Nickel in PDB 8sp2: Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form

The structure of Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form, PDB code: 8sp2 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)	74.61 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	103.53, 107.88, 114.51, 93.43, 97.63, 98.11
R / Rfree (%)	21.3 / 25.7

The binding sites of Nickel atom in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form (pdb code 8sp2). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form, PDB code: 8sp2:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form


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 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ G:Ni401 b:49.2 occ:1.00 OD2 G:ASP279 2.2 30.9 1.0 ND1 G:HIS186 2.2 43.3 1.0 OD1 G:ASP184 2.2 31.2 1.0 OD2 G:ASP277 2.4 36.6 1.0 CG G:ASP279 2.8 27.0 1.0 OD1 G:ASP279 2.9 25.3 1.0 NI G:NI402 3.0 49.9 1.0 CG G:ASP277 3.1 39.3 1.0 CE1 G:HIS186 3.1 47.5 1.0 CG G:ASP184 3.1 39.6 1.0 CG G:HIS186 3.2 47.3 1.0 OD2 G:ASP184 3.3 37.5 1.0 OD1 G:ASP277 3.7 34.7 1.0 CB G:HIS186 3.7 42.7 1.0 O G:HOH505 3.8 61.2 1.0 CB G:ASP277 3.9 36.6 1.0 N G:HIS186 4.2 46.1 1.0 NE2 G:HIS186 4.2 47.3 1.0 CB G:ASP279 4.3 27.8 1.0 CD2 G:HIS186 4.3 48.3 1.0 CB G:ASP184 4.5 40.1 1.0 CA G:HIS186 4.6 43.5 1.0 N G:CYS185 4.6 45.5 1.0 OD1 G:ASP188 4.7 41.0 1.0 ND1 G:HIS159 4.7 41.5 1.0 CB G:CYS185 4.9 48.4 1.0

Nickel binding site 2 out of 8 in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form


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 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ G:Ni402 b:49.9 occ:1.00 OD2 G:ASP184 2.1 37.5 1.0 ND1 G:HIS159 2.2 41.5 1.0 OD2 G:ASP188 2.3 43.1 1.0 OD2 G:ASP277 2.6 36.6 1.0 NI G:NI401 3.0 49.2 1.0 CG G:ASP188 3.0 44.0 1.0 OD1 G:ASP188 3.1 41.0 1.0 CG G:ASP184 3.1 39.6 1.0 CE1 G:HIS159 3.2 43.7 1.0 CG G:HIS159 3.2 39.8 1.0 OD1 G:ASP184 3.5 31.2 1.0 CB G:HIS159 3.5 41.8 1.0 CG G:ASP277 3.8 39.3 1.0 O G:ASN200 4.2 60.4 1.0 CB G:ASP277 4.3 36.6 1.0 NE2 G:HIS182 4.3 35.1 1.0 NE2 G:HIS159 4.3 37.8 1.0 CD2 G:HIS159 4.3 38.1 1.0 CB G:ASP188 4.4 48.0 1.0 ND1 G:HIS186 4.4 43.3 1.0 CB G:HIS186 4.4 42.7 1.0 CB G:ASP184 4.5 40.1 1.0 O G:HOH556 4.7 37.6 1.0 CE1 G:HIS182 4.8 35.0 1.0 OD1 G:ASP277 4.8 34.7 1.0 O G:HIS186 4.8 42.6 1.0 CG G:HIS186 4.9 47.3 1.0 OD2 G:ASP279 4.9 30.9 1.0

Nickel binding site 3 out of 8 in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form


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 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni401 b:50.0 occ:1.00 OD2 H:ASP279 2.1 33.7 1.0 OD2 H:ASP277 2.2 31.1 1.0 ND1 H:HIS186 2.2 46.2 1.0 OD1 H:ASP184 2.4 33.4 1.0 CG H:ASP279 2.8 33.8 1.0 OD1 H:ASP279 2.9 33.0 1.0 NI H:NI402 3.0 47.5 1.0 CG H:ASP277 3.0 36.9 1.0 CE1 H:HIS186 3.1 50.9 1.0 CG H:ASP184 3.1 35.0 1.0 OD2 H:ASP184 3.2 36.7 1.0 CG H:HIS186 3.3 45.7 1.0 O H:HOH522 3.6 45.4 1.0 OD1 H:ASP277 3.6 31.5 1.0 CB H:HIS186 3.7 44.0 1.0 CB H:ASP277 4.0 35.5 1.0 N H:HIS186 4.2 43.2 1.0 NE2 H:HIS186 4.2 52.5 1.0 CB H:ASP279 4.3 31.5 1.0 CD2 H:HIS186 4.3 49.4 1.0 CA H:HIS186 4.5 44.3 1.0 CB H:ASP184 4.6 35.9 1.0 ND1 H:HIS159 4.6 32.4 1.0 N H:CYS185 4.7 47.1 1.0 OD1 H:ASP188 4.7 41.4 1.0

Nickel binding site 4 out of 8 in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form


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 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni402 b:47.5 occ:1.00 OD2 H:ASP184 2.1 36.7 1.0 ND1 H:HIS159 2.1 32.4 1.0 OD2 H:ASP188 2.2 38.9 1.0 OD2 H:ASP277 2.6 31.1 1.0 CG H:ASP188 2.9 39.5 1.0 NI H:NI401 3.0 50.0 1.0 OD1 H:ASP188 3.1 41.4 1.0 CE1 H:HIS159 3.1 34.3 1.0 CG H:ASP184 3.1 35.0 1.0 CG H:HIS159 3.2 36.8 1.0 CB H:HIS159 3.5 37.4 1.0 OD1 H:ASP184 3.6 33.4 1.0 CG H:ASP277 3.7 36.9 1.0 O H:ASN200 4.1 55.3 1.0 NE2 H:HIS182 4.2 40.6 1.0 CB H:ASP277 4.2 35.5 1.0 NE2 H:HIS159 4.2 36.3 1.0 CD2 H:HIS159 4.3 36.8 1.0 CB H:ASP188 4.4 40.4 1.0 CB H:ASP184 4.4 35.9 1.0 ND1 H:HIS186 4.5 46.2 1.0 CB H:HIS186 4.5 44.0 1.0 CE1 H:HIS182 4.7 40.1 1.0 O H:HIS186 4.7 41.0 1.0 OD1 H:ASP277 4.8 31.5 1.0 OD2 H:ASP279 4.9 33.7 1.0

Nickel binding site 5 out of 8 in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ I:Ni401 b:55.9 occ:1.00 OD2 I:ASP277 2.0 38.2 1.0 OD2 I:ASP279 2.3 44.6 1.0 OD1 I:ASP184 2.3 33.8 1.0 ND1 I:HIS186 2.4 58.5 1.0 CG I:ASP279 2.9 39.8 1.0 NI I:NI402 2.9 56.3 1.0 OD1 I:ASP279 2.9 38.4 1.0 CG I:ASP277 3.1 44.3 1.0 CG I:ASP184 3.1 37.6 1.0 OD2 I:ASP184 3.2 38.2 1.0 CG I:HIS186 3.3 57.4 1.0 CE1 I:HIS186 3.3 59.1 1.0 CB I:HIS186 3.6 52.0 1.0 OD1 I:ASP277 3.8 46.4 1.0 CB I:ASP277 4.0 41.2 1.0 N I:HIS186 4.2 50.9 1.0 CB I:ASP279 4.4 38.2 1.0 NE2 I:HIS186 4.4 60.2 1.0 CD2 I:HIS186 4.4 61.1 1.0 CA I:HIS186 4.5 49.5 1.0 CB I:ASP184 4.6 39.8 1.0 SG I:CYS185 4.6 68.7 1.0 OD1 I:ASP188 4.6 39.5 1.0 ND1 I:HIS159 4.7 41.4 1.0 N I:CYS185 4.7 49.8 1.0

Nickel binding site 6 out of 8 in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ I:Ni402 b:56.3 occ:1.00 OD2 I:ASP184 2.2 38.2 1.0 ND1 I:HIS159 2.3 41.4 1.0 OD2 I:ASP188 2.4 47.5 1.0 OD2 I:ASP277 2.8 38.2 1.0 OD1 I:ASP188 2.9 39.5 1.0 NI I:NI401 2.9 55.9 1.0 CG I:ASP188 3.0 43.2 1.0 CG I:HIS159 3.2 44.7 1.0 CG I:ASP184 3.2 37.6 1.0 CE1 I:HIS159 3.3 45.1 1.0 CB I:HIS159 3.5 45.2 1.0 OD1 I:ASP184 3.6 33.8 1.0 CG I:ASP277 3.8 44.3 1.0 O I:ASN200 4.1 63.7 1.0 CB I:ASP277 4.3 41.2 1.0 NE2 I:HIS182 4.3 35.7 1.0 CD2 I:HIS159 4.4 45.7 1.0 NE2 I:HIS159 4.4 44.2 1.0 CB I:ASP188 4.5 44.6 1.0 CB I:HIS186 4.5 52.0 1.0 CB I:ASP184 4.6 39.8 1.0 ND1 I:HIS186 4.6 58.5 1.0 O I:HIS186 4.8 40.5 1.0 CE1 I:HIS182 4.8 37.7 1.0 OD1 I:ASP277 4.9 46.4 1.0

Nickel binding site 7 out of 8 in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ J:Ni401 b:59.2 occ:1.00 OD2 J:ASP277 2.0 49.5 1.0 OD2 J:ASP279 2.2 41.0 1.0 ND1 J:HIS186 2.3 66.5 1.0 OD1 J:ASP184 2.3 41.8 1.0 O J:HOH567 2.5 49.0 1.0 CG J:ASP279 2.9 38.3 1.0 NI J:NI402 2.9 63.9 1.0 OD1 J:ASP279 3.0 37.4 1.0 CG J:ASP277 3.1 45.0 1.0 CG J:ASP184 3.1 47.6 1.0 CE1 J:HIS186 3.2 63.6 1.0 OD2 J:ASP184 3.2 46.7 1.0 CG J:HIS186 3.3 67.5 1.0 CB J:HIS186 3.6 61.3 1.0 OD1 J:ASP277 3.8 47.5 1.0 CB J:ASP277 4.0 43.3 1.0 N J:HIS186 4.2 56.0 1.0 NE2 J:HIS186 4.3 65.7 1.0 CD2 J:HIS186 4.3 64.5 1.0 CB J:ASP279 4.4 35.5 1.0 CB J:ASP184 4.5 49.3 1.0 CA J:HIS186 4.6 57.2 1.0 SG J:CYS185 4.6 68.1 1.0 N J:CYS185 4.7 51.8 1.0 OD2 J:ASP188 4.7 52.8 1.0 ND1 J:HIS159 4.7 45.6 1.0 OD1 J:ASP188 4.8 49.0 1.0

Nickel binding site 8 out of 8 in the Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of Metformin Hydrolase (Mfmab) From Pseudomonas Mendocina Sp. Met-2 Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ J:Ni402 b:63.9 occ:1.00 OD2 J:ASP184 2.2 46.7 1.0 OD2 J:ASP188 2.2 52.8 1.0 ND1 J:HIS159 2.3 45.6 1.0 O J:HOH567 2.4 49.0 1.0 OD2 J:ASP277 2.8 49.5 1.0 NI J:NI401 2.9 59.2 1.0 CG J:ASP188 3.0 51.4 1.0 CG J:ASP184 3.2 47.6 1.0 OD1 J:ASP188 3.2 49.0 1.0 CG J:HIS159 3.2 43.7 1.0 CE1 J:HIS159 3.4 45.7 1.0 CB J:HIS159 3.5 43.4 1.0 OD1 J:ASP184 3.5 41.8 1.0 CG J:ASP277 3.8 45.0 1.0 O J:ASN200 4.2 68.7 1.0 NE2 J:HIS182 4.3 44.1 1.0 CB J:ASP277 4.3 43.3 1.0 CD2 J:HIS159 4.4 45.8 1.0 NE2 J:HIS159 4.4 45.1 1.0 CB J:ASP188 4.5 54.6 1.0 CB J:HIS186 4.5 61.3 1.0 CB J:ASP184 4.5 49.3 1.0 ND1 J:HIS186 4.5 66.5 1.0 CE1 J:HIS182 4.9 42.7 1.0 OD1 J:ASP277 4.9 47.5 1.0 OD2 J:ASP279 4.9 41.0 1.0 O J:HIS186 4.9 52.5 1.0 OE1 J:GLU321 5.0 64.5 1.0 CG J:HIS186 5.0 67.5 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