Manganese in PDB 7cj6: Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose

The structure of Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose, PDB code: 7cj6 was solved by H.Yoshida, A.Yoshihara, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.29 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.75, 80.87, 139.71, 90, 90, 90
R / Rfree (%)	18.1 / 25.5

The binding sites of Manganese atom in the Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose (pdb code 7cj6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose, PDB code: 7cj6:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose


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 Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:24.1 occ:1.00 OE2 A:GLU246 2.0 21.3 1.0 OE2 A:GLU152 2.0 18.1 1.0 OD2 A:ASP185 2.1 19.8 1.0 ND1 A:HIS211 2.2 16.5 1.0 O2 A:PSJ302 2.2 21.2 1.0 O3 A:PSJ302 2.4 24.7 1.0 C2 A:PSJ302 2.9 22.8 1.0 C3 A:PSJ302 2.9 26.6 1.0 CD A:GLU246 3.0 20.9 1.0 CD A:GLU152 3.1 18.1 1.0 CE1 A:HIS211 3.1 17.0 1.0 CG A:HIS211 3.2 16.1 1.0 CG A:ASP185 3.2 17.0 1.0 OE1 A:GLU246 3.3 25.4 1.0 OE1 A:GLU152 3.4 20.4 1.0 CB A:HIS211 3.5 15.9 1.0 CB A:ASP185 3.8 15.1 1.0 O A:HOH533 4.0 25.1 1.0 NH2 A:ARG217 4.1 21.0 1.0 OD1 A:ASP185 4.2 17.9 1.0 NE2 A:HIS211 4.2 16.7 1.0 CD2 A:HIS211 4.3 16.5 1.0 CG A:GLU246 4.3 20.0 1.0 C1 A:PSJ302 4.3 23.1 1.0 CG A:GLU152 4.4 17.1 1.0 C4 A:PSJ302 4.4 29.4 1.0 NE2 A:HIS188 4.4 17.2 1.0 CD2 A:HIS188 4.4 17.5 1.0 O5 A:PSJ302 4.6 39.8 1.0 O1 A:PSJ302 4.7 22.7 1.0 CB A:GLU246 4.8 20.1 1.0 NE2 A:HIS183 4.8 16.8 1.0 CE1 A:HIS183 4.9 16.5 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose


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 Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:19.4 occ:1.00 OD2 B:ASP185 2.0 14.2 1.0 OE2 B:GLU152 2.1 18.9 1.0 O2 B:PSJ302 2.2 23.3 1.0 ND1 B:HIS211 2.2 13.4 1.0 OE1 B:GLU246 2.2 20.3 1.0 O3 B:PSJ302 2.2 18.4 1.0 C2 B:PSJ302 2.9 25.4 1.0 CD B:GLU152 3.0 19.6 1.0 C3 B:PSJ302 3.0 26.3 1.0 CD B:GLU246 3.1 20.9 1.0 CE1 B:HIS211 3.1 13.9 1.0 CG B:ASP185 3.2 16.2 1.0 CG B:HIS211 3.2 13.9 1.0 OE2 B:GLU246 3.3 23.1 1.0 OE1 B:GLU152 3.3 20.7 1.0 CB B:HIS211 3.6 14.6 1.0 CB B:ASP185 3.8 16.5 1.0 O B:HOH472 4.1 19.6 1.0 NH1 B:ARG217 4.1 19.9 1.0 OD1 B:ASP185 4.2 17.6 1.0 NE2 B:HIS211 4.2 13.4 1.0 CD2 B:HIS211 4.3 13.5 1.0 CG B:GLU152 4.4 18.9 1.0 C4 B:PSJ302 4.4 30.0 1.0 C1 B:PSJ302 4.4 25.2 1.0 CG B:GLU246 4.4 20.3 1.0 CD2 B:HIS188 4.5 16.5 1.0 NE2 B:HIS188 4.5 17.3 1.0 O5 B:PSJ302 4.5 38.0 1.0 NE2 B:HIS183 4.7 15.5 1.0 CB B:GLU246 4.8 19.7 1.0 CE1 B:HIS183 4.9 14.8 1.0 O1 B:PSJ302 4.9 24.4 1.0

H.Yoshida, A.Yoshihara, S.Kato, S.Mochizuki, K.Akimitsu, K.Izumori, S.Kamitori. Crystal Structure of A Novel Homodimeric L-Ribulose 3-Epimerase From Methylomonus Sp. Febs Open Bio 2021.
ISSN: ESSN 2211-5463
PubMed: 33838083
DOI: 10.1002/2211-5463.13159