Manganese in PDB 7cj8: Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose

The structure of Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose, PDB code: 7cj8 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)	48.84 / 2.05
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	51.02, 81.05, 106.13, 99.3, 101.5, 87.24
R / Rfree (%)	16.2 / 24.1

The binding sites of Manganese atom in the Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose (pdb code 7cj8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose, PDB code: 7cj8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Crystal Structure of N-Terminal His-Tagged 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 N-Terminal His-Tagged 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:34.0 occ:1.00 O2 A:PSJ303 2.2 27.6 1.0 OD2 A:ASP185 2.2 17.5 1.0 OE2 A:GLU246 2.2 32.5 1.0 OE2 A:GLU152 2.2 23.4 1.0 O3 A:PSJ303 2.3 34.0 1.0 ND1 A:HIS211 2.4 18.2 1.0 C3 A:PSJ303 2.8 36.5 1.0 C2 A:PSJ303 2.8 30.4 1.0 CD A:GLU246 3.0 31.7 1.0 CD A:GLU152 3.1 21.6 1.0 OE1 A:GLU246 3.2 30.4 1.0 CG A:ASP185 3.3 18.2 1.0 CE1 A:HIS211 3.4 19.5 1.0 OE1 A:GLU152 3.4 23.5 1.0 CG A:HIS211 3.4 18.7 1.0 CB A:HIS211 3.7 19.6 1.0 CB A:ASP185 3.9 18.9 1.0 NH2 A:ARG217 4.1 26.0 1.0 C1 A:PSJ303 4.3 29.9 1.0 C4 A:PSJ303 4.3 38.1 1.0 OD1 A:ASP185 4.3 16.5 1.0 NE2 A:HIS188 4.4 15.4 1.0 CG A:GLU246 4.4 29.6 1.0 CG A:GLU152 4.5 20.2 1.0 CD2 A:HIS188 4.5 16.4 1.0 NE2 A:HIS211 4.5 18.5 1.0 CD2 A:HIS211 4.5 18.7 1.0 O5 A:PSJ303 4.6 41.7 1.0 O1 A:PSJ303 4.7 26.9 1.0 NE2 A:HIS183 4.9 18.7 1.0 C5 A:PSJ303 4.9 39.7 1.0 CB A:GLU246 4.9 27.0 1.0 CE1 A:HIS183 4.9 18.8 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of N-Terminal His-Tagged 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 N-Terminal His-Tagged 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:34.9 occ:1.00 OD2 B:ASP185 2.0 19.5 1.0 OE2 B:GLU246 2.1 27.9 1.0 OE2 B:GLU152 2.2 20.4 1.0 O2 B:PSJ303 2.3 29.6 1.0 ND1 B:HIS211 2.4 23.9 1.0 O3 B:PSJ303 2.5 39.6 1.0 CD B:GLU246 2.9 28.2 1.0 C3 B:PSJ303 3.0 40.5 1.0 C2 B:PSJ303 3.0 33.1 1.0 OE1 B:GLU246 3.1 29.5 1.0 CD B:GLU152 3.1 22.5 1.0 CG B:ASP185 3.2 21.0 1.0 CG B:HIS211 3.3 22.5 1.0 CE1 B:HIS211 3.3 23.8 1.0 OE1 B:GLU152 3.5 24.0 1.0 CB B:HIS211 3.5 23.5 1.0 CB B:ASP185 3.7 23.0 1.0 NH1 B:ARG217 4.0 29.8 1.0 O B:HOH427 4.1 26.4 1.0 OD1 B:ASP185 4.2 20.3 1.0 CG B:GLU246 4.2 28.0 1.0 CG B:GLU152 4.4 21.9 1.0 CD2 B:HIS188 4.5 24.0 1.0 NE2 B:HIS211 4.5 23.8 1.0 CD2 B:HIS211 4.5 23.1 1.0 C1 B:PSJ303 4.5 28.4 1.0 C4 B:PSJ303 4.5 44.2 1.0 NE2 B:HIS188 4.5 24.0 1.0 O5 B:PSJ303 4.7 50.5 1.0 NE2 B:HIS183 4.8 22.6 1.0 CE1 B:HIS183 4.9 21.0 1.0 O1 B:PSJ303 5.0 22.0 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of N-Terminal His-Tagged 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 3 of Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:38.8 occ:1.00 OE2 C:GLU246 2.1 30.8 1.0 O2 C:PSJ303 2.1 24.1 1.0 OD2 C:ASP185 2.2 19.4 1.0 OE2 C:GLU152 2.3 25.7 1.0 O3 C:PSJ303 2.3 36.0 1.0 ND1 C:HIS211 2.4 22.7 1.0 CD C:GLU246 2.8 29.2 1.0 C2 C:PSJ303 2.9 27.2 1.0 OE1 C:GLU246 3.0 34.6 1.0 C3 C:PSJ303 3.0 33.6 1.0 CD C:GLU152 3.2 23.3 1.0 CE1 C:HIS211 3.3 21.7 1.0 CG C:ASP185 3.4 19.3 1.0 CG C:HIS211 3.5 22.8 1.0 OE1 C:GLU152 3.5 28.1 1.0 CB C:HIS211 3.8 23.1 1.0 CB C:ASP185 4.0 20.8 1.0 NH2 C:ARG217 4.0 24.2 1.0 CG C:GLU246 4.3 27.2 1.0 C1 C:PSJ303 4.3 23.7 1.0 OD1 C:ASP185 4.4 18.5 1.0 C4 C:PSJ303 4.4 37.3 1.0 NE2 C:HIS188 4.5 19.1 1.0 CD2 C:HIS188 4.5 21.3 1.0 NE2 C:HIS211 4.5 22.3 1.0 CD2 C:HIS211 4.6 21.9 1.0 CG C:GLU152 4.6 23.2 1.0 O1 C:PSJ303 4.6 23.5 1.0 CB C:GLU246 4.8 25.1 1.0 O5 C:PSJ303 4.8 42.0 1.0 NE2 C:HIS183 4.9 22.3 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of N-Terminal His-Tagged 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 4 of Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:36.9 occ:1.00 O2 D:PSJ303 2.0 26.0 1.0 OE2 D:GLU152 2.1 23.8 1.0 OD2 D:ASP185 2.2 16.9 1.0 OE1 D:GLU246 2.2 25.8 1.0 O3 D:PSJ303 2.4 33.6 1.0 ND1 D:HIS211 2.5 21.1 1.0 C2 D:PSJ303 2.7 29.3 1.0 C3 D:PSJ303 2.8 35.4 1.0 CD D:GLU152 3.0 22.2 1.0 CD D:GLU246 3.1 25.3 1.0 OE1 D:GLU152 3.3 25.9 1.0 OE2 D:GLU246 3.3 26.4 1.0 CG D:ASP185 3.3 17.3 1.0 CE1 D:HIS211 3.4 21.8 1.0 CG D:HIS211 3.5 20.6 1.0 CB D:HIS211 3.8 19.6 1.0 CB D:ASP185 3.8 16.5 1.0 O D:HOH423 3.8 27.6 1.0 NH1 D:ARG217 4.1 18.6 1.0 C1 D:PSJ303 4.2 29.0 1.0 C4 D:PSJ303 4.3 39.0 1.0 OD1 D:ASP185 4.4 19.6 1.0 CG D:GLU152 4.4 21.1 1.0 O5 D:PSJ303 4.4 43.1 1.0 CD2 D:HIS188 4.4 17.8 1.0 NE2 D:HIS188 4.4 17.4 1.0 CG D:GLU246 4.5 22.8 1.0 NE2 D:HIS211 4.6 21.8 1.0 O1 D:PSJ303 4.6 24.6 1.0 CD2 D:HIS211 4.6 21.0 1.0 C5 D:PSJ303 4.8 42.1 1.0 NE2 D:HIS183 4.8 18.6 1.0 CB D:GLU246 4.9 22.5 1.0 CE1 D:HIS183 4.9 17.9 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of N-Terminal His-Tagged 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 5 of Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn301 b:34.0 occ:1.00 OE2 E:GLU246 2.0 28.4 1.0 OE2 E:GLU152 2.1 20.5 1.0 OD2 E:ASP185 2.1 21.4 1.0 O2 E:PSJ303 2.4 28.9 1.0 ND1 E:HIS211 2.4 21.5 1.0 O3 E:PSJ303 2.4 43.6 1.0 CD E:GLU246 2.9 29.2 1.0 C3 E:PSJ303 2.9 38.3 1.0 C2 E:PSJ303 3.0 31.0 1.0 CD E:GLU152 3.0 20.1 1.0 OE1 E:GLU246 3.2 32.0 1.0 CG E:ASP185 3.3 22.2 1.0 CE1 E:HIS211 3.3 22.2 1.0 OE1 E:GLU152 3.4 21.8 1.0 CG E:HIS211 3.4 20.8 1.0 CB E:HIS211 3.7 23.0 1.0 CB E:ASP185 3.8 22.6 1.0 O E:HOH412 3.9 22.3 1.0 NH2 E:ARG217 4.2 31.6 1.0 CG E:GLU246 4.2 30.0 1.0 OD1 E:ASP185 4.3 26.6 1.0 CG E:GLU152 4.4 20.6 1.0 C4 E:PSJ303 4.4 42.0 1.0 CD2 E:HIS188 4.5 21.9 1.0 NE2 E:HIS188 4.5 19.6 1.0 NE2 E:HIS211 4.5 22.0 1.0 C1 E:PSJ303 4.5 27.0 1.0 CD2 E:HIS211 4.5 22.9 1.0 O5 E:PSJ303 4.6 51.3 1.0 NE2 E:HIS183 4.8 18.4 1.0 CE1 E:HIS183 4.9 18.0 1.0 O1 E:PSJ303 5.0 23.6 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of N-Terminal His-Tagged 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 6 of Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. in Complex with D-Allulose within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn301 b:28.9 occ:1.00 OE2 F:GLU152 2.1 22.1 1.0 OE1 F:GLU246 2.1 24.8 1.0 OD2 F:ASP185 2.2 15.6 1.0 O2 F:PSJ303 2.2 27.7 1.0 ND1 F:HIS211 2.3 16.7 1.0 O3 F:PSJ303 2.5 28.1 1.0 C3 F:PSJ303 2.7 37.2 1.0 C2 F:PSJ303 2.8 33.8 1.0 CD F:GLU152 2.9 21.1 1.0 CD F:GLU246 3.0 25.5 1.0 OE1 F:GLU152 3.2 23.2 1.0 CE1 F:HIS211 3.3 18.6 1.0 CG F:ASP185 3.3 15.8 1.0 CG F:HIS211 3.3 17.4 1.0 OE2 F:GLU246 3.3 27.2 1.0 CB F:HIS211 3.5 15.5 1.0 CB F:ASP185 3.8 15.5 1.0 NH1 F:ARG217 4.0 27.1 1.0 C4 F:PSJ303 4.2 36.9 1.0 C1 F:PSJ303 4.2 32.6 1.0 O F:HOH504 4.3 26.9 1.0 CG F:GLU152 4.3 19.0 1.0 OD1 F:ASP185 4.3 17.4 1.0 CG F:GLU246 4.4 23.8 1.0 NE2 F:HIS211 4.4 20.2 1.0 CD2 F:HIS211 4.4 18.5 1.0 CD2 F:HIS188 4.6 21.8 1.0 O5 F:PSJ303 4.6 42.2 1.0 NE2 F:HIS188 4.6 20.4 1.0 NE2 F:HIS183 4.7 19.6 1.0 O1 F:PSJ303 4.8 27.2 1.0 O4 F:PSJ303 4.8 45.6 1.0 CE1 F:HIS183 4.9 19.8 1.0 C5 F:PSJ303 4.9 38.5 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