Manganese in PDB 4ytt: Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 6-Deoxy L-Psicose

The structure of Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 6-Deoxy L-Psicose, PDB code: 4ytt 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)	23.42 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.400, 126.730, 99.340, 90.00, 101.71, 90.00
R / Rfree (%)	19 / 22.6

The binding sites of Manganese atom in the Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 6-Deoxy L-Psicose (pdb code 4ytt). 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 6-Deoxy L-Psicose, PDB code: 4ytt:
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 6-Deoxy L-Psicose


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 6-Deoxy L-Psicose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:22.6 occ:1.00 OD2 A:ASP185 2.0 18.1 1.0 OE2 A:GLU152 2.1 23.4 1.0 ND1 A:HIS211 2.2 16.3 1.0 O2 A:PUD402 2.3 39.2 1.0 O3 A:PUD402 2.3 42.9 1.0 OE1 A:GLU246 2.6 30.2 1.0 CD A:GLU152 3.1 24.1 1.0 CE1 A:HIS211 3.1 17.0 1.0 CG A:ASP185 3.1 17.5 1.0 C2 A:PUD402 3.1 39.6 1.0 CG A:HIS211 3.2 17.1 1.0 C3 A:PUD402 3.3 43.3 1.0 OE1 A:GLU152 3.4 23.6 1.0 CD A:GLU246 3.5 29.5 1.0 CB A:HIS211 3.6 19.6 1.0 CB A:ASP185 3.7 17.3 1.0 OE2 A:GLU246 3.7 32.6 1.0 NH2 A:ARG217 4.1 18.6 1.0 OD1 A:ASP185 4.1 18.3 1.0 NE2 A:GLN183 4.2 17.2 1.0 NE2 A:HIS211 4.2 17.0 1.0 CD2 A:HIS188 4.3 15.4 1.0 O A:HOH504 4.3 26.7 1.0 NE2 A:HIS188 4.3 15.0 1.0 CD2 A:HIS211 4.3 18.7 1.0 C4 A:PUD402 4.3 45.0 1.0 CG A:GLU152 4.4 19.9 1.0 C1 A:PUD402 4.5 38.8 1.0 CG A:GLU246 4.9 28.0 1.0 CA A:ASP185 4.9 17.3 1.0 O5 A:PUD402 4.9 44.0 0.5 O A:HOH645 5.0 17.8 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 6-Deoxy L-Psicose


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 6-Deoxy L-Psicose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:25.5 occ:1.00 OD2 B:ASP185 2.0 18.8 1.0 OE2 B:GLU152 2.1 19.2 1.0 ND1 B:HIS211 2.2 19.4 1.0 O2 B:PUD402 2.2 39.7 1.0 O3 B:PUD402 2.5 43.9 1.0 OE1 B:GLU246 2.7 29.0 1.0 C2 B:PUD402 3.0 40.8 1.0 CE1 B:HIS211 3.0 19.9 1.0 CG B:ASP185 3.1 18.3 1.0 CD B:GLU152 3.1 21.1 1.0 CG B:HIS211 3.3 18.9 1.0 C3 B:PUD402 3.3 44.8 1.0 OE1 B:GLU152 3.5 23.0 1.0 CD B:GLU246 3.6 27.0 1.0 CB B:HIS211 3.6 17.2 1.0 CB B:ASP185 3.7 15.1 1.0 OE2 B:GLU246 3.9 29.4 1.0 OD1 B:ASP185 4.2 19.1 1.0 CD2 B:HIS188 4.2 20.1 1.0 NE2 B:HIS188 4.2 17.6 1.0 NE2 B:GLN183 4.2 16.0 1.0 NE2 B:HIS211 4.2 20.6 1.0 NH2 B:ARG217 4.2 26.6 1.0 C4 B:PUD402 4.3 47.0 1.0 CD2 B:HIS211 4.3 20.5 1.0 O B:HOH621 4.4 25.6 1.0 C1 B:PUD402 4.4 38.8 1.0 CG B:GLU152 4.5 18.6 1.0 O B:HOH624 4.9 18.9 1.0 O1 B:PUD402 5.0 32.3 1.0 CA B:ASP185 5.0 16.6 1.0 O5 B:PUD402 5.0 49.6 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 6-Deoxy L-Psicose


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 6-Deoxy L-Psicose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:26.1 occ:1.00 OD2 C:ASP185 2.0 20.3 1.0 OE2 C:GLU152 2.1 24.5 1.0 ND1 C:HIS211 2.2 20.6 1.0 O2 C:PUD402 2.3 34.9 1.0 O3 C:PUD402 2.5 41.8 1.0 OE1 C:GLU246 2.6 29.7 1.0 CE1 C:HIS211 3.0 22.5 1.0 CD C:GLU152 3.1 24.8 1.0 CG C:ASP185 3.1 21.3 1.0 C2 C:PUD402 3.2 37.5 1.0 CG C:HIS211 3.2 21.6 1.0 C3 C:PUD402 3.4 41.8 1.0 OE1 C:GLU152 3.4 22.9 1.0 CD C:GLU246 3.6 28.2 1.0 CB C:HIS211 3.6 20.6 1.0 CB C:ASP185 3.7 16.9 1.0 OE2 C:GLU246 3.8 29.6 1.0 NH2 C:ARG217 4.2 27.9 1.0 OD1 C:ASP185 4.2 21.3 1.0 NE2 C:HIS211 4.2 21.5 1.0 NE2 C:GLN183 4.2 19.3 1.0 CD2 C:HIS188 4.2 15.2 1.0 NE2 C:HIS188 4.3 15.5 1.0 CD2 C:HIS211 4.3 21.8 1.0 O C:HOH598 4.4 33.1 1.0 CG C:GLU152 4.5 20.4 1.0 C4 C:PUD402 4.5 44.6 1.0 C1 C:PUD402 4.6 36.6 1.0 O5 C:PUD402 4.9 44.4 1.0 O C:HOH566 4.9 21.8 1.0 CG C:GLU246 4.9 28.0 1.0 O1 C:PUD402 5.0 28.5 1.0 CA C:ASP185 5.0 16.7 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 6-Deoxy L-Psicose


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 6-Deoxy L-Psicose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:25.0 occ:1.00 OD2 D:ASP185 2.0 24.6 1.0 OE2 D:GLU152 2.0 29.2 1.0 O2 D:PUD402 2.2 41.0 1.0 ND1 D:HIS211 2.2 23.6 1.0 O3 D:PUD402 2.6 49.1 1.0 OE1 D:GLU246 2.7 30.2 1.0 CD D:GLU152 3.1 29.2 1.0 CG D:ASP185 3.1 24.2 1.0 C2 D:PUD402 3.1 44.1 1.0 CE1 D:HIS211 3.1 24.1 1.0 CG D:HIS211 3.3 23.8 1.0 C3 D:PUD402 3.4 47.3 1.0 OE1 D:GLU152 3.5 29.1 1.0 CB D:HIS211 3.6 23.4 1.0 CD D:GLU246 3.7 29.0 1.0 CB D:ASP185 3.7 22.4 1.0 OE2 D:GLU246 3.9 32.4 1.0 NH2 D:ARG217 4.1 19.9 1.0 NE2 D:GLN183 4.1 23.0 1.0 OD1 D:ASP185 4.2 24.3 1.0 CD2 D:HIS188 4.3 19.5 1.0 NE2 D:HIS211 4.3 24.4 1.0 O D:HOH572 4.3 24.1 1.0 CG D:GLU152 4.4 27.1 1.0 CD2 D:HIS211 4.4 23.6 1.0 NE2 D:HIS188 4.4 18.2 1.0 C4 D:PUD402 4.4 49.1 1.0 C1 D:PUD402 4.5 44.1 1.0 O5 D:PUD402 4.9 48.9 1.0 O1 D:PUD402 4.9 40.4 1.0 CA D:ASP185 4.9 20.5 1.0 O D:HOH507 4.9 29.8 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