Manganese in PDB 3vnl: Crystal Structures of D-Psicose 3-Epimerase with D-Tagatose From Clostridium Cellulolyticum H10

The structure of Crystal Structures of D-Psicose 3-Epimerase with D-Tagatose From Clostridium Cellulolyticum H10, PDB code: 3vnl was solved by H.C.Chan, Y.Zhu, Y.Hu, T.P.Ko, C.H.Huang, F.Ren, C.C.Chen, R.T.Guo, Y.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.073, 115.371, 91.530, 90.00, 104.77, 90.00
R / Rfree (%)	18.7 / 22.9

The binding sites of Manganese atom in the Crystal Structures of D-Psicose 3-Epimerase with D-Tagatose From Clostridium Cellulolyticum H10 (pdb code 3vnl). 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 Structures of D-Psicose 3-Epimerase with D-Tagatose From Clostridium Cellulolyticum H10, PDB code: 3vnl:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structures of D-Psicose 3-Epimerase with D-Tagatose From Clostridium Cellulolyticum H10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structures of D-Psicose 3-Epimerase with D-Tagatose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn7102 b:29.0 occ:1.00 O2 A:TAG7101 1.9 47.3 1.0 ND1 A:HIS209 2.1 24.3 1.0 OD2 A:ASP183 2.2 27.2 1.0 OE2 A:GLU150 2.2 35.2 1.0 OE1 A:GLU244 2.3 30.8 1.0 C2 A:TAG7101 2.7 47.3 1.0 C3 A:TAG7101 2.8 50.0 1.0 CE1 A:HIS209 2.9 25.6 1.0 CD A:GLU244 3.1 33.4 1.0 OE2 A:GLU244 3.1 34.9 1.0 O3 A:TAG7101 3.2 53.2 1.0 CD A:GLU150 3.2 32.8 1.0 CG A:HIS209 3.2 24.9 1.0 CG A:ASP183 3.3 28.2 1.0 OE1 A:GLU150 3.4 32.4 1.0 CB A:HIS209 3.6 26.1 1.0 CB A:ASP183 3.9 32.6 1.0 NE2 A:HIS209 4.1 22.9 1.0 O A:HOH7218 4.1 27.9 1.0 C1 A:TAG7101 4.2 47.8 1.0 C4 A:TAG7101 4.2 48.2 1.0 CD2 A:HIS209 4.2 19.8 1.0 CE A:MET181 4.3 29.9 1.0 CD2 A:HIS186 4.3 30.0 1.0 OD1 A:ASP183 4.3 28.4 1.0 NH1 A:ARG215 4.3 31.6 1.0 NE2 A:HIS186 4.4 27.0 1.0 O4 A:TAG7101 4.4 48.1 1.0 CG A:GLU244 4.6 34.2 1.0 CG A:GLU150 4.6 32.3 1.0 O1 A:TAG7101 4.9 40.5 1.0 CB A:GLU244 5.0 31.7 1.0

Manganese binding site 2 out of 4 in the Crystal Structures of D-Psicose 3-Epimerase with D-Tagatose From Clostridium Cellulolyticum H10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structures of D-Psicose 3-Epimerase with D-Tagatose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:33.9 occ:1.00 OE2 B:GLU150 2.0 36.0 1.0 OD2 B:ASP183 2.1 28.0 1.0 ND1 B:HIS209 2.1 33.1 1.0 OE1 B:GLU244 2.2 37.4 1.0 O2 B:TAG301 2.2 48.0 1.0 C2 B:TAG301 2.9 49.7 1.0 C3 B:TAG301 2.9 54.3 1.0 O3 B:TAG301 2.9 55.4 1.0 CE1 B:HIS209 3.0 34.3 1.0 CD B:GLU150 3.0 36.2 1.0 CD B:GLU244 3.1 37.3 1.0 CG B:HIS209 3.2 35.1 1.0 CG B:ASP183 3.2 30.3 1.0 OE1 B:GLU150 3.3 34.2 1.0 OE2 B:GLU244 3.3 38.4 1.0 CB B:HIS209 3.6 33.0 1.0 CB B:ASP183 3.9 30.9 1.0 O B:HOH414 4.0 31.2 1.0 NE2 B:HIS209 4.1 37.4 1.0 CD2 B:HIS209 4.2 35.0 1.0 OD1 B:ASP183 4.3 31.0 1.0 NH1 B:ARG215 4.4 33.3 1.0 C4 B:TAG301 4.4 55.8 1.0 CG B:GLU150 4.4 32.6 1.0 CE B:MET181 4.4 34.5 1.0 C1 B:TAG301 4.4 48.9 1.0 CD2 B:HIS186 4.4 30.9 1.0 NE2 B:HIS186 4.5 30.8 1.0 CG B:GLU244 4.5 40.2 1.0 O4 B:TAG301 4.8 56.8 1.0 O1 B:TAG301 5.0 38.1 1.0

Manganese binding site 3 out of 4 in the Crystal Structures of D-Psicose 3-Epimerase with D-Tagatose From Clostridium Cellulolyticum H10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structures of D-Psicose 3-Epimerase with D-Tagatose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn302 b:36.0 occ:1.00 O2 C:TAG301 2.1 55.3 1.0 OE2 C:GLU150 2.1 38.9 1.0 OE1 C:GLU244 2.2 41.8 1.0 OD2 C:ASP183 2.2 34.9 1.0 ND1 C:HIS209 2.2 42.6 1.0 O3 C:TAG301 2.6 61.2 1.0 C2 C:TAG301 2.7 58.7 1.0 C3 C:TAG301 2.9 62.6 1.0 CD C:GLU244 3.0 42.8 1.0 CE1 C:HIS209 3.1 42.0 1.0 CD C:GLU150 3.1 39.2 1.0 OE2 C:GLU244 3.1 45.9 1.0 CG C:HIS209 3.3 41.0 1.0 CG C:ASP183 3.3 34.6 1.0 OE1 C:GLU150 3.5 41.3 1.0 CB C:HIS209 3.7 36.1 1.0 CB C:ASP183 3.9 35.4 1.0 O C:HOH469 4.0 38.5 1.0 C1 C:TAG301 4.1 57.7 1.0 CD2 C:HIS186 4.2 34.9 1.0 NE2 C:HIS209 4.3 43.1 1.0 OD1 C:ASP183 4.3 37.1 1.0 NE2 C:HIS186 4.4 34.8 1.0 CD2 C:HIS209 4.4 42.1 1.0 C4 C:TAG301 4.4 64.0 1.0 NH1 C:ARG215 4.4 37.4 1.0 CE C:MET181 4.4 35.6 1.0 CG C:GLU150 4.5 38.2 1.0 CG C:GLU244 4.5 42.7 1.0 O1 C:TAG301 4.9 48.6 1.0 CB C:GLU244 5.0 36.3 1.0

Manganese binding site 4 out of 4 in the Crystal Structures of D-Psicose 3-Epimerase with D-Tagatose From Clostridium Cellulolyticum H10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structures of D-Psicose 3-Epimerase with D-Tagatose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn302 b:36.9 occ:1.00 O2 D:TAG301 1.9 61.1 1.0 OD2 D:ASP183 2.1 35.2 1.0 OE2 D:GLU150 2.1 35.1 1.0 ND1 D:HIS209 2.1 40.3 1.0 OE1 D:GLU244 2.3 41.2 1.0 C2 D:TAG301 2.9 62.6 1.0 CD D:GLU244 3.0 42.8 1.0 CE1 D:HIS209 3.0 43.7 1.0 OE2 D:GLU244 3.1 46.4 1.0 CD D:GLU150 3.1 38.7 1.0 CG D:HIS209 3.2 41.1 1.0 CG D:ASP183 3.3 35.1 1.0 C3 D:TAG301 3.4 64.5 1.0 OE1 D:GLU150 3.5 39.4 1.0 CB D:HIS209 3.6 38.3 1.0 CB D:ASP183 3.9 31.2 1.0 O D:HOH427 3.9 36.4 1.0 NE2 D:HIS209 4.2 41.1 1.0 C1 D:TAG301 4.3 61.2 1.0 CD2 D:HIS209 4.3 42.0 1.0 NE2 D:HIS186 4.3 34.5 1.0 OD1 D:ASP183 4.3 32.6 1.0 O4 D:TAG301 4.3 62.4 1.0 O3 D:TAG301 4.4 67.6 1.0 CE D:MET181 4.4 34.4 1.0 CD2 D:HIS186 4.4 35.6 1.0 NH1 D:ARG215 4.4 37.0 1.0 CG D:GLU244 4.5 43.8 1.0 CG D:GLU150 4.5 34.3 1.0 C4 D:TAG301 4.5 63.6 1.0 O1 D:TAG301 4.8 55.3 1.0 CB D:GLU244 4.9 40.0 1.0

H.C.Chan, Y.Zhu, Y.Hu, T.P.Ko, C.H.Huang, F.Ren, C.C.Chen, Y.Ma, R.T.Guo, Y.Sun. Crystal Structures of D-Psicose 3-Epimerase From Clostridium Cellulolyticum H10 and Its Complex with Ketohexose Sugars. Protein Cell V. 3 123 2012.
ISSN: ISSN 1674-800X
PubMed: 22426981
DOI: 10.1007/S13238-012-2026-5