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

The structure of Crystal Structures of D-Psicose 3-Epimerase with D-Fructose From Clostridium Cellulolyticum H10, PDB code: 3vnk 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 / 2.02
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.040, 115.209, 91.375, 90.00, 105.08, 90.00
R / Rfree (%)	18.6 / 22.7

The binding sites of Manganese atom in the Crystal Structures of D-Psicose 3-Epimerase with D-Fructose From Clostridium Cellulolyticum H10 (pdb code 3vnk). 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-Fructose From Clostridium Cellulolyticum H10, PDB code: 3vnk:
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-Fructose 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-Fructose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:25.2 occ:1.00 OE2 A:GLU150 2.2 29.5 1.0 ND1 A:HIS209 2.2 18.6 1.0 O2 A:FUD301 2.2 42.0 1.0 OD2 A:ASP183 2.2 21.9 1.0 OE1 A:GLU244 2.3 26.5 1.0 C3 A:FUD301 2.7 44.4 1.0 C2 A:FUD301 2.8 43.0 1.0 O3 A:FUD301 3.0 46.3 1.0 CE1 A:HIS209 3.1 19.4 1.0 CD A:GLU150 3.1 30.1 1.0 CD A:GLU244 3.2 30.0 1.0 CG A:HIS209 3.2 21.0 1.0 CG A:ASP183 3.3 23.7 1.0 OE2 A:GLU244 3.3 30.1 1.0 OE1 A:GLU150 3.4 31.3 1.0 CB A:HIS209 3.5 21.2 1.0 CB A:ASP183 3.9 24.5 1.0 C4 A:FUD301 4.1 45.0 1.0 O A:HOH465 4.1 30.5 1.0 NE2 A:HIS209 4.2 19.1 1.0 C1 A:FUD301 4.3 41.2 1.0 CD2 A:HIS209 4.3 19.2 1.0 OD1 A:ASP183 4.3 27.1 1.0 NH1 A:ARG215 4.3 25.2 1.0 CD2 A:HIS186 4.4 23.3 1.0 NE2 A:HIS186 4.4 21.7 1.0 CG A:GLU150 4.5 29.2 1.0 CG A:GLU244 4.6 28.6 1.0 CE A:MET181 4.6 21.9 1.0 O4 A:FUD301 4.7 41.7 1.0 O1 A:FUD301 4.8 37.2 1.0 CB A:GLU244 4.9 24.9 1.0

Manganese binding site 2 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Fructose 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-Fructose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:62.6 occ:1.00 O D:HOH522 3.2 42.8 1.0 O D:HOH612 3.5 51.7 1.0 O A:HOH455 3.7 37.5 1.0 NH2 A:ARG220 3.8 33.8 1.0 NE A:ARG220 3.9 35.5 1.0 NZ A:LYS216 4.0 29.6 1.0 CZ A:ARG220 4.3 36.2 1.0 ND2 A:ASN265 4.4 48.7 1.0 O A:HOH516 4.5 36.9 1.0 MN D:MN303 4.7 48.7 1.0 CD A:LYS216 4.7 25.3 1.0 CE A:LYS216 4.8 28.7 1.0 O A:HOH566 4.8 55.0 1.0 OE1 A:GLU275 4.9 53.0 1.0 OD1 D:ASP192 5.0 37.7 1.0 CD A:ARG220 5.0 34.1 1.0

Manganese binding site 3 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Fructose 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-Fructose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1302 b:24.8 occ:1.00 OD2 B:ASP183 2.1 21.4 1.0 ND1 B:HIS209 2.2 22.6 1.0 OE2 B:GLU150 2.2 27.4 1.0 OE1 B:GLU244 2.3 29.5 1.0 O2 B:FUD1301 2.3 32.8 1.0 O3 B:FUD1301 2.3 35.5 1.0 C2 B:FUD1301 3.0 33.3 1.0 C3 B:FUD1301 3.0 36.7 1.0 CE1 B:HIS209 3.0 25.4 1.0 CD B:GLU244 3.1 31.5 1.0 CD B:GLU150 3.1 27.4 1.0 CG B:ASP183 3.2 24.2 1.0 CG B:HIS209 3.2 25.0 1.0 OE2 B:GLU244 3.4 34.6 1.0 OE1 B:GLU150 3.4 29.2 1.0 CB B:HIS209 3.6 21.8 1.0 CB B:ASP183 3.8 27.7 1.0 O B:HOH1587 4.2 28.0 1.0 NE2 B:HIS209 4.2 23.8 1.0 OD1 B:ASP183 4.2 28.1 1.0 CD2 B:HIS186 4.3 26.9 1.0 CD2 B:HIS209 4.3 23.6 1.0 NE2 B:HIS186 4.3 27.6 1.0 CG B:GLU244 4.4 32.4 1.0 NH1 B:ARG215 4.4 27.8 1.0 C4 B:FUD1301 4.5 39.9 1.0 C1 B:FUD1301 4.5 30.7 1.0 CG B:GLU150 4.5 27.6 1.0 CE B:MET181 4.7 25.6 1.0 O4 B:FUD1301 4.9 41.4 1.0 CB B:GLU244 4.9 29.2 1.0 O1 B:FUD1301 4.9 27.5 1.0 O5 B:FUD1301 5.0 42.0 1.0

Manganese binding site 4 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Fructose 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-Fructose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1303 b:48.2 occ:1.00 O D:HOH500 2.2 40.3 1.0 O C:HOH450 2.3 27.8 1.0 O B:HOH1583 2.4 52.2 1.0 OD2 B:ASP192 2.5 38.2 1.0 CG B:ASP192 3.4 33.7 1.0 O C:HOH545 3.7 50.4 1.0 O C:ARG220 3.8 30.2 1.0 CB B:ASP192 3.8 28.1 1.0 OE2 D:GLU230 3.9 42.6 1.0 O C:HOH419 4.2 26.7 1.0 OD1 B:ASP192 4.3 32.4 1.0 NH1 C:ARG220 4.4 46.9 1.0 NZ C:LYS216 4.5 29.8 1.0 O C:HOH544 4.5 37.1 1.0 MN C:MN303 4.6 61.5 1.0 CD D:GLU230 4.8 40.9 1.0 CG D:GLU230 4.8 37.9 1.0 C C:ARG220 4.8 30.7 1.0 CB C:ARG220 5.0 32.8 1.0 CA B:ASP192 5.0 27.9 1.0

Manganese binding site 5 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Fructose 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-Fructose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn302 b:29.4 occ:1.00 OE2 C:GLU150 2.1 34.9 1.0 O2 C:FUD301 2.2 35.5 1.0 ND1 C:HIS209 2.2 36.5 1.0 OE1 C:GLU244 2.2 37.4 1.0 OD2 C:ASP183 2.2 27.9 1.0 O3 C:FUD301 2.5 41.9 1.0 C2 C:FUD301 2.9 39.9 1.0 C3 C:FUD301 3.0 42.7 1.0 CE1 C:HIS209 3.0 36.3 1.0 CD C:GLU244 3.1 39.1 1.0 CD C:GLU150 3.2 32.1 1.0 OE2 C:GLU244 3.3 41.1 1.0 CG C:HIS209 3.3 34.7 1.0 CG C:ASP183 3.3 29.0 1.0 OE1 C:GLU150 3.5 29.6 1.0 CB C:HIS209 3.7 31.0 1.0 CB C:ASP183 3.9 28.4 1.0 O C:HOH457 4.1 37.1 1.0 NE2 C:HIS209 4.2 32.8 1.0 CD2 C:HIS186 4.3 28.2 1.0 NE2 C:HIS186 4.3 29.2 1.0 OD1 C:ASP183 4.3 31.2 1.0 CD2 C:HIS209 4.3 34.8 1.0 C1 C:FUD301 4.4 40.2 1.0 NH1 C:ARG215 4.4 31.4 1.0 C4 C:FUD301 4.5 44.4 1.0 CG C:GLU244 4.5 38.8 1.0 CG C:GLU150 4.6 30.4 1.0 CE C:MET181 4.7 30.5 1.0 O1 C:FUD301 4.8 37.1 1.0 CB C:GLU244 4.9 35.1 1.0 O5 C:FUD301 4.9 49.7 1.0

Manganese binding site 6 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Fructose 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-Fructose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn303 b:61.5 occ:1.00 NH1 C:ARG220 2.9 46.9 1.0 O B:HOH1583 3.0 52.2 1.0 O C:HOH437 3.7 43.1 1.0 NZ C:LYS216 3.9 29.8 1.0 CZ C:ARG220 4.1 41.7 1.0 O C:HOH423 4.3 57.8 1.0 CD C:LYS216 4.4 29.1 1.0 CE C:LYS216 4.6 32.1 1.0 MN B:MN1303 4.6 48.2 1.0 NH2 C:ARG220 4.7 45.1 1.0 O C:HOH419 4.7 26.7 1.0 OD2 B:ASP192 4.9 38.2 1.0

Manganese binding site 7 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Fructose 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-Fructose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn302 b:29.0 occ:1.00 OE2 D:GLU150 2.1 30.0 1.0 OD2 D:ASP183 2.1 29.4 1.0 O2 D:FUD301 2.2 38.0 1.0 OE1 D:GLU244 2.3 30.2 1.0 ND1 D:HIS209 2.4 31.1 1.0 O3 D:FUD301 2.5 41.1 1.0 C2 D:FUD301 2.9 37.5 1.0 C3 D:FUD301 3.0 40.7 1.0 CD D:GLU244 3.1 34.5 1.0 CD D:GLU150 3.2 31.6 1.0 OE2 D:GLU244 3.2 36.1 1.0 CE1 D:HIS209 3.3 32.6 1.0 CG D:ASP183 3.3 29.0 1.0 CG D:HIS209 3.4 30.8 1.0 OE1 D:GLU150 3.6 32.0 1.0 CB D:HIS209 3.7 28.7 1.0 CB D:ASP183 3.9 28.0 1.0 O D:HOH419 4.2 30.9 1.0 NE2 D:HIS186 4.2 27.8 1.0 OD1 D:ASP183 4.3 29.7 1.0 CD2 D:HIS186 4.4 28.0 1.0 C1 D:FUD301 4.4 37.5 1.0 NH1 D:ARG215 4.4 25.8 1.0 NE2 D:HIS209 4.4 31.1 1.0 C4 D:FUD301 4.5 41.0 1.0 CD2 D:HIS209 4.5 31.0 1.0 CG D:GLU150 4.5 30.8 1.0 CG D:GLU244 4.6 33.3 1.0 CE D:MET181 4.7 27.4 1.0 O1 D:FUD301 4.7 30.6 1.0 CB D:GLU244 4.9 31.0 1.0

Manganese binding site 8 out of 8 in the Crystal Structures of D-Psicose 3-Epimerase with D-Fructose 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-Fructose From Clostridium Cellulolyticum H10 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn303 b:48.7 occ:1.00 O B:HOH1470 2.4 33.1 1.0 OD1 D:ASP192 2.5 37.7 1.0 O D:HOH522 2.6 42.8 1.0 CG D:ASP192 3.5 31.1 1.0 O B:HOH1465 3.7 51.9 1.0 O A:ARG220 3.8 26.0 1.0 CB D:ASP192 3.8 27.0 1.0 OE2 B:GLU230 3.8 38.4 1.0 OD2 D:ASP192 4.5 27.8 1.0 O B:HOH1415 4.5 44.1 1.0 O A:HOH433 4.5 25.6 1.0 CG B:GLU230 4.6 34.1 1.0 NZ A:LYS216 4.6 29.6 1.0 CD B:GLU230 4.7 37.4 1.0 NH2 A:ARG220 4.7 33.8 1.0 MN A:MN303 4.7 62.6 1.0 C A:ARG220 4.8 24.6 1.0 CB A:ARG220 4.9 27.1 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