Manganese in PDB 7cj9: Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. with Additional C-Terminal Residues

The structure of Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. with Additional C-Terminal Residues, PDB code: 7cj9 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)	45.71 / 1.58
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	80.43, 92.77, 93.78, 87.67, 98.64, 115.6
R / Rfree (%)	17.7 / 22.7

The binding sites of Manganese atom in the Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. with Additional C-Terminal Residues (pdb code 7cj9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. with Additional C-Terminal Residues, PDB code: 7cj9:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in the Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. with Additional C-Terminal Residues


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. with Additional C-Terminal Residues within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:20.5 occ:1.00 OD2 A:ASP185 2.1 15.8 1.0 O3 A:FUD302 2.1 26.2 1.0 O2 A:FUD302 2.1 15.8 1.0 OE2 A:GLU246 2.1 20.0 1.0 OE2 A:GLU152 2.2 16.6 1.0 ND1 A:HIS211 2.3 16.3 1.0 C2 A:FUD302 3.0 19.7 1.0 C3 A:FUD302 3.0 25.4 1.0 CD A:GLU246 3.1 21.5 1.0 CD A:GLU152 3.1 15.7 1.0 CE1 A:HIS211 3.2 16.9 1.0 CG A:ASP185 3.3 14.1 1.0 CG A:HIS211 3.3 14.8 1.0 OE1 A:GLU246 3.4 25.5 1.0 OE1 A:GLU152 3.4 18.3 1.0 CB A:HIS211 3.6 13.9 1.0 O A:HOH446 3.9 22.2 1.0 CB A:ASP185 3.9 13.2 1.0 NH2 A:ARG217 4.2 15.0 1.0 OD1 A:ASP185 4.3 15.5 1.0 NE2 A:HIS211 4.3 16.2 1.0 C4 A:FUD302 4.4 29.0 1.0 CD2 A:HIS211 4.4 14.4 1.0 C1 A:FUD302 4.4 17.4 1.0 CG A:GLU246 4.4 18.5 1.0 CG A:GLU152 4.4 13.5 1.0 NE2 A:HIS188 4.5 12.7 1.0 O4 A:FUD302 4.5 41.3 1.0 CD2 A:HIS188 4.5 14.6 1.0 NE2 A:HIS183 4.8 12.9 1.0 CB A:GLU246 4.8 17.5 1.0 O1 A:FUD302 4.8 14.4 1.0 CE1 A:HIS183 4.9 14.7 1.0

Manganese binding site 2 out of 8 in the Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. with Additional C-Terminal Residues


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. with Additional C-Terminal Residues within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:21.8 occ:1.00 OE1 B:GLU246 2.1 19.9 1.0 OD2 B:ASP185 2.1 15.5 1.0 O2 B:FUD302 2.1 19.0 1.0 OE2 B:GLU152 2.2 18.8 1.0 O3 B:FUD302 2.2 26.8 1.0 ND1 B:HIS211 2.2 17.5 1.0 C2 B:FUD302 3.0 22.0 1.0 CD B:GLU246 3.1 21.1 1.0 CD B:GLU152 3.1 15.9 1.0 CE1 B:HIS211 3.1 19.1 1.0 C3 B:FUD302 3.2 25.2 1.0 CG B:ASP185 3.3 14.2 1.0 CG B:HIS211 3.3 16.3 1.0 OE2 B:GLU246 3.4 24.7 1.0 OE1 B:GLU152 3.4 20.6 1.0 CB B:HIS211 3.6 15.5 1.0 CB B:ASP185 3.9 15.8 1.0 O B:HOH505 4.0 22.7 1.0 O4 B:FUD302 4.1 34.3 1.0 NH1 B:ARG217 4.2 19.5 1.0 NE2 B:HIS211 4.3 16.4 1.0 C4 B:FUD302 4.3 31.6 1.0 OD1 B:ASP185 4.3 17.3 1.0 CD2 B:HIS211 4.4 18.0 1.0 CG B:GLU246 4.4 22.4 1.0 NE2 B:HIS188 4.4 14.8 1.0 CG B:GLU152 4.5 16.1 1.0 CD2 B:HIS188 4.5 15.8 1.0 C1 B:FUD302 4.5 18.7 1.0 NE2 B:HIS183 4.8 16.9 1.0 CB B:GLU246 4.9 20.7 1.0 O1 B:FUD302 4.9 17.1 1.0 CE1 B:HIS183 5.0 17.7 1.0

Manganese binding site 3 out of 8 in the Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. with Additional C-Terminal Residues


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. with Additional C-Terminal Residues within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn304 b:17.9 occ:1.00 OD2 C:ASP185 2.1 15.8 1.0 OE2 C:GLU246 2.1 17.8 1.0 OE2 C:GLU152 2.1 15.8 1.0 O3 C:FUD305 2.1 20.4 1.0 O2 C:FUD305 2.2 16.1 1.0 ND1 C:HIS211 2.3 15.3 1.0 C2 C:FUD305 3.0 18.6 1.0 CD C:GLU246 3.0 18.1 1.0 CD C:GLU152 3.1 15.0 1.0 C3 C:FUD305 3.1 20.1 1.0 CG C:ASP185 3.2 14.2 1.0 CE1 C:HIS211 3.2 15.5 1.0 CG C:HIS211 3.3 15.0 1.0 OE1 C:GLU246 3.4 17.4 1.0 OE1 C:GLU152 3.4 16.7 1.0 CB C:HIS211 3.6 14.6 1.0 CB C:ASP185 3.8 13.3 1.0 O C:HOH525 4.1 18.8 1.0 OD1 C:ASP185 4.2 16.2 1.0 NH2 C:ARG217 4.2 20.5 1.0 O4 C:FUD305 4.2 26.1 1.0 C4 C:FUD305 4.3 22.4 1.0 CG C:GLU246 4.3 17.0 1.0 NE2 C:HIS211 4.4 13.8 1.0 O5 C:FUD305 4.4 38.0 1.0 CG C:GLU152 4.4 14.1 1.0 CD2 C:HIS211 4.4 15.2 1.0 NE2 C:HIS188 4.4 13.3 1.0 C1 C:FUD305 4.5 16.2 1.0 CD2 C:HIS188 4.5 13.2 1.0 NE2 C:HIS183 4.8 13.2 1.0 O1 C:FUD305 4.9 16.4 1.0 C5 C:FUD305 4.9 25.8 1.0

Manganese binding site 4 out of 8 in the Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. with Additional C-Terminal Residues


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. with Additional C-Terminal Residues within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn302 b:21.3 occ:1.00 OD2 D:ASP185 2.1 15.9 1.0 OE2 D:GLU152 2.1 17.3 1.0 O2 D:FUD303 2.1 17.8 1.0 OE1 D:GLU246 2.2 19.9 1.0 O3 D:FUD303 2.2 26.3 1.0 ND1 D:HIS211 2.2 15.9 1.0 C2 D:FUD303 2.9 22.3 1.0 CD D:GLU246 3.1 23.3 1.0 CD D:GLU152 3.1 15.5 1.0 C3 D:FUD303 3.1 25.7 1.0 CE1 D:HIS211 3.1 18.1 1.0 CG D:ASP185 3.3 13.9 1.0 OE2 D:GLU246 3.3 28.9 1.0 CG D:HIS211 3.3 15.5 1.0 OE1 D:GLU152 3.4 19.0 1.0 CB D:HIS211 3.7 15.6 1.0 CB D:ASP185 3.9 14.7 1.0 O D:HOH486 4.0 22.0 1.0 O4 D:FUD303 4.2 30.7 1.0 NH1 D:ARG217 4.2 16.4 1.0 C4 D:FUD303 4.3 29.7 1.0 OD1 D:ASP185 4.3 15.9 1.0 NE2 D:HIS211 4.3 17.2 1.0 O5 D:FUD303 4.4 45.7 1.0 C1 D:FUD303 4.4 19.3 1.0 CD2 D:HIS211 4.4 15.5 1.0 CG D:GLU246 4.4 22.6 1.0 CG D:GLU152 4.4 15.7 1.0 CD2 D:HIS188 4.5 15.2 1.0 NE2 D:HIS188 4.5 15.2 1.0 NE2 D:HIS183 4.8 15.1 1.0 O1 D:FUD303 4.8 17.3 1.0 CB D:GLU246 4.9 20.2 1.0 CE1 D:HIS183 5.0 15.8 1.0 C5 D:FUD303 5.0 29.6 1.0

Manganese binding site 5 out of 8 in the Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. with Additional C-Terminal Residues


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. with Additional C-Terminal Residues within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn302 b:21.2 occ:1.00 OD2 E:ASP185 2.1 15.9 1.0 OE2 E:GLU152 2.1 17.4 1.0 OE1 E:GLU246 2.1 20.3 1.0 O3 E:FUD303 2.1 22.6 1.0 O2 E:FUD303 2.2 17.7 1.0 ND1 E:HIS211 2.3 17.2 1.0 C2 E:FUD303 3.0 20.4 1.0 CD E:GLU246 3.0 26.9 1.0 C3 E:FUD303 3.1 24.7 1.0 CD E:GLU152 3.1 18.4 1.0 CE1 E:HIS211 3.2 17.7 1.0 CG E:ASP185 3.2 15.2 1.0 OE2 E:GLU246 3.3 29.6 1.0 CG E:HIS211 3.3 16.2 1.0 OE1 E:GLU152 3.4 20.3 1.0 CB E:HIS211 3.6 15.0 1.0 CB E:ASP185 3.9 15.6 1.0 O E:HOH473 4.0 24.0 1.0 O4 E:FUD303 4.1 32.6 1.0 NH1 E:ARG217 4.2 17.0 1.0 C4 E:FUD303 4.2 27.6 1.0 OD1 E:ASP185 4.3 17.6 1.0 NE2 E:HIS211 4.4 17.6 1.0 C1 E:FUD303 4.4 18.0 1.0 CG E:GLU152 4.4 15.2 1.0 CG E:GLU246 4.4 25.2 1.0 CD2 E:HIS188 4.4 15.0 1.0 CD2 E:HIS211 4.4 17.1 1.0 NE2 E:HIS188 4.4 14.7 1.0 NE2 E:HIS183 4.8 13.8 1.0 O1 E:FUD303 4.9 16.1 1.0 CB E:GLU246 4.9 24.0 1.0

Manganese binding site 6 out of 8 in the Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. with Additional C-Terminal Residues


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. with Additional C-Terminal Residues within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn303 b:19.0 occ:1.00 OE2 F:GLU152 2.1 14.7 1.0 OD2 F:ASP185 2.1 14.8 1.0 OE2 F:GLU246 2.1 16.5 1.0 O3 F:FUD304 2.1 19.3 1.0 O2 F:FUD304 2.2 16.5 1.0 ND1 F:HIS211 2.2 16.0 1.0 C2 F:FUD304 3.0 18.5 1.0 CD F:GLU152 3.0 15.0 1.0 CD F:GLU246 3.1 16.6 1.0 C3 F:FUD304 3.1 19.5 1.0 CE1 F:HIS211 3.1 15.8 1.0 CG F:ASP185 3.2 13.4 1.0 CG F:HIS211 3.3 15.4 1.0 OE1 F:GLU152 3.4 18.1 1.0 OE1 F:GLU246 3.4 19.2 1.0 CB F:HIS211 3.6 14.1 1.0 CB F:ASP185 3.9 13.7 1.0 O F:HOH527 4.1 20.9 1.0 O4 F:FUD304 4.2 23.1 1.0 OD1 F:ASP185 4.3 16.0 1.0 C4 F:FUD304 4.3 23.7 1.0 NH2 F:ARG217 4.3 20.4 1.0 NE2 F:HIS211 4.3 16.2 1.0 CG F:GLU152 4.4 14.9 1.0 CD2 F:HIS211 4.4 15.3 1.0 CG F:GLU246 4.4 15.7 1.0 C1 F:FUD304 4.5 17.4 1.0 CD2 F:HIS188 4.5 14.2 1.0 NE2 F:HIS188 4.5 14.4 1.0 NE2 F:HIS183 4.8 14.0 1.0 O5 F:FUD304 4.8 36.7 1.0 O1 F:FUD304 4.9 14.1 1.0

Manganese binding site 7 out of 8 in the Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. with Additional C-Terminal Residues


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. with Additional C-Terminal Residues within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn301 b:23.9 occ:1.00 OD2 G:ASP185 2.1 17.1 1.0 OE2 G:GLU152 2.1 21.4 1.0 OE1 G:GLU246 2.2 22.8 1.0 O2 G:FUD302 2.2 21.3 1.0 ND1 G:HIS211 2.2 20.6 1.0 O3 G:FUD302 2.3 29.7 1.0 C2 G:FUD302 3.0 25.4 1.0 CD G:GLU152 3.1 20.7 1.0 CD G:GLU246 3.1 22.5 1.0 C3 G:FUD302 3.1 29.6 1.0 CE1 G:HIS211 3.1 21.5 1.0 CG G:HIS211 3.3 20.1 1.0 CG G:ASP185 3.3 18.7 1.0 OE2 G:GLU246 3.4 24.5 1.0 OE1 G:GLU152 3.4 21.4 1.0 CB G:HIS211 3.6 20.9 1.0 CB G:ASP185 3.9 17.0 1.0 O G:HOH473 4.0 25.1 1.0 NH1 G:ARG217 4.2 20.6 1.0 O4 G:FUD302 4.3 32.3 1.0 NE2 G:HIS211 4.3 19.0 1.0 OD1 G:ASP185 4.3 20.6 1.0 C4 G:FUD302 4.4 31.6 1.0 CD2 G:HIS211 4.4 21.5 1.0 NE2 G:HIS188 4.4 16.9 1.0 CD2 G:HIS188 4.4 16.7 1.0 C1 G:FUD302 4.4 23.2 1.0 CG G:GLU152 4.4 18.2 1.0 CG G:GLU246 4.5 24.8 1.0 NE2 G:HIS183 4.8 18.0 1.0 CB G:GLU246 4.9 23.0 1.0 O1 G:FUD302 4.9 18.9 1.0 CE1 G:HIS183 5.0 18.9 1.0

Manganese binding site 8 out of 8 in the Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. with Additional C-Terminal Residues


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of N-Terminal His-Tagged D-Allulose 3-Epimerase From Methylomonas Sp. with Additional C-Terminal Residues within 5.0Å range: probe atom residue distance (Å) B Occ H:Mn301 b:20.6 occ:1.00 OD2 H:ASP185 2.1 14.1 1.0 OE2 H:GLU246 2.1 17.8 1.0 O2 H:FUD302 2.1 15.3 1.0 OE2 H:GLU152 2.2 17.0 1.0 O3 H:FUD302 2.2 28.9 1.0 ND1 H:HIS211 2.3 17.6 1.0 C2 H:FUD302 3.0 18.9 1.0 CD H:GLU246 3.1 19.2 1.0 CD H:GLU152 3.1 15.7 1.0 CE1 H:HIS211 3.1 17.4 1.0 C3 H:FUD302 3.2 25.3 1.0 CG H:ASP185 3.2 13.0 1.0 CG H:HIS211 3.3 15.1 1.0 OE1 H:GLU246 3.4 25.8 1.0 OE1 H:GLU152 3.4 19.5 1.0 CB H:HIS211 3.7 13.9 1.0 CB H:ASP185 3.9 13.4 1.0 O H:HOH499 3.9 23.7 1.0 NH2 H:ARG217 4.2 17.7 1.0 OD1 H:ASP185 4.2 14.0 1.0 NE2 H:HIS211 4.3 15.3 1.0 CD2 H:HIS211 4.4 16.2 1.0 CG H:GLU246 4.4 17.1 1.0 C1 H:FUD302 4.4 17.0 1.0 CG H:GLU152 4.5 14.2 1.0 C4 H:FUD302 4.5 31.5 1.0 NE2 H:HIS188 4.5 14.4 1.0 CD2 H:HIS188 4.5 14.9 1.0 O4 H:FUD302 4.5 34.6 1.0 NE2 H:HIS183 4.8 14.2 1.0 O1 H:FUD302 4.8 14.7 1.0 CB H:GLU246 4.8 15.9 1.0 CE1 H:HIS183 5.0 13.3 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