Manganese in PDB 7cj7: Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with L-Tagatose

The structure of Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with L-Tagatose, PDB code: 7cj7 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)	39.25 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.056, 81.777, 140.033, 90, 90, 90
R / Rfree (%)	14.8 / 19

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

Magnesium

(Mg)

1 atom

The binding sites of Manganese atom in the Crystal Structure of Homo Dimeric D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with L-Tagatose (pdb code 7cj7). 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 L-Tagatose, PDB code: 7cj7:
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 L-Tagatose


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 L-Tagatose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:20.1 occ:1.00 OD2 A:ASP185 2.0 8.4 1.0 OE2 A:GLU152 2.1 11.6 1.0 OE2 A:GLU246 2.1 12.4 1.0 O2 A:SOL301 2.1 14.2 1.0 ND1 A:HIS211 2.2 7.8 1.0 O3 A:SOL301 2.3 13.9 1.0 C2 A:SOL301 2.9 16.3 1.0 C3 A:SOL301 3.1 18.4 1.0 CE1 A:HIS211 3.1 8.5 1.0 CD A:GLU152 3.1 11.6 1.0 CD A:GLU246 3.1 14.7 1.0 CG A:ASP185 3.2 8.7 1.0 CG A:HIS211 3.3 7.9 1.0 OE1 A:GLU246 3.4 18.0 1.0 OE1 A:GLU152 3.5 14.4 1.0 CB A:HIS211 3.6 8.1 1.0 CB A:ASP185 3.8 8.2 1.0 O A:HOH468 3.9 17.5 1.0 OD1 A:ASP185 4.2 9.2 1.0 NH2 A:ARG217 4.2 13.6 1.0 NE2 A:HIS211 4.2 8.7 1.0 C1 A:SOL301 4.3 18.3 1.0 CD2 A:HIS211 4.4 8.5 1.0 C4 A:SOL301 4.4 21.2 1.0 CG A:GLU152 4.4 10.3 1.0 CG A:GLU246 4.4 13.4 1.0 CD2 A:HIS188 4.5 8.7 1.0 NE2 A:HIS188 4.5 9.0 1.0 O4 A:SOL301 4.5 28.4 1.0 NE2 A:HIS183 4.6 10.2 1.0 O1 A:SOL301 4.8 16.0 1.0 CB A:GLU246 4.8 11.9 1.0 CE1 A:HIS183 4.9 9.8 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 L-Tagatose


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 L-Tagatose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:21.6 occ:1.00 OD2 B:ASP185 2.0 10.8 1.0 OE2 B:GLU152 2.1 13.5 1.0 OE1 B:GLU246 2.1 13.2 1.0 O2 B:LTG303 2.2 14.4 1.0 ND1 B:HIS211 2.2 8.6 1.0 O3 B:LTG303 2.3 15.5 1.0 C2 B:LTG303 3.0 17.6 1.0 CD B:GLU152 3.1 12.9 1.0 CE1 B:HIS211 3.1 9.1 1.0 CD B:GLU246 3.1 14.2 1.0 C3 B:LTG303 3.1 19.6 1.0 CG B:ASP185 3.2 10.2 1.0 CG B:HIS211 3.3 8.5 1.0 OE2 B:GLU246 3.4 18.2 1.0 OE1 B:GLU152 3.5 16.1 1.0 CB B:HIS211 3.7 8.8 1.0 O B:HOH438 3.8 16.2 1.0 CB B:ASP185 3.8 10.3 1.0 OD1 B:ASP185 4.2 11.1 1.0 NH1 B:ARG217 4.2 13.2 1.0 NE2 B:HIS211 4.3 9.3 1.0 CD2 B:HIS211 4.4 8.5 1.0 CG B:GLU152 4.4 11.0 1.0 C1 B:LTG303 4.4 15.9 1.0 CG B:GLU246 4.4 12.8 1.0 C4 B:LTG303 4.5 26.1 1.0 CD2 B:HIS188 4.5 9.1 1.0 NE2 B:HIS188 4.6 8.9 1.0 NE2 B:HIS183 4.6 10.7 1.0 CB B:GLU246 4.8 11.4 1.0 CE1 B:HIS183 4.8 10.5 1.0 O1 B:LTG303 4.9 14.5 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