Manganese in PDB 2hk1: Crystal Structure of D-Psicose 3-Epimerase (Dpease) in the Presence of D-Fructose

The structure of Crystal Structure of D-Psicose 3-Epimerase (Dpease) in the Presence of D-Fructose, PDB code: 2hk1 was solved by K.Kim, H.J.Kim, D.K.Oh, S.S.Cha, S.Rhee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.50 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.900, 113.500, 133.800, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 23.9

The binding sites of Manganese atom in the Crystal Structure of D-Psicose 3-Epimerase (Dpease) in the Presence of D-Fructose (pdb code 2hk1). 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 Structure of D-Psicose 3-Epimerase (Dpease) in the Presence of D-Fructose, PDB code: 2hk1:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of D-Psicose 3-Epimerase (Dpease) in the Presence of D-Fructose


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 D-Psicose 3-Epimerase (Dpease) in the Presence of D-Fructose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1004 b:32.8 occ:1.00 OE2 A:GLU150 2.2 31.4 1.0 ND1 A:HIS209 2.2 24.7 1.0 OD2 A:ASP183 2.3 28.1 1.0 O2 A:FUD1300 2.3 56.6 1.0 OE1 A:GLU244 2.4 39.4 1.0 O3 A:FUD1300 2.5 57.2 1.0 C2 A:FUD1300 3.1 59.1 1.0 CE1 A:HIS209 3.1 27.1 1.0 CD A:GLU244 3.2 37.9 1.0 CD A:GLU150 3.2 33.1 1.0 OE2 A:GLU244 3.3 39.6 1.0 C3 A:FUD1300 3.3 62.0 1.0 CG A:HIS209 3.3 24.7 1.0 OE1 A:GLU150 3.4 33.8 1.0 CG A:ASP183 3.4 30.6 1.0 CB A:HIS209 3.7 24.8 1.0 CB A:ASP183 4.0 26.7 1.0 O A:HOH1311 4.3 28.5 1.0 NE2 A:HIS209 4.3 24.3 1.0 NE2 A:HIS186 4.3 28.7 1.0 CD2 A:HIS186 4.4 31.7 1.0 CD2 A:HIS209 4.4 26.0 1.0 C1 A:FUD1300 4.5 56.9 1.0 OD1 A:ASP183 4.5 32.1 1.0 CG A:GLU150 4.6 33.5 1.0 CG A:GLU244 4.6 37.1 1.0 C4 A:FUD1300 4.6 65.3 1.0 O4 A:FUD1300 4.6 68.1 1.0 NH1 A:ARG215 4.7 29.6 1.0 CE A:MSE181 4.9 58.6 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of D-Psicose 3-Epimerase (Dpease) in the Presence of D-Fructose


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 D-Psicose 3-Epimerase (Dpease) in the Presence of D-Fructose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1002 b:36.9 occ:1.00 OD2 B:ASP183 2.1 37.5 1.0 OE2 B:GLU150 2.2 34.2 1.0 OE1 B:GLU244 2.3 42.2 1.0 O2 B:FUD1301 2.3 61.8 1.0 O3 B:FUD1301 2.4 64.4 1.0 ND1 B:HIS209 2.4 37.3 1.0 C2 B:FUD1301 3.1 63.9 1.0 CD B:GLU244 3.2 42.5 1.0 CD B:GLU150 3.2 36.2 1.0 C3 B:FUD1301 3.2 67.0 1.0 CG B:ASP183 3.3 35.4 1.0 OE2 B:GLU244 3.3 44.7 1.0 CG B:HIS209 3.4 36.0 1.0 CE1 B:HIS209 3.4 37.4 1.0 OE1 B:GLU150 3.6 41.0 1.0 CB B:HIS209 3.6 34.4 1.0 CB B:ASP183 3.8 33.1 1.0 CE B:MSE181 4.1 60.2 1.0 OD1 B:ASP183 4.3 37.1 1.0 CD2 B:HIS186 4.4 30.3 1.0 NE2 B:HIS186 4.4 31.5 1.0 NE2 B:HIS209 4.5 37.4 1.0 CD2 B:HIS209 4.5 37.9 1.0 CG B:GLU150 4.5 32.8 1.0 O B:HOH1329 4.5 41.4 1.0 C4 B:FUD1301 4.6 70.3 1.0 C1 B:FUD1301 4.6 62.2 1.0 CG B:GLU244 4.6 41.2 1.0 O4 B:FUD1301 4.6 71.9 1.0 NH1 B:ARG215 4.6 29.4 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of D-Psicose 3-Epimerase (Dpease) in the Presence of D-Fructose


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 D-Psicose 3-Epimerase (Dpease) in the Presence of D-Fructose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1003 b:35.0 occ:1.00 OD2 C:ASP183 2.1 33.5 1.0 ND1 C:HIS209 2.2 31.6 1.0 OE2 C:GLU150 2.2 31.9 1.0 O2 C:FUD1302 2.3 42.7 1.0 O3 C:FUD1302 2.4 47.7 1.0 OE1 C:GLU244 2.4 42.7 1.0 C2 C:FUD1302 3.1 49.3 1.0 CE1 C:HIS209 3.2 32.0 1.0 C3 C:FUD1302 3.2 53.6 1.0 CD C:GLU150 3.2 32.4 1.0 CG C:HIS209 3.3 31.7 1.0 CD C:GLU244 3.3 41.0 1.0 CG C:ASP183 3.3 32.9 1.0 OE2 C:GLU244 3.4 45.4 1.0 OE1 C:GLU150 3.5 32.2 1.0 CB C:HIS209 3.6 31.1 1.0 CB C:ASP183 3.9 30.7 1.0 O C:HOH1316 4.0 32.6 1.0 CE C:MSE181 4.3 64.2 1.0 NE2 C:HIS209 4.3 32.1 1.0 OD1 C:ASP183 4.3 35.9 1.0 NE2 C:HIS186 4.3 26.6 1.0 CD2 C:HIS209 4.4 31.4 1.0 CD2 C:HIS186 4.4 27.8 1.0 C1 C:FUD1302 4.5 47.5 1.0 C4 C:FUD1302 4.6 58.9 1.0 CG C:GLU150 4.6 33.5 1.0 NH1 C:ARG215 4.6 34.6 1.0 CG C:GLU244 4.7 39.7 1.0 O4 C:FUD1302 4.7 62.9 1.0 CB C:GLU244 5.0 34.9 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of D-Psicose 3-Epimerase (Dpease) in the Presence of D-Fructose


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 D-Psicose 3-Epimerase (Dpease) in the Presence of D-Fructose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1001 b:38.5 occ:1.00 OD2 D:ASP183 2.2 34.6 1.0 OE2 D:GLU150 2.3 32.0 1.0 ND1 D:HIS209 2.3 28.9 1.0 O2 D:FUD1303 2.3 53.3 1.0 OE1 D:GLU244 2.3 37.8 1.0 O3 D:FUD1303 2.3 59.2 1.0 C2 D:FUD1303 3.0 58.6 1.0 CD D:GLU244 3.1 38.2 1.0 C3 D:FUD1303 3.2 62.4 1.0 CD D:GLU150 3.2 35.5 1.0 CE1 D:HIS209 3.2 28.5 1.0 OE2 D:GLU244 3.3 42.3 1.0 CG D:ASP183 3.3 31.2 1.0 CG D:HIS209 3.3 28.2 1.0 OE1 D:GLU150 3.4 39.4 1.0 CB D:HIS209 3.6 29.1 1.0 CB D:ASP183 3.9 30.6 1.0 CE D:MSE181 4.2 67.4 1.0 O D:HOH1309 4.3 35.5 1.0 OD1 D:ASP183 4.3 36.0 1.0 NE2 D:HIS209 4.4 28.9 1.0 CD2 D:HIS186 4.4 29.1 1.0 CD2 D:HIS209 4.4 28.2 1.0 NE2 D:HIS186 4.4 29.7 1.0 C4 D:FUD1303 4.5 65.7 1.0 C1 D:FUD1303 4.5 57.1 1.0 CG D:GLU244 4.5 39.6 1.0 NH1 D:ARG215 4.6 32.4 1.0 O4 D:FUD1303 4.6 67.6 1.0 CG D:GLU150 4.6 33.3 1.0 CB D:GLU244 5.0 38.0 1.0

K.Kim, H.J.Kim, D.K.Oh, S.S.Cha, S.Rhee. Crystal Structure of D-Psicose 3-Epimerase From Agrobacterium Tumefaciens and Its Complex with True Substrate D-Fructose: A Pivotal Role of Metal in Catalysis, An Active Site For the Non-Phosphorylated Substrate, and Its Conformational Changes J.Mol.Biol. V. 361 920 2006.
ISSN: ISSN 0022-2836
PubMed: 16876192
DOI: 10.1016/J.JMB.2006.06.069