Manganese in PDB 6wn6: Crystal Structure of 3-Keto-D-Glucoside 4-Epimerase, Ycjr, From E. Coli, Apo Form

The structure of Crystal Structure of 3-Keto-D-Glucoside 4-Epimerase, Ycjr, From E. Coli, Apo Form, PDB code: 6wn6 was solved by M.F.Mabanglo, F.M.Raushel, K.Mukherjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.91 / 1.86
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	116.576, 116.576, 247.725, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 19.9

The binding sites of Manganese atom in the Crystal Structure of 3-Keto-D-Glucoside 4-Epimerase, Ycjr, From E. Coli, Apo Form (pdb code 6wn6). 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 3-Keto-D-Glucoside 4-Epimerase, Ycjr, From E. Coli, Apo Form, PDB code: 6wn6:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of 3-Keto-D-Glucoside 4-Epimerase, Ycjr, From E. Coli, Apo Form


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 3-Keto-D-Glucoside 4-Epimerase, Ycjr, From E. Coli, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:16.2 occ:1.00 OE2 A:GLU149 1.9 17.5 1.0 OD2 A:ASP182 1.9 17.3 1.0 OE1 A:GLU243 2.0 18.8 1.0 ND1 A:HIS208 2.1 18.7 1.0 CD A:GLU149 2.8 21.1 1.0 CD A:GLU243 2.9 19.9 1.0 CG A:ASP182 3.0 23.0 1.0 CG A:HIS208 3.0 19.9 1.0 CE1 A:HIS208 3.1 19.8 1.0 OE1 A:GLU149 3.1 15.9 1.0 CB A:HIS208 3.3 17.9 1.0 OE2 A:GLU243 3.4 18.9 1.0 CB A:ASP182 3.4 16.8 1.0 O A:HOH423 3.8 19.0 1.0 O1 A:EDO302 4.0 20.9 1.0 CG A:GLU243 4.0 20.3 1.0 OD1 A:ASP182 4.1 18.8 1.0 CG A:GLU149 4.1 15.7 1.0 NE2 A:HIS208 4.2 20.2 1.0 CD2 A:HIS208 4.2 18.8 1.0 CB A:GLU243 4.2 21.1 1.0 CD2 A:HIS185 4.2 15.6 1.0 NH2 A:ARG214 4.3 19.8 1.0 NH1 A:ARG214 4.3 20.8 1.0 NE2 A:HIS185 4.3 16.3 1.0 CD1 A:ILE180 4.6 21.2 1.0 CA A:ASP182 4.7 17.3 1.0 CZ A:ARG214 4.8 21.7 1.0 CA A:HIS208 4.9 18.9 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of 3-Keto-D-Glucoside 4-Epimerase, Ycjr, From E. Coli, Apo Form


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 3-Keto-D-Glucoside 4-Epimerase, Ycjr, From E. Coli, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:16.8 occ:1.00 OE1 B:GLU243 1.8 20.8 1.0 OE2 B:GLU149 1.9 18.3 1.0 OD2 B:ASP182 2.0 18.6 1.0 ND1 B:HIS208 2.1 18.7 1.0 CD B:GLU149 2.8 18.5 1.0 CD B:GLU243 2.8 20.6 1.0 CG B:ASP182 3.0 20.5 1.0 OE1 B:GLU149 3.0 16.3 1.0 CG B:HIS208 3.1 18.7 1.0 CE1 B:HIS208 3.1 19.8 1.0 CB B:HIS208 3.3 18.9 1.0 CB B:ASP182 3.4 17.4 1.0 OE2 B:GLU243 3.5 18.4 1.0 O B:HOH420 3.8 21.3 1.0 O1 B:EDO307 3.9 21.5 1.0 CG B:GLU243 3.9 18.4 1.0 CB B:GLU243 4.1 18.1 1.0 CG B:GLU149 4.1 16.4 1.0 OD1 B:ASP182 4.1 19.1 1.0 NE2 B:HIS208 4.2 19.9 1.0 CD2 B:HIS208 4.2 19.7 1.0 CD2 B:HIS185 4.2 16.2 1.0 NH2 B:ARG214 4.3 19.8 1.0 NE2 B:HIS185 4.3 18.0 1.0 NH1 B:ARG214 4.4 19.5 1.0 CD1 B:ILE180 4.6 21.1 1.0 CA B:ASP182 4.7 18.0 1.0 CZ B:ARG214 4.8 22.8 1.0 CA B:HIS208 4.9 20.4 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of 3-Keto-D-Glucoside 4-Epimerase, Ycjr, From E. Coli, Apo Form


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 3-Keto-D-Glucoside 4-Epimerase, Ycjr, From E. Coli, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:13.7 occ:1.00 OE2 C:GLU149 1.8 15.3 1.0 OE2 C:GLU243 1.9 16.5 1.0 OD2 C:ASP182 2.0 14.9 1.0 ND1 C:HIS208 2.0 14.1 1.0 CD C:GLU149 2.7 14.3 1.0 CD C:GLU243 2.9 17.4 1.0 CE1 C:HIS208 3.0 14.1 1.0 CG C:ASP182 3.0 13.9 1.0 CG C:HIS208 3.0 14.4 1.0 OE1 C:GLU149 3.0 13.8 1.0 CB C:HIS208 3.3 14.6 1.0 CB C:ASP182 3.4 14.0 1.0 OE1 C:GLU243 3.5 13.7 1.0 O C:HOH417 3.8 19.5 1.0 O2 C:EDO303 4.0 20.8 1.0 CG C:GLU243 4.0 15.4 1.0 CG C:GLU149 4.1 13.5 1.0 NE2 C:HIS208 4.1 14.4 1.0 OD1 C:ASP182 4.1 14.0 1.0 CD2 C:HIS208 4.1 15.7 1.0 CB C:GLU243 4.2 14.1 1.0 CD2 C:HIS185 4.2 13.3 1.0 NE2 C:HIS185 4.3 13.3 1.0 NH2 C:ARG214 4.3 13.1 1.0 NH1 C:ARG214 4.4 15.1 1.0 CD1 C:ILE180 4.5 17.7 1.0 CA C:ASP182 4.6 14.4 1.0 CZ C:ARG214 4.8 18.2 1.0 CA C:HIS208 4.9 15.1 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of 3-Keto-D-Glucoside 4-Epimerase, Ycjr, From E. Coli, Apo Form


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 3-Keto-D-Glucoside 4-Epimerase, Ycjr, From E. Coli, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:13.4 occ:1.00 OE2 D:GLU149 1.8 14.2 1.0 OE1 D:GLU243 1.9 17.0 1.0 OD2 D:ASP182 2.0 14.3 1.0 ND1 D:HIS208 2.1 15.9 1.0 CD D:GLU149 2.8 15.2 1.0 CD D:GLU243 2.9 16.6 1.0 CG D:ASP182 3.0 15.9 1.0 CG D:HIS208 3.0 15.0 1.0 CE1 D:HIS208 3.1 13.7 1.0 OE1 D:GLU149 3.1 13.8 1.0 CB D:HIS208 3.3 14.2 1.0 CB D:ASP182 3.4 13.7 1.0 OE2 D:GLU243 3.4 15.6 1.0 O D:HOH420 3.9 19.0 1.0 O1 D:EDO302 3.9 19.6 1.0 CG D:GLU243 4.0 15.3 1.0 CG D:GLU149 4.1 13.1 1.0 OD1 D:ASP182 4.1 14.8 1.0 NE2 D:HIS208 4.2 16.0 1.0 CB D:GLU243 4.2 14.5 1.0 CD2 D:HIS208 4.2 15.7 1.0 CD2 D:HIS185 4.2 12.9 1.0 NH1 D:ARG214 4.3 15.2 1.0 NE2 D:HIS185 4.3 14.4 1.0 NH2 D:ARG214 4.3 13.6 1.0 CD1 D:ILE180 4.6 18.5 1.0 CA D:ASP182 4.7 14.1 1.0 CZ D:ARG214 4.8 18.1 1.0 CA D:HIS208 4.9 14.7 1.0

M.F.Mabanglo, J.P.Huddleston, K.Mukherjee, Z.W.Taylor, F.M.Raushel. Structure and Reaction Mechanism of Ycjr, An Epimerase That Facilitates the Interconversion of D-Gulosides to D-Glucosides Inescherichia Coli. Biochemistry 2020.
ISSN: ISSN 0006-2960
PubMed: 32437133
DOI: 10.1021/ACS.BIOCHEM.0C00334