Manganese in PDB 4pfh: Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-IDF8

The structure of Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-IDF8, PDB code: 4pfh was solved by C.S.Hee, A.Bosshart, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.74 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.460, 86.740, 61.820, 90.00, 99.10, 90.00
R / Rfree (%)	14.4 / 17.7

The binding sites of Manganese atom in the Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-IDF8 (pdb code 4pfh). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-IDF8, PDB code: 4pfh:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-IDF8


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 Engineered D-Tagatose 3-Epimerase Pcdte-IDF8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:14.6 occ:1.00 O2 A:FUD504 2.0 18.3 0.7 OD2 A:ASP185 2.1 7.5 1.0 OE2 A:GLU152 2.2 9.4 1.0 OE1 A:GLU246 2.3 11.7 1.0 ND1 A:HIS211 2.3 7.5 1.0 O2 A:PSJ503 2.3 19.6 0.3 O3 A:PSJ503 2.4 19.8 0.3 O3 A:FUD504 2.4 27.3 0.7 C2 A:FUD504 3.0 28.6 0.7 C2 A:PSJ503 3.0 21.2 0.3 CD A:GLU246 3.1 14.2 1.0 C3 A:PSJ503 3.1 22.0 0.3 CE1 A:HIS211 3.2 7.8 1.0 CG A:ASP185 3.2 7.0 1.0 CD A:GLU152 3.2 9.9 1.0 C3 A:FUD504 3.2 34.9 0.7 OE2 A:GLU246 3.2 22.2 1.0 CG A:HIS211 3.4 6.7 1.0 OE1 A:GLU152 3.6 12.1 1.0 CB A:HIS211 3.7 6.3 1.0 CB A:ASP185 3.9 6.2 1.0 O A:HOH813 3.9 20.8 1.0 OD1 A:ASP185 4.2 8.1 1.0 NH2 A:ARG217 4.3 8.4 1.0 NE2 A:HIS211 4.4 7.6 1.0 NE2 A:GLN183 4.4 11.1 1.0 C1 A:FUD504 4.4 26.6 0.7 C1 A:PSJ503 4.4 20.9 0.3 CD2 A:HIS211 4.5 7.4 1.0 CG A:GLU246 4.5 13.1 1.0 CG A:GLU152 4.5 7.7 1.0 C4 A:PSJ503 4.5 22.2 0.3 C4 A:FUD504 4.6 38.7 0.7 CD2 A:HIS188 4.6 4.4 1.0 NE2 A:HIS188 4.6 4.3 1.0 O5 A:PSJ503 4.7 23.5 0.3 O4 A:FUD504 4.7 48.8 0.7 O A:HOH672 4.7 15.3 1.0 CB A:GLU246 4.9 10.6 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-IDF8


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 Engineered D-Tagatose 3-Epimerase Pcdte-IDF8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:15.6 occ:1.00 O B:HOH628 2.2 15.1 1.0 NE2 A:HIS116 2.2 14.0 1.0 NE2 B:HIS116 2.2 17.2 1.0 O A:HOH625 2.2 17.9 1.0 CD2 A:HIS116 3.1 14.8 1.0 CE1 B:HIS116 3.2 16.6 1.0 CD2 B:HIS116 3.2 18.4 1.0 CE1 A:HIS116 3.2 13.9 1.0 CG A:HIS116 4.3 14.1 1.0 ND1 A:HIS116 4.3 14.0 1.0 ND1 B:HIS116 4.3 16.9 1.0 CG B:HIS116 4.4 18.4 1.0 O B:HOH649 4.4 25.6 1.0 O A:TYR157 4.5 5.4 1.0 O B:HOH648 4.5 24.2 1.0 O B:TYR157 4.5 8.4 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-IDF8


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 Engineered D-Tagatose 3-Epimerase Pcdte-IDF8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:16.9 occ:1.00 OD2 B:ASP185 2.1 8.1 1.0 O2 B:PSJ502 2.1 8.8 0.3 OE2 B:GLU152 2.2 13.4 1.0 OE1 B:GLU246 2.2 13.5 1.0 O3 B:PSJ502 2.2 9.0 0.3 O2 B:FUD503 2.3 28.0 0.7 ND1 B:HIS211 2.4 10.8 1.0 O3 B:FUD503 2.5 28.6 0.7 C2 B:PSJ502 2.9 9.7 0.3 C3 B:PSJ502 2.9 10.7 0.3 CD B:GLU246 3.0 16.3 1.0 C2 B:FUD503 3.1 30.3 0.7 OE2 B:GLU246 3.2 24.1 1.0 CG B:ASP185 3.2 7.7 1.0 CD B:GLU152 3.2 12.4 1.0 CE1 B:HIS211 3.3 10.8 1.0 C3 B:FUD503 3.4 35.7 0.7 CG B:HIS211 3.4 9.3 1.0 OE1 B:GLU152 3.6 14.8 1.0 CB B:HIS211 3.8 8.3 1.0 CB B:ASP185 3.9 7.3 1.0 O B:HOH740 4.0 23.4 1.0 OD1 B:ASP185 4.2 8.7 1.0 NH2 B:ARG217 4.3 7.7 1.0 C4 B:PSJ502 4.3 11.3 0.3 C1 B:PSJ502 4.3 9.3 0.3 NE2 B:HIS211 4.4 10.5 1.0 O4 B:FUD503 4.4 39.0 0.7 CG B:GLU246 4.5 13.5 1.0 NE2 B:GLN183 4.5 12.5 1.0 CD2 B:HIS211 4.5 10.7 1.0 C4 B:FUD503 4.5 38.8 0.7 CG B:GLU152 4.6 10.9 1.0 C1 B:FUD503 4.6 28.9 0.7 CD2 B:HIS188 4.6 5.7 1.0 O5 B:PSJ502 4.6 13.0 0.3 NE2 B:HIS188 4.6 5.7 1.0 O B:HOH679 4.8 14.3 1.0 O1 B:PSJ502 4.9 8.8 0.3 CB B:GLU246 4.9 10.7 1.0 O1 B:FUD503 5.0 25.7 0.7

A.Bosshart, C.S.Hee, M.Bechtold, T.Schirmer, S.Panke. Divergent Evolution of A Thermostable D-Tagatose Epimerase Towards Improved Activity For Two Different Hexose Substrates To Be Published.