Zinc in PDB 8snk: Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Mutant (Mfma/D188N)

The structure of Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Mutant (Mfma/D188N), PDB code: 8snk was solved by L.J.Tassoulas, J.A.Rankin, M.H.Elias, L.P.Wackett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.75 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.7, 162.3, 152.7, 90, 101.1, 90
R / Rfree (%)	18.8 / 22.3

The binding sites of Zinc atom in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Mutant (Mfma/D188N) (pdb code 8snk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Mutant (Mfma/D188N), PDB code: 8snk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Mutant (Mfma/D188N)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Mutant (Mfma/D188N) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn401 b:30.1 occ:1.00 OD2 I:ASP277 2.1 21.9 1.0 OD1 I:ASP184 2.1 22.5 1.0 OD2 I:ASP279 2.2 23.3 1.0 O I:HOH635 2.2 32.6 1.0 ND1 I:HIS186 2.4 29.8 1.0 OD1 I:ASP279 2.7 20.8 1.0 CG I:ASP279 2.7 20.9 1.0 CG I:ASP277 3.0 21.8 1.0 CG I:ASP184 3.1 26.9 1.0 CE1 I:HIS186 3.3 37.2 1.0 OD2 I:ASP184 3.4 26.0 1.0 CG I:HIS186 3.4 31.9 1.0 OD1 I:ASP277 3.7 21.4 1.0 CB I:HIS186 3.8 26.8 1.0 O I:HOH517 3.8 47.1 1.0 CB I:ASP277 4.0 23.5 1.0 N I:HIS186 4.2 23.7 1.0 CB I:ASP279 4.2 20.0 1.0 NE2 I:HIS186 4.4 32.8 1.0 CB I:ASP184 4.5 21.6 1.0 ND1 I:HIS159 4.5 25.1 1.0 CD2 I:HIS186 4.5 35.2 1.0 CA I:HIS186 4.6 24.7 1.0 N I:CYS185 4.6 25.0 1.0 ND2 I:ASN188 4.6 38.6 1.0 CB I:CYS185 4.9 27.3 1.0 CA I:ASP184 4.9 22.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Mutant (Mfma/D188N)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Mutant (Mfma/D188N) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:29.5 occ:1.00 O A:HOH679 2.0 34.4 1.0 OD1 A:ASP184 2.1 21.1 1.0 OD2 A:ASP277 2.2 22.3 1.0 OD2 A:ASP279 2.2 24.4 1.0 ND1 A:HIS186 2.2 27.9 1.0 OD1 A:ASP279 2.8 22.1 1.0 CG A:ASP279 2.8 22.2 1.0 CG A:ASP184 3.1 23.3 1.0 CG A:ASP277 3.1 24.6 1.0 CE1 A:HIS186 3.1 34.1 1.0 CG A:HIS186 3.2 29.6 1.0 OD2 A:ASP184 3.3 23.8 1.0 CB A:HIS186 3.6 27.5 1.0 OD1 A:ASP277 3.8 23.5 1.0 CB A:ASP277 4.0 24.6 1.0 N A:HIS186 4.2 26.2 1.0 O A:HOH505 4.2 33.5 1.0 NE2 A:HIS186 4.3 34.8 1.0 CB A:ASP279 4.3 20.8 1.0 CD2 A:HIS186 4.3 31.3 1.0 CB A:ASP184 4.4 22.1 1.0 N A:CYS185 4.5 21.0 1.0 ND1 A:HIS159 4.5 25.1 1.0 CA A:HIS186 4.6 24.2 1.0 ND2 A:ASN188 4.6 32.5 1.0 CA A:ASP184 4.9 23.4 1.0 CB A:CYS185 4.9 27.4 1.0

L.J.Tassoulas, J.A.Rankin, M.H.Elias, L.P.Wackett. Dinickel Enzyme Evolved to Metabolize the Pharmaceutical Metformin and Its Implications For Wastewater and Human Microbiomes. Proc.Natl.Acad.Sci.Usa V. 121 52121 2024.
ISSN: ESSN 1091-6490
PubMed: 38408229
DOI: 10.1073/PNAS.2312652121