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

The structure of Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose From Clostridium Cellulolyticum H10, PDB code: 3vnm 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 / 2.12
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.924, 115.225, 91.614, 90.00, 105.73, 90.00
R / Rfree (%)	19 / 23.2

The binding sites of Manganese atom in the Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose From Clostridium Cellulolyticum H10 (pdb code 3vnm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose From Clostridium Cellulolyticum H10, PDB code: 3vnm:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose 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-Sorbose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:33.2 occ:1.00 O2 A:SDD301 2.0 43.5 1.0 ND1 A:HIS209 2.1 29.6 1.0 OD2 A:ASP183 2.2 28.7 1.0 OE2 A:GLU150 2.2 39.9 1.0 OE1 A:GLU244 2.3 36.2 1.0 O3 A:SDD301 2.5 46.2 1.0 CE1 A:HIS209 2.9 31.1 1.0 C2 A:SDD301 3.0 46.9 1.0 CD A:GLU244 3.1 37.9 1.0 OE2 A:GLU244 3.1 37.5 1.0 CD A:GLU150 3.2 39.8 1.0 CG A:HIS209 3.2 30.3 1.0 CG A:ASP183 3.3 32.3 1.0 C3 A:SDD301 3.4 44.3 1.0 OE1 A:GLU150 3.4 39.9 1.0 CB A:HIS209 3.6 29.1 1.0 CB A:ASP183 3.9 33.2 1.0 O A:HOH425 4.1 33.7 1.0 NE2 A:HIS209 4.1 25.9 1.0 O4 A:SDD301 4.1 38.5 1.0 CD2 A:HIS209 4.2 27.1 1.0 NH1 A:ARG215 4.3 34.4 1.0 OD1 A:ASP183 4.3 31.3 1.0 C4 A:SDD301 4.4 45.4 1.0 C1 A:SDD301 4.4 45.7 1.0 CD2 A:HIS186 4.4 36.6 1.0 NE2 A:HIS186 4.5 38.0 1.0 CE A:MET181 4.5 37.0 1.0 CG A:GLU244 4.5 38.7 1.0 CG A:GLU150 4.6 38.2 1.0 O1 A:SDD301 4.9 46.1 1.0 CB A:GLU244 4.9 33.7 1.0

Manganese binding site 2 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose 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-Sorbose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:71.4 occ:1.00 O D:HOH509 3.2 45.6 1.0 O D:HOH516 3.3 39.4 1.0 O A:HOH415 3.6 39.7 1.0 NH2 A:ARG220 3.6 40.5 1.0 NE A:ARG220 3.7 41.0 1.0 NZ A:LYS216 3.8 35.3 1.0 CZ A:ARG220 4.2 40.1 1.0 O A:HOH583 4.6 45.4 1.0 MN B:MN304 4.6 50.0 1.0 CE A:LYS216 4.7 38.9 1.0 CD A:LYS216 4.8 36.4 1.0 ND2 A:ASN265 4.9 59.9 1.0 OD2 D:ASP192 4.9 43.8 1.0 CD A:ARG220 4.9 43.1 1.0 O A:HOH417 5.0 37.5 1.0

Manganese binding site 3 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose 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-Sorbose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:35.0 occ:1.00 ND1 B:HIS209 2.0 38.4 1.0 OE2 B:GLU150 2.1 39.7 1.0 OD2 B:ASP183 2.1 32.6 1.0 O2 B:SDD301 2.2 45.8 1.0 O3 B:SDD301 2.4 46.4 1.0 OE1 B:GLU244 2.4 37.3 1.0 CE1 B:HIS209 2.8 40.8 1.0 CD B:GLU150 3.0 41.7 1.0 C2 B:SDD301 3.0 46.5 1.0 CG B:HIS209 3.2 39.0 1.0 CD B:GLU244 3.2 44.7 1.0 C3 B:SDD301 3.2 46.6 1.0 OE1 B:GLU150 3.3 42.8 1.0 OE2 B:GLU244 3.3 44.3 1.0 CG B:ASP183 3.3 39.0 1.0 CB B:HIS209 3.6 36.9 1.0 CB B:ASP183 4.0 37.7 1.0 NE2 B:HIS209 4.0 39.8 1.0 O B:HOH421 4.0 36.5 1.0 CD2 B:HIS209 4.2 37.8 1.0 O4 B:SDD301 4.3 47.3 1.0 CD2 B:HIS186 4.3 33.0 1.0 OD1 B:ASP183 4.4 36.7 1.0 NH1 B:ARG215 4.4 39.8 1.0 C4 B:SDD301 4.4 46.9 1.0 NE2 B:HIS186 4.4 34.8 1.0 CG B:GLU150 4.4 41.4 1.0 C1 B:SDD301 4.5 46.1 1.0 CG B:GLU244 4.6 44.7 1.0 CE B:MET181 4.7 41.9 1.0 O1 B:SDD301 4.9 43.1 1.0 CB B:GLU244 5.0 41.2 1.0

Manganese binding site 4 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose 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-Sorbose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn303 b:50.2 occ:1.00 O D:HOH515 2.2 47.8 1.0 O D:HOH514 2.2 43.3 1.0 OD2 B:ASP192 2.2 46.3 1.0 O B:HOH549 2.4 45.6 1.0 O C:HOH509 2.4 39.0 1.0 ND1 D:HIS290 2.5 60.2 1.0 CE1 D:HIS290 3.2 60.2 1.0 CG B:ASP192 3.3 43.0 1.0 OE2 D:GLU230 3.6 51.3 1.0 CG D:HIS290 3.7 61.6 1.0 O C:ARG220 3.7 39.3 1.0 CB B:ASP192 3.8 39.4 1.0 CB D:HIS290 4.1 63.3 1.0 NH1 C:ARG220 4.3 50.5 1.0 OD1 B:ASP192 4.3 37.9 1.0 CA D:HIS290 4.3 65.8 1.0 NZ C:LYS216 4.4 38.5 1.0 NE2 D:HIS290 4.4 59.2 1.0 O D:HIS290 4.5 66.5 1.0 MN C:MN303 4.6 72.1 1.0 CD D:GLU230 4.6 50.4 1.0 CG D:GLU230 4.7 45.3 1.0 CD2 D:HIS290 4.7 61.8 1.0 CB C:ARG220 4.8 43.4 1.0 C C:ARG220 4.9 40.9 1.0 C D:HIS290 4.9 65.8 1.0

Manganese binding site 5 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose From Clostridium Cellulolyticum H10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn304 b:50.0 occ:1.00 O D:HOH516 2.3 39.4 1.0 O B:HOH546 2.3 34.7 1.0 OD2 D:ASP192 2.4 43.8 1.0 O A:HOH588 2.4 37.4 1.0 ND1 B:HIS290 2.4 59.3 1.0 O D:HOH509 2.4 45.6 1.0 CE1 B:HIS290 3.0 59.8 1.0 CG D:ASP192 3.3 41.5 1.0 OE2 B:GLU230 3.6 42.6 1.0 CG B:HIS290 3.7 60.6 1.0 CB D:ASP192 3.7 37.1 1.0 O A:ARG220 3.9 39.1 1.0 CB B:HIS290 4.2 60.5 1.0 O A:HOH417 4.2 37.5 1.0 CA B:HIS290 4.3 62.0 1.0 NE2 B:HIS290 4.3 60.5 1.0 OD1 D:ASP192 4.3 38.2 1.0 NZ A:LYS216 4.4 35.3 1.0 CD B:GLU230 4.5 43.1 1.0 CG B:GLU230 4.6 39.8 1.0 CD2 B:HIS290 4.6 58.8 1.0 MN A:MN303 4.6 71.4 1.0 NH2 A:ARG220 4.8 40.5 1.0 O B:HIS290 4.9 62.0 1.0 C A:ARG220 5.0 37.5 1.0 CA D:ASP192 5.0 37.3 1.0 CB A:ARG220 5.0 37.8 1.0

Manganese binding site 6 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose From Clostridium Cellulolyticum H10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn302 b:38.9 occ:1.00 OE1 C:GLU244 2.1 38.4 1.0 OD2 C:ASP183 2.2 37.4 1.0 ND1 C:HIS209 2.2 43.2 1.0 O2 C:SDD301 2.2 48.0 1.0 OE2 C:GLU150 2.3 44.2 1.0 O3 C:SDD301 2.6 51.3 1.0 CD C:GLU244 3.0 44.4 1.0 CE1 C:HIS209 3.1 45.5 1.0 C2 C:SDD301 3.2 52.4 1.0 CD C:GLU150 3.3 44.1 1.0 CG C:HIS209 3.3 42.8 1.0 OE2 C:GLU244 3.3 47.1 1.0 CG C:ASP183 3.3 38.8 1.0 C3 C:SDD301 3.4 53.0 1.0 OE1 C:GLU150 3.6 42.9 1.0 CB C:HIS209 3.6 40.2 1.0 CB C:ASP183 3.9 38.4 1.0 O C:HOH429 4.1 42.0 1.0 O4 C:SDD301 4.2 51.6 1.0 CE C:MET181 4.2 44.0 1.0 NE2 C:HIS209 4.3 44.3 1.0 CD2 C:HIS186 4.3 38.7 1.0 OD1 C:ASP183 4.3 39.1 1.0 CD2 C:HIS209 4.4 43.9 1.0 NE2 C:HIS186 4.4 41.3 1.0 C4 C:SDD301 4.4 53.8 1.0 CG C:GLU244 4.4 45.0 1.0 NH1 C:ARG215 4.4 46.4 1.0 C1 C:SDD301 4.5 51.8 1.0 CG C:GLU150 4.6 42.5 1.0 CB C:GLU244 4.9 41.5 1.0

Manganese binding site 7 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose From Clostridium Cellulolyticum H10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn303 b:72.1 occ:1.00 O B:HOH549 3.1 45.6 1.0 O C:HOH430 3.3 41.5 1.0 O D:HOH514 3.4 43.3 1.0 NZ C:LYS216 3.5 38.5 1.0 NH1 C:ARG220 3.6 50.5 1.0 CD C:ARG220 4.2 48.2 1.0 O C:HOH438 4.3 46.3 1.0 CD C:LYS216 4.5 37.6 1.0 CZ C:ARG220 4.6 52.9 1.0 MN B:MN303 4.6 50.2 1.0 CE C:LYS216 4.6 39.8 1.0 OD2 B:ASP192 4.8 46.3 1.0 NE C:ARG220 4.8 51.8 1.0

Manganese binding site 8 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose From Clostridium Cellulolyticum H10


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structures of D-Psicose 3-Epimerase with D-Sorbose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn302 b:36.9 occ:1.00 OD2 D:ASP183 2.1 34.9 1.0 O2 D:SDD301 2.2 46.2 1.0 OE2 D:GLU150 2.2 34.0 1.0 ND1 D:HIS209 2.2 37.9 1.0 O3 D:SDD301 2.2 46.9 1.0 OE1 D:GLU244 2.3 41.6 1.0 CD D:GLU244 3.0 43.4 1.0 C2 D:SDD301 3.0 47.6 1.0 OE2 D:GLU244 3.0 45.2 1.0 CE1 D:HIS209 3.1 40.0 1.0 C3 D:SDD301 3.2 50.0 1.0 CD D:GLU150 3.2 33.6 1.0 CG D:ASP183 3.3 32.3 1.0 CG D:HIS209 3.3 37.7 1.0 OE1 D:GLU150 3.5 35.6 1.0 CB D:HIS209 3.7 36.8 1.0 CB D:ASP183 4.0 34.6 1.0 O4 D:SDD301 4.0 46.1 1.0 O D:HOH493 4.1 39.2 1.0 C4 D:SDD301 4.2 49.2 1.0 OD1 D:ASP183 4.3 30.6 1.0 NE2 D:HIS186 4.3 36.7 1.0 NE2 D:HIS209 4.3 39.6 1.0 NH1 D:ARG215 4.4 38.7 1.0 CD2 D:HIS209 4.4 38.9 1.0 CD2 D:HIS186 4.4 36.5 1.0 CG D:GLU244 4.4 42.2 1.0 CE D:MET181 4.4 35.9 1.0 C1 D:SDD301 4.5 46.7 1.0 CG D:GLU150 4.6 32.9 1.0 CB D:GLU244 4.9 38.8 1.0 C5 D:SDD301 4.9 51.3 1.0 O1 D:SDD301 5.0 42.6 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