Manganese in PDB 8x3g: Crystal Structure of Metformin Hydrolase From Aminobacter

The structure of Crystal Structure of Metformin Hydrolase From Aminobacter, PDB code: 8x3g was solved by T.Li, N.Y.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.47 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.43, 152.522, 173.572, 90, 90, 90
R / Rfree (%)	15.3 / 18.2

The binding sites of Manganese atom in the Crystal Structure of Metformin Hydrolase From Aminobacter (pdb code 8x3g). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Metformin Hydrolase From Aminobacter, PDB code: 8x3g:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Metformin Hydrolase From Aminobacter


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 Metformin Hydrolase From Aminobacter within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:26.7 occ:1.00 OD2 A:ASP183 2.2 15.9 1.0 OD2 A:ASP187 2.2 18.6 1.0 ND1 A:HIS158 2.4 14.8 1.0 O1 A:GOL401 2.5 28.2 1.0 OD2 A:ASP276 2.5 15.6 1.0 C3 A:GOL401 2.5 23.2 1.0 O3 A:GOL401 2.7 42.1 1.0 MN A:MN403 2.7 39.9 1.0 CG A:ASP183 3.1 18.5 1.0 CG A:ASP187 3.2 19.3 1.0 OD1 A:ASP183 3.3 16.2 1.0 CG A:HIS158 3.3 14.7 1.0 CE1 A:HIS158 3.3 17.3 1.0 C1 A:GOL401 3.4 29.1 1.0 C2 A:GOL401 3.5 25.2 1.0 OD1 A:ASP187 3.5 20.8 1.0 O2 A:GOL401 3.5 26.5 1.0 CB A:HIS158 3.6 14.5 1.0 CG A:ASP276 3.6 15.0 1.0 CB A:ASP276 4.1 14.7 1.0 NE2 A:HIS181 4.4 18.0 1.0 O A:ASN199 4.4 19.8 1.0 OD2 A:ASP278 4.4 24.9 1.0 NE2 A:HIS158 4.5 14.2 1.0 CD2 A:HIS158 4.5 12.5 1.0 CB A:ASP183 4.5 14.9 1.0 ND1 A:HIS185 4.6 16.7 1.0 CB A:ASP187 4.6 14.7 1.0 CB A:HIS185 4.6 12.7 1.0 OD1 A:ASP276 4.7 17.3 1.0 OE2 A:GLU320 4.8 17.8 1.0 O A:HIS185 4.9 16.1 1.0 O A:HOH683 4.9 14.8 1.0 CG A:GLU320 5.0 16.1 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Metformin Hydrolase From Aminobacter


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 Metformin Hydrolase From Aminobacter within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:39.9 occ:1.00 OD2 A:ASP278 1.7 24.9 1.0 OD2 A:ASP276 2.2 15.6 1.0 OD1 A:ASP183 2.3 16.2 1.0 O2 A:GOL401 2.4 26.5 1.0 ND1 A:HIS185 2.5 16.7 1.0 CG A:ASP278 2.7 19.0 1.0 MN A:MN402 2.7 26.7 1.0 O1 A:GOL401 2.8 28.2 1.0 OD1 A:ASP278 3.0 20.1 1.0 CG A:ASP276 3.1 15.0 1.0 CG A:ASP183 3.1 18.5 1.0 OD2 A:ASP183 3.3 15.9 1.0 CE1 A:HIS185 3.3 17.2 1.0 C2 A:GOL401 3.4 25.2 1.0 CG A:HIS185 3.5 17.3 1.0 C3 A:GOL401 3.5 23.2 1.0 O A:HOH557 3.5 25.9 1.0 C1 A:GOL401 3.6 29.1 1.0 OD1 A:ASP276 3.7 17.3 1.0 CB A:HIS185 3.8 12.7 1.0 CB A:ASP276 4.0 14.7 1.0 CB A:ASP278 4.0 17.0 1.0 N A:HIS185 4.3 14.2 1.0 O3 A:GOL401 4.3 42.1 1.0 NE2 A:HIS185 4.4 15.5 1.0 CD2 A:HIS185 4.6 16.5 1.0 CB A:ASP183 4.6 14.9 1.0 OD2 A:ASP187 4.6 18.6 1.0 N A:CYS184 4.6 14.9 1.0 CA A:HIS185 4.7 15.2 1.0 ND1 A:HIS158 4.7 14.8 1.0 OD1 A:ASP187 4.8 20.8 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Metformin Hydrolase From Aminobacter


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 Metformin Hydrolase From Aminobacter within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:30.8 occ:1.00 O2 B:GOL401 1.9 21.5 1.0 C2 B:GOL401 2.1 26.2 1.0 O1 B:GOL401 2.3 23.5 1.0 OD2 B:ASP187 2.4 17.5 1.0 ND1 B:HIS158 2.5 13.7 1.0 MN B:MN403 2.6 47.5 1.0 OD2 B:ASP276 2.7 12.3 1.0 OD2 B:ASP183 2.7 18.4 1.0 C1 B:GOL401 2.7 28.6 1.0 CG B:ASP187 3.3 21.6 1.0 CG B:HIS158 3.3 13.4 1.0 C3 B:GOL401 3.3 31.3 1.0 CB B:HIS158 3.3 14.7 1.0 O3 B:GOL401 3.4 26.5 1.0 OD1 B:ASP187 3.5 19.6 1.0 CG B:ASP183 3.6 13.9 1.0 CE1 B:HIS158 3.6 13.0 1.0 OD1 B:ASP183 3.7 14.4 1.0 CG B:ASP276 3.8 14.2 1.0 O B:ASN199 4.1 16.9 1.0 OE2 B:GLU320 4.4 19.4 1.0 CB B:ASP276 4.4 15.3 1.0 OD2 B:ASP278 4.5 28.0 1.0 CD2 B:HIS158 4.5 13.1 1.0 ND1 B:HIS185 4.6 16.1 1.0 NE2 B:HIS158 4.6 13.1 1.0 CB B:ASP187 4.7 14.2 1.0 NE2 B:HIS181 4.7 14.5 1.0 CB B:HIS185 4.7 18.0 1.0 CG B:GLU320 4.8 15.7 1.0 O B:HOH693 4.8 14.6 1.0 CA B:HIS158 4.8 13.5 1.0 OD1 B:ASP276 4.8 16.6 1.0 O B:HOH516 4.9 30.9 1.0 CB B:ASP183 5.0 10.1 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Metformin Hydrolase From Aminobacter


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 Metformin Hydrolase From Aminobacter within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn403 b:47.5 occ:1.00 OD2 B:ASP278 2.1 28.0 1.0 OD1 B:ASP183 2.2 14.4 1.0 OD2 B:ASP276 2.3 12.3 1.0 O1 B:GOL401 2.4 23.5 1.0 O3 B:GOL401 2.4 26.5 1.0 ND1 B:HIS185 2.4 16.1 1.0 MN B:MN402 2.6 30.8 1.0 C2 B:GOL401 2.9 26.2 1.0 CG B:ASP183 3.0 13.9 1.0 OD2 B:ASP183 3.1 18.4 1.0 CG B:ASP278 3.1 14.0 1.0 CG B:ASP276 3.2 14.2 1.0 C3 B:GOL401 3.3 31.3 1.0 CG B:HIS185 3.3 19.2 1.0 OD1 B:ASP278 3.4 17.5 1.0 C1 B:GOL401 3.4 28.6 1.0 CE1 B:HIS185 3.4 18.1 1.0 CB B:HIS185 3.5 18.0 1.0 O B:HOH516 3.7 30.9 1.0 O2 B:GOL401 3.7 21.5 1.0 OD1 B:ASP276 4.0 16.6 1.0 CB B:ASP276 4.1 15.3 1.0 N B:HIS185 4.2 11.5 1.0 OD2 B:ASP187 4.2 17.5 1.0 OD1 B:ASP187 4.4 19.6 1.0 CB B:ASP278 4.4 15.8 1.0 CA B:HIS185 4.5 12.4 1.0 CB B:ASP183 4.5 10.1 1.0 ND1 B:HIS158 4.5 13.7 1.0 CD2 B:HIS185 4.5 15.1 1.0 NE2 B:HIS185 4.5 15.1 1.0 CG B:ASP187 4.7 21.6 1.0 N B:CYS184 4.8 12.4 1.0 O B:HIS185 4.9 13.5 1.0

T.Li, Z.J.Xu, S.T.Zhang, J.Xu, P.Pan, N.Y.Zhou. Discovery of A Ni 2+ -Dependent Heterohexameric Metformin Hydrolase. Nat Commun V. 15 6121 2024.
ISSN: ESSN 2041-1723
PubMed: 39033196
DOI: 10.1038/S41467-024-50409-7