Nickel in PDB 6isr: Structure of Lipase Mutant with Cys-His-Asp Catalytic Triad

All present enzymatic activity of Structure of Lipase Mutant with Cys-His-Asp Catalytic Triad:
3.1.1.3;

The structure of Structure of Lipase Mutant with Cys-His-Asp Catalytic Triad, PDB code: 6isr was solved by Y.X.Cen, J.H.Zhou, Q.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.25 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.288, 44.559, 132.947, 90.00, 89.41, 90.00
R / Rfree (%)	17.9 / 22.8

The binding sites of Nickel atom in the Structure of Lipase Mutant with Cys-His-Asp Catalytic Triad (pdb code 6isr). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of Lipase Mutant with Cys-His-Asp Catalytic Triad, PDB code: 6isr:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of Lipase Mutant with Cys-His-Asp Catalytic Triad


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Lipase Mutant with Cys-His-Asp Catalytic Triad within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:70.7 occ:1.00 NE2 A:HIS224 2.4 46.0 1.0 O A:HOH525 2.7 43.5 1.0 SG A:CYS105 2.7 46.0 1.0 CB A:CYS105 3.0 41.7 1.0 CD2 A:HIS224 3.1 44.9 1.0 CE1 A:HIS224 3.5 45.9 1.0 CA A:PRO280 4.3 90.5 1.0 CG A:HIS224 4.3 44.6 1.0 N A:THR40 4.4 35.5 1.0 CA A:CYS105 4.5 37.7 1.0 ND1 A:HIS224 4.5 46.2 1.0 O A:THR40 4.6 37.2 1.0 CA A:GLY39 4.7 35.2 1.0 CG2 A:ILE189 4.7 32.6 1.0 CB A:PRO280 4.7 90.5 1.0 C A:GLY39 4.9 34.3 1.0 O A:PRO280 4.9 90.5 1.0 N A:PRO280 5.0 91.2 1.0

Nickel binding site 2 out of 2 in the Structure of Lipase Mutant with Cys-His-Asp Catalytic Triad


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Lipase Mutant with Cys-His-Asp Catalytic Triad within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:69.9 occ:1.00 NE2 B:HIS224 2.3 48.2 1.0 SG B:CYS105 2.6 43.3 1.0 O B:HOH525 2.8 41.3 1.0 CB B:CYS105 2.9 40.1 1.0 CD2 B:HIS224 3.2 48.1 1.0 CE1 B:HIS224 3.4 47.7 1.0 CB B:PRO280 4.0 93.9 1.0 CG B:HIS224 4.4 47.1 1.0 CA B:CYS105 4.4 36.3 1.0 N B:THR40 4.4 38.2 1.0 CD B:PRO280 4.4 92.3 1.0 CA B:PRO280 4.5 94.6 1.0 ND1 B:HIS224 4.5 47.7 1.0 CG B:PRO280 4.5 92.7 1.0 CG2 B:ILE189 4.6 30.1 1.0 O B:THR40 4.6 43.6 1.0 CA B:GLY39 4.8 36.1 1.0 N B:PRO280 4.8 93.0 1.0 CB B:THR40 4.9 40.9 1.0 C B:GLY39 5.0 36.9 1.0

Y.Cen, W.Singh, M.Arkin, T.S.Moody, M.Huang, J.Zhou, Q.Wu, M.T.Reetz. Artificial Cysteine-Lipases with High Activity and Altered Catalytic Mechanism Created By Laboratory Evolution. Nat Commun V. 10 3198 2019.
ISSN: ESSN 2041-1723
PubMed: 31324776
DOI: 10.1038/S41467-019-11155-3