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

The structure of Crystal Structures of D-Psicose 3-Epimerase with D-Psicose From Clostridium Cellulolyticum H10, PDB code: 3vnj 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 / 2.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.883, 115.499, 91.577, 90.00, 105.16, 90.00
R / Rfree (%)	18.2 / 22

The binding sites of Manganese atom in the Crystal Structures of D-Psicose 3-Epimerase with D-Psicose From Clostridium Cellulolyticum H10 (pdb code 3vnj). 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-Psicose From Clostridium Cellulolyticum H10, PDB code: 3vnj:
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-Psicose 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-Psicose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:28.0 occ:1.00 O2 A:PSJ301 2.1 37.7 1.0 ND1 A:HIS209 2.2 26.1 1.0 OD2 A:ASP183 2.2 26.3 1.0 OE2 A:GLU150 2.2 31.5 1.0 OE1 A:GLU244 2.4 34.4 1.0 O3 A:PSJ301 2.5 36.9 1.0 C2 A:PSJ301 2.9 40.5 1.0 CE1 A:HIS209 3.0 25.8 1.0 CD A:GLU150 3.2 30.8 1.0 CD A:GLU244 3.2 35.3 1.0 C3 A:PSJ301 3.2 41.0 1.0 CG A:HIS209 3.2 26.1 1.0 OE2 A:GLU244 3.3 37.3 1.0 CG A:ASP183 3.3 28.0 1.0 OE1 A:GLU150 3.4 31.3 1.0 CB A:HIS209 3.6 23.9 1.0 CB A:ASP183 3.9 27.3 1.0 O A:HOH437 4.1 28.4 1.0 NE2 A:HIS209 4.2 24.9 1.0 CD2 A:HIS209 4.3 26.0 1.0 CD2 A:HIS186 4.3 27.4 1.0 NE2 A:HIS186 4.3 25.6 1.0 OD1 A:ASP183 4.4 28.1 1.0 NH1 A:ARG215 4.4 27.0 1.0 C1 A:PSJ301 4.4 38.9 1.0 O5 A:PSJ301 4.6 45.4 1.0 CE A:MET181 4.6 28.4 1.0 CG A:GLU150 4.6 30.4 1.0 C4 A:PSJ301 4.6 41.9 1.0 CG A:GLU244 4.6 33.0 1.0 O1 A:PSJ301 4.9 36.6 1.0 C5 A:PSJ301 4.9 45.8 1.0 CB A:GLU244 5.0 28.8 1.0

Manganese binding site 2 out of 4 in the Crystal Structures of D-Psicose 3-Epimerase with D-Psicose 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-Psicose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:27.5 occ:1.00 ND1 B:HIS209 2.1 28.3 1.0 OE2 B:GLU150 2.1 32.0 1.0 OD2 B:ASP183 2.1 25.1 1.0 O2 B:PSJ301 2.2 42.1 1.0 O3 B:PSJ301 2.2 39.6 1.0 OE1 B:GLU244 2.3 32.6 1.0 C2 B:PSJ301 2.9 39.5 1.0 CE1 B:HIS209 3.0 29.6 1.0 C3 B:PSJ301 3.0 42.5 1.0 CD B:GLU150 3.1 32.8 1.0 CD B:GLU244 3.1 35.5 1.0 CG B:HIS209 3.2 28.7 1.0 OE2 B:GLU244 3.3 36.9 1.0 CG B:ASP183 3.3 28.6 1.0 OE1 B:GLU150 3.3 33.1 1.0 CB B:HIS209 3.6 24.9 1.0 CB B:ASP183 3.8 30.9 1.0 O B:HOH414 4.1 31.0 1.0 NE2 B:HIS209 4.1 27.5 1.0 CD2 B:HIS209 4.3 25.7 1.0 OD1 B:ASP183 4.3 32.0 1.0 CD2 B:HIS186 4.3 28.9 1.0 C4 B:PSJ301 4.4 44.7 1.0 C1 B:PSJ301 4.4 38.4 1.0 NE2 B:HIS186 4.4 29.4 1.0 CG B:GLU150 4.5 32.9 1.0 NH1 B:ARG215 4.5 37.5 1.0 CE B:MET181 4.5 32.5 1.0 CG B:GLU244 4.6 35.9 1.0 O5 B:PSJ301 4.6 47.4 1.0 C5 B:PSJ301 4.8 47.1 1.0 O1 B:PSJ301 4.8 35.2 1.0 CB B:GLU244 5.0 30.4 1.0

Manganese binding site 3 out of 4 in the Crystal Structures of D-Psicose 3-Epimerase with D-Psicose 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-Psicose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn302 b:31.4 occ:1.00 OE2 C:GLU150 2.2 34.3 1.0 OE1 C:GLU244 2.2 35.9 1.0 ND1 C:HIS209 2.2 35.8 1.0 OD2 C:ASP183 2.3 32.4 1.0 O2 C:PSJ301 2.3 37.0 1.0 O3 C:PSJ301 2.3 42.0 1.0 CD C:GLU244 3.0 38.3 1.0 C2 C:PSJ301 3.0 39.9 1.0 CE1 C:HIS209 3.1 37.9 1.0 C3 C:PSJ301 3.1 43.0 1.0 OE2 C:GLU244 3.1 42.1 1.0 CD C:GLU150 3.2 34.5 1.0 CG C:HIS209 3.3 36.0 1.0 CG C:ASP183 3.4 30.2 1.0 OE1 C:GLU150 3.5 34.4 1.0 CB C:HIS209 3.6 32.4 1.0 CB C:ASP183 3.9 30.1 1.0 O C:HOH504 4.0 37.8 1.0 NE2 C:HIS209 4.3 37.4 1.0 CD2 C:HIS186 4.3 31.6 1.0 NH1 C:ARG215 4.4 32.1 1.0 CD2 C:HIS209 4.4 37.4 1.0 OD1 C:ASP183 4.4 30.2 1.0 NE2 C:HIS186 4.4 32.5 1.0 CG C:GLU244 4.5 39.7 1.0 C4 C:PSJ301 4.5 45.9 1.0 C1 C:PSJ301 4.5 40.4 1.0 CE C:MET181 4.5 36.9 1.0 CG C:GLU150 4.6 34.1 1.0 O5 C:PSJ301 4.6 51.4 1.0 C5 C:PSJ301 4.8 49.6 1.0 O1 C:PSJ301 4.9 33.0 1.0 CB C:GLU244 4.9 37.7 1.0

Manganese binding site 4 out of 4 in the Crystal Structures of D-Psicose 3-Epimerase with D-Psicose 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-Psicose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn302 b:34.5 occ:1.00 OE2 D:GLU150 2.0 32.7 1.0 OD2 D:ASP183 2.2 34.1 1.0 OE1 D:GLU244 2.3 41.3 1.0 O2 D:PSJ301 2.3 38.9 1.0 ND1 D:HIS209 2.4 34.9 1.0 O3 D:PSJ301 2.4 40.9 1.0 CD D:GLU150 3.0 34.8 1.0 CD D:GLU244 3.1 42.3 1.0 C2 D:PSJ301 3.1 38.5 1.0 OE2 D:GLU244 3.2 46.2 1.0 C3 D:PSJ301 3.2 41.9 1.0 CG D:ASP183 3.3 32.8 1.0 CE1 D:HIS209 3.3 34.9 1.0 CG D:HIS209 3.4 33.0 1.0 OE1 D:GLU150 3.4 34.7 1.0 CB D:HIS209 3.7 32.9 1.0 CB D:ASP183 3.9 30.1 1.0 NE2 D:HIS186 4.2 32.3 1.0 O D:HOH419 4.3 33.9 1.0 CD2 D:HIS186 4.3 31.6 1.0 OD1 D:ASP183 4.4 30.4 1.0 CG D:GLU150 4.4 33.4 1.0 NH1 D:ARG215 4.4 33.4 1.0 NE2 D:HIS209 4.5 33.1 1.0 CG D:GLU244 4.5 42.4 1.0 CD2 D:HIS209 4.5 35.2 1.0 C1 D:PSJ301 4.6 38.9 1.0 CE D:MET181 4.6 31.5 1.0 C4 D:PSJ301 4.6 42.3 1.0 O5 D:PSJ301 4.8 44.5 1.0 O1 D:PSJ301 4.9 35.0 1.0 C5 D:PSJ301 4.9 44.0 1.0 CB D:GLU244 4.9 37.1 1.0 O D:HOH566 5.0 42.5 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