Manganese in PDB 7cj5: Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose

The structure of Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose, PDB code: 7cj5 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)	19.94 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.42, 70.54, 140.22, 90, 90, 90
R / Rfree (%)	12.6 / 15.9

The structure of Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose (pdb code 7cj5). 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-Fructose, PDB code: 7cj5:
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-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 Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:21.1 occ:1.00 OE2 A:GLU152 2.0 12.8 1.0 OD2 A:ASP185 2.0 11.7 1.0 OE2 A:GLU246 2.1 14.9 1.0 O2 A:FUD302 2.2 14.7 1.0 O3 A:FUD302 2.2 18.1 1.0 ND1 A:HIS211 2.3 10.8 1.0 C2 A:FUD302 3.0 16.6 1.0 CD A:GLU152 3.1 13.8 1.0 CD A:GLU246 3.1 15.1 1.0 C3 A:FUD302 3.1 18.5 1.0 CG A:ASP185 3.2 11.2 1.0 CE1 A:HIS211 3.2 11.7 1.0 CG A:HIS211 3.3 11.9 1.0 OE1 A:GLU246 3.4 15.4 1.0 OE1 A:GLU152 3.5 14.5 1.0 CB A:HIS211 3.5 12.6 1.0 CB A:ASP185 3.8 10.6 1.0 O A:HOH448 4.0 15.1 1.0 O4 A:FUD302 4.1 23.6 1.0 OD1 A:ASP185 4.2 13.3 1.0 C4 A:FUD302 4.3 21.0 1.0 NH2 A:ARG217 4.3 16.8 1.0 CG A:GLU152 4.4 13.1 1.0 NE2 A:HIS211 4.4 11.2 1.0 CD2 A:HIS211 4.4 12.1 1.0 CG A:GLU246 4.4 14.4 1.0 CD2 A:HIS188 4.4 12.3 1.0 NE2 A:HIS188 4.4 11.9 1.0 C1 A:FUD302 4.4 14.5 1.0 NE2 A:HIS183 4.8 12.2 1.0 O1 A:FUD302 4.9 14.6 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-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 Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Fructose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:23.6 occ:1.00 OD2 B:ASP185 2.1 15.0 1.0 OE2 B:GLU152 2.1 14.6 1.0 O2 B:FUD302 2.2 17.2 1.0 OE1 B:GLU246 2.2 15.6 1.0 ND1 B:HIS211 2.3 13.2 1.0 O3 B:FUD302 2.3 21.2 1.0 C2 B:FUD302 2.9 19.8 1.0 C3 B:FUD302 3.0 23.7 1.0 CD B:GLU246 3.1 17.2 1.0 CD B:GLU152 3.1 15.8 1.0 CE1 B:HIS211 3.2 12.6 1.0 CG B:ASP185 3.2 14.3 1.0 OE2 B:GLU246 3.3 20.8 1.0 CG B:HIS211 3.3 14.1 1.0 OE1 B:GLU152 3.4 18.9 1.0 CB B:HIS211 3.6 15.1 1.0 CB B:ASP185 3.8 14.7 1.0 O B:HOH426 3.9 19.3 1.0 NH1 B:ARG217 4.1 14.0 1.0 OD1 B:ASP185 4.2 15.1 1.0 NE2 B:HIS211 4.3 12.9 1.0 C1 B:FUD302 4.4 18.5 1.0 C4 B:FUD302 4.4 28.2 1.0 CD2 B:HIS211 4.4 14.3 1.0 CG B:GLU152 4.4 14.6 1.0 CG B:GLU246 4.4 16.0 1.0 CD2 B:HIS188 4.4 12.1 1.0 NE2 B:HIS188 4.5 12.3 1.0 NE2 B:HIS183 4.7 16.0 1.0 O4 B:FUD302 4.7 33.3 1.0 O1 B:FUD302 4.8 15.9 1.0 CB B:GLU246 4.9 14.7 1.0 CE1 B:HIS183 4.9 16.1 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