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

The structure of Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with L-Erythrulose, PDB code: 4ytu 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)	20.86 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.720, 124.800, 94.720, 90.00, 99.09, 90.00
R / Rfree (%)	22.3 / 26.6

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


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 L-Erythrulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:38.6 occ:1.00 OD2 A:ASP185 2.1 35.0 1.0 OE2 A:GLU152 2.2 35.7 1.0 ND1 A:HIS211 2.3 26.7 1.0 O2 A:LER402 2.3 53.2 1.0 O3 A:LER402 2.7 59.0 1.0 OE1 A:GLU246 2.9 32.3 1.0 CE1 A:HIS211 3.2 25.2 1.0 CD A:GLU152 3.2 34.3 1.0 C2 A:LER402 3.2 54.8 1.0 CG A:ASP185 3.3 31.9 1.0 CG A:HIS211 3.3 25.8 1.0 C3 A:LER402 3.6 56.7 1.0 CB A:HIS211 3.6 23.0 1.0 OE1 A:GLU152 3.7 33.8 1.0 CD A:GLU246 3.7 33.7 1.0 CB A:ASP185 3.8 30.2 1.0 OE2 A:GLU246 3.9 36.2 1.0 CD2 A:HIS188 4.1 21.6 1.0 NE2 A:HIS188 4.2 21.1 1.0 NH2 A:ARG217 4.2 31.1 1.0 O A:HOH531 4.2 23.3 1.0 OD1 A:ASP185 4.3 33.6 1.0 NE2 A:HIS211 4.3 24.0 1.0 NE2 A:GLN183 4.4 25.4 1.0 CD2 A:HIS211 4.4 25.8 1.0 CG A:GLU152 4.5 31.8 1.0 C4 A:LER402 4.6 57.5 1.0 C1 A:LER402 4.6 52.0 1.0 O1 A:LER402 4.8 48.2 1.0 O A:HOH577 4.9 27.3 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 L-Erythrulose


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 L-Erythrulose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:53.8 occ:1.00 ND1 B:HIS211 2.0 24.5 1.0 OD2 B:ASP185 2.0 37.0 1.0 OE2 B:GLU152 2.3 36.4 1.0 O2 B:LER402 2.5 46.3 1.0 O3 B:LER402 2.8 49.9 1.0 OE1 B:GLU246 2.8 30.1 1.0 CE1 B:HIS211 2.9 24.1 1.0 CG B:HIS211 3.1 22.8 1.0 CG B:ASP185 3.2 35.8 1.0 C2 B:LER402 3.4 47.6 1.0 CD B:GLU152 3.4 35.2 1.0 CB B:HIS211 3.5 22.1 1.0 CD B:GLU246 3.6 31.5 1.0 C3 B:LER402 3.7 48.6 1.0 CB B:ASP185 3.8 32.5 1.0 OE2 B:GLU246 3.8 34.0 1.0 OE1 B:GLU152 4.0 38.8 1.0 NE2 B:GLN183 4.0 24.2 1.0 NE2 B:HIS211 4.1 23.8 1.0 CD2 B:HIS211 4.2 23.8 1.0 OD1 B:ASP185 4.2 37.6 1.0 CD2 B:HIS188 4.3 24.1 1.0 NE2 B:HIS188 4.4 24.3 1.0 O B:HOH528 4.4 32.8 1.0 NH2 B:ARG217 4.6 28.8 1.0 CG B:GLU152 4.6 34.0 1.0 C4 B:LER402 4.7 48.0 1.0 C1 B:LER402 4.8 46.4 1.0 O B:HOH613 4.9 32.9 1.0 O4 B:LER402 5.0 45.4 1.0 CG B:GLU246 5.0 30.8 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 L-Erythrulose


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 L-Erythrulose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:47.6 occ:1.00 OD2 C:ASP185 2.0 36.1 1.0 OE2 C:GLU152 2.1 39.6 1.0 ND1 C:HIS211 2.5 27.2 1.0 O2 C:LER402 2.6 45.6 1.0 OE1 C:GLU246 2.9 35.4 1.0 O3 C:LER402 2.9 47.7 1.0 CG C:ASP185 3.0 36.4 1.0 CD C:GLU152 3.3 38.5 1.0 CG C:HIS211 3.4 28.0 1.0 CB C:ASP185 3.4 33.5 1.0 CE1 C:HIS211 3.4 24.6 1.0 C2 C:LER402 3.5 46.0 1.0 CB C:HIS211 3.6 27.4 1.0 C3 C:LER402 3.8 46.6 1.0 CD2 C:HIS188 4.0 22.9 1.0 CD C:GLU246 4.0 33.3 1.0 NE2 C:GLN183 4.0 35.3 1.0 OE1 C:GLU152 4.0 42.0 1.0 NE2 C:HIS188 4.1 25.0 1.0 OD1 C:ASP185 4.1 40.7 1.0 CG C:GLU152 4.3 37.5 1.0 NH2 C:ARG217 4.3 27.5 1.0 OE2 C:GLU246 4.4 34.3 1.0 O C:HOH519 4.4 40.5 1.0 CD2 C:HIS211 4.5 26.7 1.0 NE2 C:HIS211 4.5 26.0 1.0 CA C:ASP185 4.7 30.6 1.0 C1 C:LER402 4.9 44.5 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 L-Erythrulose


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 L-Erythrulose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:39.2 occ:1.00 OD2 D:ASP185 1.9 39.4 1.0 O2 D:LER402 2.2 56.7 1.0 OE2 D:GLU152 2.3 40.5 1.0 ND1 D:HIS211 2.6 31.7 1.0 O3 D:LER402 2.8 59.7 1.0 CG D:ASP185 3.0 39.2 1.0 OE1 D:GLU246 3.1 38.4 1.0 CD D:GLU152 3.1 38.0 1.0 C2 D:LER402 3.2 57.3 1.0 CE1 D:HIS211 3.4 31.1 1.0 C3 D:LER402 3.6 58.8 1.0 CB D:ASP185 3.6 35.5 1.0 CG D:HIS211 3.6 30.9 1.0 OE1 D:GLU152 3.7 39.6 1.0 CB D:HIS211 4.0 32.0 1.0 CD2 D:HIS188 4.0 26.6 1.0 OD1 D:ASP185 4.1 41.8 1.0 CD D:GLU246 4.1 38.2 1.0 NH2 D:ARG217 4.1 22.9 1.0 CG D:GLU152 4.1 36.6 1.0 NE2 D:HIS188 4.2 28.3 1.0 OE2 D:GLU246 4.2 38.3 1.0 NE2 D:GLN183 4.3 33.2 1.0 C1 D:LER402 4.5 57.0 1.0 O D:HOH551 4.5 24.4 1.0 C4 D:LER402 4.5 60.0 1.0 NE2 D:HIS211 4.6 31.8 1.0 O1 D:LER402 4.7 55.5 1.0 CD2 D:HIS211 4.7 31.0 1.0 O D:HOH600 4.9 38.8 1.0 O4 D:LER402 5.0 58.3 1.0 CA D:ASP185 5.0 34.6 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