Manganese in PDB 4pgl: Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-ILS6

The structure of Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-ILS6, PDB code: 4pgl 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)	36.85 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	102.810, 47.440, 126.380, 90.00, 102.49, 90.00
R / Rfree (%)	15.2 / 18.1

The binding sites of Manganese atom in the Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-ILS6 (pdb code 4pgl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-ILS6, PDB code: 4pgl:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-ILS6


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-ILS6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:22.4 occ:1.00 O3 A:LTG505 2.1 19.9 0.3 OD2 A:ASP185 2.1 11.9 1.0 OE2 A:GLU152 2.2 14.0 1.0 O2 A:LTG505 2.3 17.9 0.3 ND1 A:HIS211 2.3 13.8 1.0 O2 A:SOL502 2.3 38.5 0.7 O3 A:SOL502 2.4 47.7 0.7 OE1 A:GLU246 2.6 18.0 1.0 C2 A:LTG505 3.0 19.8 0.3 C3 A:SOL502 3.0 49.9 0.7 C2 A:SOL502 3.1 44.8 0.7 CE1 A:HIS211 3.1 13.2 1.0 C3 A:LTG505 3.1 21.3 0.3 CD A:GLU152 3.2 14.7 1.0 CG A:ASP185 3.2 12.8 1.0 CD A:GLU246 3.3 17.9 1.0 CG A:HIS211 3.4 13.2 1.0 OE2 A:GLU246 3.4 19.8 1.0 OE1 A:GLU152 3.5 14.9 1.0 CB A:HIS211 3.7 12.8 1.0 CB A:ASP185 3.7 13.0 1.0 O A:HOH653 4.0 25.7 1.0 NH2 A:ARG217 4.0 19.2 1.0 OD1 A:ASP185 4.3 14.4 1.0 NE2 A:HIS211 4.3 14.2 1.0 NE2 A:HIS188 4.3 12.4 1.0 C4 A:LTG505 4.3 24.1 0.3 CD2 A:HIS188 4.3 13.2 1.0 NE2 A:HIS183 4.3 14.0 1.0 CD2 A:HIS211 4.4 14.1 1.0 C1 A:LTG505 4.5 18.9 0.3 CE1 A:HIS183 4.5 13.5 1.0 C4 A:SOL502 4.5 56.5 0.7 C1 A:SOL502 4.5 40.4 0.7 CG A:GLU152 4.5 14.7 1.0 CG A:GLU246 4.8 16.0 1.0 O1 A:LTG505 4.8 16.6 0.3 O1 A:SOL502 4.8 29.5 0.7

Manganese binding site 2 out of 5 in the Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-ILS6


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-ILS6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn506 b:13.5 occ:1.00 NE2 A:HIS297 2.2 20.4 1.0 NE2 C:HIS297 2.2 17.3 1.0 NE2 C:HIS293 2.2 21.2 1.0 NE2 A:HIS293 2.3 18.4 1.0 CE1 C:HIS297 3.0 18.4 1.0 CE1 A:HIS293 3.1 19.6 1.0 CD2 A:HIS297 3.1 23.3 1.0 CE1 C:HIS293 3.2 22.5 1.0 CE1 A:HIS297 3.2 21.3 1.0 CD2 C:HIS293 3.2 19.4 1.0 CD2 C:HIS297 3.3 16.5 1.0 CD2 A:HIS293 3.5 17.6 1.0 ND1 C:HIS297 4.2 19.8 1.0 CG A:HIS297 4.3 26.1 1.0 ND1 A:HIS293 4.3 20.4 1.0 ND1 A:HIS297 4.3 21.1 1.0 ND1 C:HIS293 4.3 22.2 1.0 CG C:HIS293 4.4 19.5 1.0 CG C:HIS297 4.4 18.8 1.0 CG A:HIS293 4.5 19.9 1.0

Manganese binding site 3 out of 5 in the Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-ILS6


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-ILS6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:28.0 occ:1.00 O2 B:LTG503 2.0 29.6 0.3 O2 B:SOL504 2.1 38.7 0.7 OD2 B:ASP185 2.1 16.1 1.0 OE2 B:GLU152 2.2 17.2 1.0 ND1 B:HIS211 2.3 14.6 1.0 OE1 B:GLU246 2.5 21.2 1.0 O3 B:SOL504 2.5 47.0 0.7 C2 B:LTG503 3.0 32.2 0.3 C2 B:SOL504 3.0 45.8 0.7 O3 B:LTG503 3.1 34.2 0.3 CE1 B:HIS211 3.1 14.4 1.0 CG B:ASP185 3.2 16.8 1.0 CD B:GLU152 3.2 18.4 1.0 CD B:GLU246 3.2 23.2 1.0 CG B:HIS211 3.3 14.8 1.0 C3 B:SOL504 3.3 50.3 0.7 OE2 B:GLU246 3.4 26.6 1.0 C3 B:LTG503 3.5 33.4 0.3 OE1 B:GLU152 3.6 17.9 1.0 CB B:HIS211 3.6 14.8 1.0 CB B:ASP185 3.7 16.8 1.0 NH2 B:ARG217 4.0 22.5 1.0 OD1 B:ASP185 4.3 16.0 1.0 NE2 B:HIS211 4.3 14.6 1.0 C1 B:LTG503 4.3 29.8 0.3 NE2 B:HIS188 4.3 13.7 1.0 CD2 B:HIS188 4.3 13.7 1.0 NE2 B:HIS183 4.4 15.9 1.0 O B:HOH659 4.4 11.5 0.5 CD2 B:HIS211 4.4 14.9 1.0 C1 B:SOL504 4.4 40.5 0.7 O1 B:LTG503 4.4 27.1 0.3 CE1 B:HIS183 4.5 16.3 1.0 CG B:GLU152 4.6 17.3 1.0 CG B:GLU246 4.6 20.7 1.0 C4 B:SOL504 4.6 52.4 0.7 O4 B:SOL504 4.7 51.4 0.7 O1 B:SOL504 4.8 37.3 0.7 C4 B:LTG503 4.9 34.4 0.3 CB B:GLU246 5.0 19.6 1.0 CA B:ASP185 5.0 16.5 1.0

Manganese binding site 4 out of 5 in the Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-ILS6


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 Engineered D-Tagatose 3-Epimerase Pcdte-ILS6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:21.2 occ:1.00 OD2 C:ASP185 2.1 12.2 1.0 OE2 C:GLU152 2.2 13.9 1.0 O2 C:LTG303 2.2 23.8 0.3 O2 C:SOL304 2.3 34.8 0.7 O3 C:SOL304 2.3 35.3 0.7 ND1 C:HIS211 2.3 13.2 1.0 OE1 C:GLU246 2.5 21.6 1.0 O3 C:LTG303 2.5 25.3 0.3 C2 C:LTG303 3.0 24.5 0.3 C2 C:SOL304 3.1 35.2 0.7 CE1 C:HIS211 3.2 12.3 1.0 C3 C:LTG303 3.2 26.2 0.3 CD C:GLU152 3.2 12.8 1.0 CG C:ASP185 3.2 12.7 1.0 C3 C:SOL304 3.2 39.0 0.7 CD C:GLU246 3.3 21.3 1.0 CG C:HIS211 3.4 11.9 1.0 OE2 C:GLU246 3.4 22.3 1.0 OE1 C:GLU152 3.5 13.4 1.0 CB C:ASP185 3.7 12.2 1.0 CB C:HIS211 3.7 11.9 1.0 NH2 C:ARG217 4.0 17.0 1.0 OD1 C:ASP185 4.3 14.1 1.0 O C:HOH437 4.3 5.0 0.5 NE2 C:HIS188 4.3 12.6 1.0 NE2 C:HIS211 4.3 12.0 1.0 CD2 C:HIS188 4.3 12.1 1.0 O4 C:SOL304 4.4 33.3 0.7 NE2 C:HIS183 4.4 12.4 1.0 CD2 C:HIS211 4.5 12.0 1.0 C4 C:SOL304 4.5 40.2 0.7 C1 C:LTG303 4.5 22.2 0.3 C1 C:SOL304 4.5 28.4 0.7 CG C:GLU152 4.5 12.5 1.0 CE1 C:HIS183 4.5 12.3 1.0 C4 C:LTG303 4.6 29.2 0.3 CG C:GLU246 4.7 18.2 1.0 O1 C:LTG303 4.8 20.3 0.3 O1 C:SOL304 4.9 25.3 0.7 O5 C:LTG303 5.0 31.8 0.3

Manganese binding site 5 out of 5 in the Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-ILS6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Engineered D-Tagatose 3-Epimerase Pcdte-ILS6 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn501 b:26.2 occ:1.00 O2 D:LTG503 2.1 28.2 0.3 O2 D:SOL504 2.1 32.9 0.7 OD2 D:ASP185 2.2 14.7 1.0 OE2 D:GLU152 2.2 16.5 1.0 ND1 D:HIS211 2.3 15.7 1.0 O3 D:SOL504 2.3 40.7 0.7 OE1 D:GLU246 2.6 19.9 1.0 O3 D:LTG503 2.9 32.8 0.3 C2 D:SOL504 3.0 39.7 0.7 C2 D:LTG503 3.0 30.8 0.3 CE1 D:HIS211 3.1 15.7 1.0 C3 D:SOL504 3.1 44.2 0.7 CD D:GLU152 3.2 16.9 1.0 CG D:ASP185 3.3 14.3 1.0 CD D:GLU246 3.3 20.6 1.0 C3 D:LTG503 3.4 32.5 0.3 CG D:HIS211 3.4 14.9 1.0 OE2 D:GLU246 3.4 24.6 1.0 OE1 D:GLU152 3.5 17.8 1.0 CB D:ASP185 3.8 14.7 1.0 CB D:HIS211 3.8 14.9 1.0 NH2 D:ARG217 4.0 16.7 1.0 NE2 D:HIS211 4.3 16.1 1.0 OD1 D:ASP185 4.3 14.1 1.0 NE2 D:HIS188 4.3 14.4 1.0 NE2 D:HIS183 4.4 15.9 1.0 O D:HOH659 4.4 25.9 1.0 CD2 D:HIS188 4.4 14.6 1.0 C1 D:SOL504 4.4 34.6 0.7 C1 D:LTG503 4.4 28.7 0.3 CD2 D:HIS211 4.4 16.4 1.0 C4 D:SOL504 4.5 48.6 0.7 CE1 D:HIS183 4.5 15.4 1.0 CG D:GLU152 4.5 15.5 1.0 O4 D:SOL504 4.6 47.7 0.7 O1 D:LTG503 4.7 25.4 0.3 CG D:GLU246 4.7 20.4 1.0 C4 D:LTG503 4.8 34.5 0.3 O1 D:SOL504 4.8 28.2 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.