:GLU246 3.9 20.5 1.0 CD2 B:HIS188 4.1 13.7 1.0 NE2 B:HIS211 4.1 14.2 1.0 NE2 B:GLN183 4.2 13.5 1.0 NH2 B:ARG217 4.2 20.9 1.0 OD1 B:ASP185 4.2 15.0 1.0 NE2 B:HIS188 4.2 15.6 1.0 CD2 B:HIS211 4.3 13.9 1.0 O B:HOH638 4.3 21.9 1.0 CG B:GLU152 4.4 16.4 1.0 O B:HOH642 4.7 19.1 1.0 CA B:ASP185 4.9 12.3 1.0 O B:HOH693 5.0 17.5 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 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 C66S From Pseudomonas Cichorii in Complex with 1-Deoxy D-Tagatose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:22.9 occ:1.00 OD2 C:ASP185 2.0 14.0 1.0 OE2 C:GLU152 2.1 21.7 1.0 O C:HOH734 2.1 20.9 1.0 ND1 C:HIS211 2.2 15.4 1.0 OE1 C:GLU246 2.8 18.8 1.0 CD C:GLU152 3.1 19.4 1.0 CE1 C:HIS211 3.1 18.0 1.0 CG C:ASP185 3.1 16.2 1.0 CG C:HIS211 3.2 16.8 1.0 OE1 C:GLU152 3.4 21.6 1.0 CB C:HIS211 3.6 14.0 1.0 CB C:ASP185 3.6 14.6 1.0 CD C:GLU246 3.7 19.1 1.0 OE2 C:GLU246 3.8 21.5 1.0 CD2 C:HIS188 4.0 13.0 1.0 NE2 C:HIS188 4.1 12.2 1.0 NH2 C:ARG217 4.1 20.6 1.0 OD1 C:ASP185 4.2 14.2 1.0 O C:HOH672 4.2 24.2 1.0 NE2 C:GLN183 4.2 14.2 1.0 NE2 C:HIS211 4.2 18.0 1.0 CD2 C:HIS211 4.3 15.8 1.0 CG C:GLU152 4.4 16.2 1.0 CA C:ASP185 4.9 13.7 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 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 C66S From Pseudomonas Cichorii in Complex with 1-Deoxy D-Tagatose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:20.6 occ:1.00 OD2 D:ASP185 1.9 17.8 1.0 OE2 D:GLU152 2.1 23.4 1.0 O D:HOH675 2.2 18.4 1.0 ND1 D:HIS211 2.2 15.8 1.0 OE1 D:GLU246 2.7 19.2 1.0 CG D:ASP185 3.0 17.8 1.0 CD D:GLU152 3.1 22.4 1.0 CE1 D:HIS211 3.1 15.1 1.0 CG D:HIS211 3.2 15.8 1.0 OE1 D:GLU152 3.4 23.8 1.0 CB D:HIS211 3.5 15.5 1.0 CB D:ASP185 3.6 17.7 1.0 CD D:GLU246 3.6 20.5 1.0 OE2 D:GLU246 3.8 25.2 1.0 OD1 D:ASP185 4.1 18.6 1.0 NH2 D:ARG217 4.1 16.3 1.0 CD2 D:HIS188 4.1 12.4 1.0 NE2 D:GLN183 4.1 15.9 1.0 NE2 D:HIS188 4.2 13.8 1.0 O D:HOH551 4.2 19.0 1.0 NE2 D:HIS211 4.2 17.3 1.0 CD2 D:HIS211 4.3 16.6 1.0 CG D:GLU152 4.4 20.8 1.0 O D:HOH560 4.8 20.7 1.0 CA D:ASP185 4.9 15.6 1.0 CG D:GLU246 5.0 19.9 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