Manganese in PDB 4q7i: Crystal Structure of Engineered Thermostable D-Tagatose 3-Epimerase Pcdte-VAR8

The structure of Crystal Structure of Engineered Thermostable D-Tagatose 3-Epimerase Pcdte-VAR8, PDB code: 4q7i 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)	53.73 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.470, 47.500, 124.730, 90.00, 103.68, 90.00
R / Rfree (%)	17.6 / 20.8

The binding sites of Manganese atom in the Crystal Structure of Engineered Thermostable D-Tagatose 3-Epimerase Pcdte-VAR8 (pdb code 4q7i). 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 Thermostable D-Tagatose 3-Epimerase Pcdte-VAR8, PDB code: 4q7i:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the Crystal Structure of Engineered Thermostable D-Tagatose 3-Epimerase Pcdte-VAR8


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 Thermostable D-Tagatose 3-Epimerase Pcdte-VAR8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:15.8 occ:1.00 OD2 A:ASP185 2.0 14.4 1.0 OE2 A:GLU152 2.1 15.3 1.0 ND1 A:HIS211 2.2 13.3 1.0 OE1 A:GLU246 2.2 21.7 1.0 O2 A:GOL602 2.3 19.5 1.0 O1 A:GOL602 2.3 33.9 1.0 CD A:GLU246 3.0 21.7 1.0 CE1 A:HIS211 3.1 13.8 1.0 CG A:ASP185 3.1 13.7 1.0 CD A:GLU152 3.2 14.5 1.0 OE2 A:GLU246 3.2 26.4 1.0 C2 A:GOL602 3.2 26.9 1.0 CG A:HIS211 3.3 14.2 1.0 C1 A:GOL602 3.4 33.7 1.0 OE1 A:GLU152 3.5 15.6 1.0 CB A:HIS211 3.6 14.4 1.0 CB A:ASP185 3.8 13.9 1.0 NH1 A:ARG217 4.1 18.1 1.0 O A:HOH732 4.1 23.4 1.0 OD1 A:ASP185 4.1 14.6 1.0 NE2 A:HIS211 4.3 13.9 1.0 CD2 A:HIS211 4.4 14.2 1.0 CD2 A:HIS188 4.4 13.2 1.0 CG A:GLU246 4.5 20.8 1.0 NE2 A:GLN183 4.5 15.0 1.0 NE2 A:HIS188 4.5 13.5 1.0 CG A:GLU152 4.5 14.6 1.0 C3 A:GOL602 4.6 27.0 1.0 O A:HOH921 4.7 42.6 1.0 O3 A:GOL602 4.7 21.1 1.0 CB A:GLU246 4.9 19.5 1.0

Manganese binding site 2 out of 5 in the Crystal Structure of Engineered Thermostable D-Tagatose 3-Epimerase Pcdte-VAR8


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 Thermostable D-Tagatose 3-Epimerase Pcdte-VAR8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn604 b:33.7 occ:0.50 MN A:MN604 0.0 33.7 0.5 NE2 A:HIS116 1.5 45.0 1.0 MN A:MN604 1.5 39.2 0.5 N3 A:IMD605 2.1 29.7 1.0 CE1 A:HIS116 2.5 38.4 1.0 CD2 A:HIS116 2.5 41.5 1.0 C2 A:IMD605 2.7 40.2 1.0 O A:HOH751 2.8 25.4 0.5 O B:HOH905 3.0 49.8 1.0 NE2 B:HIS116 3.2 54.8 1.0 C4 A:IMD605 3.4 44.2 1.0 ND1 A:HIS116 3.6 37.9 1.0 CG A:HIS116 3.6 38.5 1.0 N1 A:IMD605 4.0 37.4 1.0 O A:HOH751 4.1 25.4 0.5 CE1 B:HIS116 4.1 52.9 1.0 CD2 B:HIS116 4.2 55.7 1.0 C5 A:IMD605 4.3 37.2 1.0 O A:TYR157 4.5 21.3 1.0

Manganese binding site 3 out of 5 in the Crystal Structure of Engineered Thermostable D-Tagatose 3-Epimerase Pcdte-VAR8


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 Thermostable D-Tagatose 3-Epimerase Pcdte-VAR8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn604 b:39.2 occ:0.50 MN A:MN604 0.0 39.2 0.5 MN A:MN604 1.5 33.7 0.5 NE2 B:HIS116 1.8 54.8 1.0 O A:HOH751 2.4 25.4 0.5 O B:HOH905 2.4 49.8 1.0 N3 A:IMD605 2.5 29.7 1.0 CE1 B:HIS116 2.6 52.9 1.0 CD2 B:HIS116 2.9 55.7 1.0 NE2 A:HIS116 3.0 45.0 1.0 C4 A:IMD605 3.3 44.2 1.0 C2 A:IMD605 3.6 40.2 1.0 ND1 B:HIS116 3.8 56.1 1.0 CE1 A:HIS116 3.8 38.4 1.0 CG B:HIS116 3.9 56.1 1.0 O A:HOH751 4.0 25.4 0.5 CD2 A:HIS116 4.0 41.5 1.0 O B:TYR157 4.2 29.0 1.0 C5 A:IMD605 4.6 37.2 1.0 N1 A:IMD605 4.7 37.4 1.0 ND1 A:HIS116 5.0 37.9 1.0

Manganese binding site 4 out of 5 in the Crystal Structure of Engineered Thermostable D-Tagatose 3-Epimerase Pcdte-VAR8


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 Thermostable D-Tagatose 3-Epimerase Pcdte-VAR8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn606 b:19.8 occ:0.50 NE2 A:HIS98 2.3 30.2 1.0 CD2 A:HIS98 3.2 29.2 1.0 CE1 A:HIS98 3.4 29.1 1.0 CG A:HIS98 4.4 27.8 1.0 ND1 A:HIS98 4.5 27.6 1.0

Manganese binding site 5 out of 5 in the Crystal Structure of Engineered Thermostable D-Tagatose 3-Epimerase Pcdte-VAR8


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 Thermostable D-Tagatose 3-Epimerase Pcdte-VAR8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:17.2 occ:1.00 O2 B:GOL602 2.0 22.9 1.0 OD2 B:ASP185 2.0 20.2 1.0 OE2 B:GLU152 2.2 20.5 1.0 ND1 B:HIS211 2.2 19.6 1.0 OE1 B:GLU246 2.3 19.9 1.0 O1 B:GOL602 2.5 34.2 1.0 CD B:GLU246 3.0 19.8 1.0 CE1 B:HIS211 3.1 19.4 1.0 CD B:GLU152 3.1 20.8 1.0 OE2 B:GLU246 3.2 20.4 1.0 CG B:ASP185 3.2 20.7 1.0 C2 B:GOL602 3.2 32.3 1.0 CG B:HIS211 3.3 19.9 1.0 C1 B:GOL602 3.5 35.2 1.0 OE1 B:GLU152 3.5 20.5 1.0 CB B:HIS211 3.6 20.3 1.0 CB B:ASP185 3.9 21.3 1.0 NH1 B:ARG217 4.0 20.2 1.0 O B:HOH724 4.1 19.7 1.0 OD1 B:ASP185 4.2 20.8 1.0 NE2 B:HIS211 4.3 19.4 1.0 CD2 B:HIS211 4.4 19.8 1.0 CD2 B:HIS188 4.4 21.5 1.0 C3 B:GOL602 4.4 30.9 1.0 NE2 B:HIS188 4.4 21.3 1.0 CG B:GLU246 4.4 19.7 1.0 NE2 B:GLN183 4.5 20.4 1.0 CG B:GLU152 4.5 21.6 1.0 O3 B:GOL602 4.8 24.0 1.0 CB B:GLU246 4.9 19.8 1.0

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.