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

The structure of Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy 3-Keto D-Galactitol, PDB code: 4yts 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)	32.46 / 2.14
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.503, 126.733, 99.520, 90.00, 101.89, 90.00
R / Rfree (%)	20.3 / 25.5

The binding sites of Manganese atom in the Crystal Structure of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii in Complex with 1-Deoxy 3-Keto D-Galactitol (pdb code 4yts). 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 3-Keto D-Galactitol, PDB code: 4yts:
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 3-Keto D-Galactitol


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 3-Keto D-Galactitol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:18.2 occ:1.00 OE2 A:GLU152 2.1 19.6 1.0 ND1 A:HIS211 2.1 14.9 1.0 OD2 A:ASP185 2.1 16.8 1.0 O3 A:TGS402 2.1 28.1 1.0 OE1 A:GLU246 2.3 26.3 1.0 O4 A:TGS402 2.4 28.5 1.0 CE1 A:HIS211 3.0 13.7 1.0 C3 A:TGS402 3.0 28.6 1.0 CD A:GLU152 3.1 23.7 1.0 C4 A:TGS402 3.2 29.2 1.0 CG A:HIS211 3.2 15.2 1.0 CD A:GLU246 3.3 26.8 1.0 CG A:ASP185 3.3 13.2 1.0 OE2 A:GLU246 3.5 28.1 1.0 OE1 A:GLU152 3.5 26.6 1.0 CB A:HIS211 3.6 15.9 1.0 CB A:ASP185 3.9 18.7 1.0 NH2 A:ARG217 4.1 20.2 1.0 NE2 A:HIS211 4.1 15.9 1.0 CD2 A:HIS188 4.2 16.2 1.0 NE2 A:HIS188 4.3 17.3 1.0 CD2 A:HIS211 4.3 16.8 1.0 NE2 A:GLN183 4.3 17.7 1.0 OD1 A:ASP185 4.3 14.9 1.0 CG A:GLU152 4.4 21.9 1.0 C2 A:TGS402 4.4 28.1 1.0 C5 A:TGS402 4.5 30.6 1.0 CG A:GLU246 4.7 28.3 1.0 O5 A:TGS402 4.7 32.2 1.0 O2 A:TGS402 4.8 26.5 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 3-Keto D-Galactitol


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 3-Keto D-Galactitol within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:19.2 occ:1.00 ND1 B:HIS211 2.1 20.7 1.0 OD2 B:ASP185 2.1 23.7 1.0 OE2 B:GLU152 2.1 19.1 1.0 O3 B:TGS403 2.3 22.9 1.0 O4 B:TGS403 2.3 25.4 1.0 OE1 B:GLU246 2.5 27.2 1.0 CE1 B:HIS211 2.9 19.6 1.0 C3 B:TGS403 3.1 24.9 1.0 CD B:GLU152 3.2 17.6 1.0 C4 B:TGS403 3.2 25.1 1.0 CG B:HIS211 3.2 20.3 1.0 CG B:ASP185 3.3 21.3 1.0 CD B:GLU246 3.3 26.3 1.0 OE2 B:GLU246 3.3 28.9 1.0 OE1 B:GLU152 3.5 20.4 1.0 CB B:HIS211 3.7 22.0 1.0 CB B:ASP185 3.9 19.4 1.0 NE2 B:HIS211 4.1 21.9 1.0 NH2 B:ARG217 4.2 25.5 1.0 CD2 B:HIS211 4.2 18.1 1.0 CD2 B:HIS188 4.2 24.4 1.0 NE2 B:HIS188 4.3 22.9 1.0 OD1 B:ASP185 4.3 20.6 1.0 NE2 B:GLN183 4.3 12.9 1.0 C2 B:TGS403 4.5 25.1 1.0 CG B:GLU152 4.5 16.1 1.0 C5 B:TGS403 4.5 25.1 1.0 O B:HOH518 4.7 27.8 1.0 CG B:GLU246 4.7 25.4 1.0 O5 B:TGS403 4.8 28.6 1.0 O2 B:TGS403 4.9 24.7 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 3-Keto D-Galactitol


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 3-Keto D-Galactitol within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:17.1 occ:1.00 O3 C:TGS402 2.0 17.0 1.0 OE2 C:GLU152 2.1 25.2 1.0 OD2 C:ASP185 2.1 10.8 1.0 ND1 C:HIS211 2.2 19.1 1.0 O4 C:TGS402 2.3 17.3 1.0 OE1 C:GLU246 2.5 22.7 1.0 C3 C:TGS402 2.8 21.8 1.0 CE1 C:HIS211 3.0 21.8 1.0 C4 C:TGS402 3.0 20.3 1.0 CD C:GLU152 3.1 23.2 1.0 CG C:ASP185 3.3 19.1 1.0 CG C:HIS211 3.3 21.0 1.0 CD C:GLU246 3.4 26.1 1.0 OE1 C:GLU152 3.5 25.2 1.0 OE2 C:GLU246 3.5 25.5 1.0 CB C:HIS211 3.8 17.5 1.0 CB C:ASP185 3.8 18.9 1.0 NE2 C:HIS211 4.2 22.2 1.0 NE2 C:GLN183 4.2 28.6 1.0 C2 C:TGS402 4.3 21.7 1.0 CD2 C:HIS188 4.3 21.9 1.0 C5 C:TGS402 4.3 24.2 1.0 OD1 C:ASP185 4.3 20.7 1.0 CD2 C:HIS211 4.3 20.4 1.0 NE2 C:HIS188 4.4 21.4 1.0 NH2 C:ARG217 4.4 27.5 1.0 CG C:GLU152 4.4 22.6 1.0 O5 C:TGS402 4.5 25.2 1.0 O C:HOH520 4.5 19.9 1.0 O C:HOH507 4.7 33.2 1.0 O2 C:TGS402 4.7 21.9 1.0 CG C:GLU246 4.8 26.6 1.0 O C:HOH517 4.9 32.1 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 3-Keto D-Galactitol


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 3-Keto D-Galactitol within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn402 b:25.9 occ:1.00 OD2 D:ASP185 2.0 26.2 1.0 OE2 D:GLU152 2.1 29.3 1.0 O4 D:TGS403 2.2 31.4 1.0 ND1 D:HIS211 2.3 25.3 1.0 O3 D:TGS403 2.4 22.4 1.0 OE1 D:GLU246 2.4 36.6 1.0 CD D:GLU152 3.1 29.4 1.0 C3 D:TGS403 3.1 27.8 1.0 CG D:ASP185 3.2 27.4 1.0 C4 D:TGS403 3.2 29.8 1.0 CE1 D:HIS211 3.2 26.7 1.0 CG D:HIS211 3.3 26.5 1.0 OE1 D:GLU152 3.4 25.8 1.0 CD D:GLU246 3.4 34.9 1.0 CB D:HIS211 3.6 25.9 1.0 OE2 D:GLU246 3.7 38.8 1.0 CB D:ASP185 3.8 27.6 1.0 O D:HOH533 3.9 27.0 1.0 OD1 D:ASP185 4.2 28.9 1.0 NH2 D:ARG217 4.2 19.4 1.0 NE2 D:HIS188 4.2 22.4 1.0 CD2 D:HIS188 4.2 22.6 1.0 NE2 D:GLN183 4.3 28.2 1.0 NE2 D:HIS211 4.4 25.5 1.0 CD2 D:HIS211 4.4 25.7 1.0 CG D:GLU152 4.4 29.6 1.0 C5 D:TGS403 4.4 32.4 1.0 O5 D:TGS403 4.5 33.3 1.0 C2 D:TGS403 4.6 28.0 1.0 CG D:GLU246 4.8 35.6 1.0 O D:HOH560 4.9 19.7 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