Nickel in PDB 8snf: Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 with NI2+2 Bound

The structure of Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 with NI2+2 Bound, PDB code: 8snf 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)	19.87 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	83.4, 96.4, 96.7, 115.5, 106.2, 101.1
R / Rfree (%)	17.2 / 21.9

The binding sites of Nickel atom in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 with NI2+2 Bound (pdb code 8snf). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 with NI2+2 Bound, PDB code: 8snf:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 with NI2+2 Bound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 with NI2+2 Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni401 b:112.8 occ:1.00 OD1 D:ASP279 2.2 98.1 1.0 OD2 D:ASP184 2.5 67.0 1.0 NI D:NI402 2.5 87.4 1.0 ND1 D:HIS186 2.6 108.9 1.0 OD2 D:ASP277 2.7 67.1 1.0 CG D:ASP279 3.1 81.8 1.0 OD1 D:ASP184 3.2 66.0 1.0 CG D:ASP184 3.2 66.5 1.0 CG D:ASP277 3.3 67.5 1.0 OD2 D:ASP279 3.4 83.0 1.0 CE1 D:HIS186 3.4 105.9 1.0 CG D:HIS186 3.5 99.4 1.0 CB D:HIS186 3.8 83.6 1.0 OD1 D:ASP277 3.8 67.4 1.0 O D:HOH522 4.0 83.1 1.0 N D:HIS186 4.2 64.8 1.0 CB D:ASP277 4.2 68.3 1.0 OD1 D:ASP188 4.3 75.2 1.0 OD2 D:ASP188 4.5 88.9 1.0 NE2 D:HIS186 4.5 110.0 1.0 ND1 D:HIS159 4.5 64.2 1.0 CB D:ASP279 4.5 74.4 1.0 CD2 D:HIS186 4.5 104.8 1.0 CA D:HIS186 4.6 78.1 1.0 CB D:ASP184 4.7 66.5 1.0 CG D:ASP188 4.8 74.2 1.0 N D:CYS185 4.9 61.0 1.0 CB D:CYS185 4.9 70.0 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 with NI2+2 Bound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 with NI2+2 Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni402 b:87.4 occ:1.00 OD1 D:ASP184 2.2 66.0 1.0 OD2 D:ASP188 2.3 88.9 1.0 ND1 D:HIS159 2.3 64.2 1.0 OD2 D:ASP277 2.5 67.1 1.0 NI D:NI401 2.5 112.8 1.0 CG D:ASP188 3.1 74.2 1.0 CG D:ASP184 3.2 66.5 1.0 CE1 D:HIS159 3.2 73.3 1.0 CG D:HIS159 3.2 64.8 1.0 OD1 D:ASP188 3.2 75.2 1.0 OD2 D:ASP184 3.4 67.0 1.0 CB D:HIS159 3.5 68.4 1.0 CG D:ASP277 3.6 67.5 1.0 CB D:ASP277 4.1 68.3 1.0 O D:ASN200 4.1 82.9 1.0 NE2 D:HIS159 4.3 63.7 1.0 CD2 D:HIS159 4.3 66.5 1.0 NE2 D:HIS182 4.4 63.9 1.0 CB D:ASP188 4.5 71.6 1.0 CB D:ASP184 4.5 66.5 1.0 ND1 D:HIS186 4.6 108.9 1.0 OD1 D:ASP277 4.6 67.4 1.0 OD1 D:ASP279 4.6 98.1 1.0 CB D:HIS186 4.8 83.6 1.0 O D:HIS186 5.0 75.4 1.0 CE1 D:HIS182 5.0 72.2 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 with NI2+2 Bound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 with NI2+2 Bound within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni401 b:95.2 occ:1.00 OD2 F:ASP184 2.3 76.6 1.0 OD2 F:ASP188 2.3 89.7 1.0 ND1 F:HIS159 2.4 68.1 1.0 OD2 F:ASP277 2.5 73.8 1.0 NI F:NI402 2.6 125.5 1.0 CG F:ASP188 3.1 85.9 1.0 CG F:ASP184 3.2 71.8 1.0 CG F:HIS159 3.3 64.7 1.0 OD1 F:ASP188 3.3 91.8 1.0 CE1 F:HIS159 3.3 75.5 1.0 OD1 F:ASP184 3.4 66.2 1.0 CB F:HIS159 3.5 61.5 1.0 CG F:ASP277 3.6 62.5 1.0 CB F:ASP277 4.0 62.4 1.0 O F:ASN200 4.1 87.7 1.0 NE2 F:HIS182 4.3 66.2 1.0 CD2 F:HIS159 4.4 72.5 1.0 NE2 F:HIS159 4.4 74.8 1.0 CB F:ASP188 4.5 87.3 1.0 CB F:ASP184 4.6 70.5 1.0 OD1 F:ASP277 4.7 68.8 1.0 OD2 F:ASP279 4.8 108.3 1.0 CE1 F:HIS182 4.9 77.7 1.0 CB F:HIS186 5.0 88.6 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 with NI2+2 Bound


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 with NI2+2 Bound within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni402 b:125.5 occ:1.00 OD2 F:ASP279 2.5 108.3 1.0 OD1 F:ASP184 2.5 66.2 1.0 NI F:NI401 2.6 95.2 1.0 OD2 F:ASP277 2.6 73.8 1.0 ND1 F:HIS186 2.9 116.0 1.0 CG F:ASP184 3.3 71.8 1.0 OD2 F:ASP184 3.3 76.6 1.0 CG F:ASP279 3.3 82.5 1.0 CG F:ASP277 3.4 62.5 1.0 OD1 F:ASP279 3.5 83.1 1.0 CG F:HIS186 3.7 102.4 1.0 CB F:HIS186 3.8 88.6 1.0 CE1 F:HIS186 3.9 116.0 1.0 OD1 F:ASP277 4.0 68.8 1.0 OD1 F:ASP188 4.2 91.8 1.0 CB F:ASP277 4.3 62.4 1.0 N F:HIS186 4.3 80.9 1.0 OD2 F:ASP188 4.5 89.7 1.0 ND1 F:HIS159 4.6 68.1 1.0 CA F:HIS186 4.6 86.5 1.0 CB F:ASP279 4.7 70.9 1.0 CB F:ASP184 4.7 70.5 1.0 CG F:ASP188 4.7 85.9 1.0 CB F:CYS185 4.8 74.3 1.0 CD2 F:HIS186 4.9 115.4 1.0 NE2 F:HIS186 4.9 117.1 1.0 N F:CYS185 5.0 73.0 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