Nickel in PDB 4zfb: Cytochrome P450 Pentamutant From BM3 Bound to Palmitic Acid

All present enzymatic activity of Cytochrome P450 Pentamutant From BM3 Bound to Palmitic Acid:
1.14.14.1; 1.6.2.4;

The structure of Cytochrome P450 Pentamutant From BM3 Bound to Palmitic Acid, PDB code: 4zfb was solved by W.E.Rogers, T.Othman, D.K.Heidary, T.Huxford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	117.93 / 2.84
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.679, 55.679, 707.577, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 27.4

The structure of Cytochrome P450 Pentamutant From BM3 Bound to Palmitic Acid also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Nickel atom in the Cytochrome P450 Pentamutant From BM3 Bound to Palmitic Acid (pdb code 4zfb). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Cytochrome P450 Pentamutant From BM3 Bound to Palmitic Acid, PDB code: 4zfb:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Cytochrome P450 Pentamutant From BM3 Bound to Palmitic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Cytochrome P450 Pentamutant From BM3 Bound to Palmitic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni504 b:59.0 occ:1.00 OE2 A:GLU348 2.0 55.7 1.0 OD2 A:ASP338 2.0 51.5 1.0 CG A:ASP338 3.0 51.2 1.0 CD A:GLU348 3.2 60.0 1.0 OD1 A:ASP338 3.4 53.5 1.0 OE1 A:GLU348 3.9 56.3 1.0 CG A:GLU348 4.2 59.8 1.0 CB A:ASP338 4.3 47.4 1.0

Nickel binding site 2 out of 4 in the Cytochrome P450 Pentamutant From BM3 Bound to Palmitic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Cytochrome P450 Pentamutant From BM3 Bound to Palmitic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni505 b:76.5 occ:1.00 CE1 A:HIS138 2.2 64.3 1.0 NE2 A:HIS138 2.3 63.8 1.0 NE2 A:HIS426 2.3 69.1 1.0 O A:HOH606 3.0 56.9 1.0 CD2 A:HIS426 3.1 64.8 1.0 CE1 A:HIS426 3.4 70.5 1.0 ND1 A:HIS138 3.5 62.3 1.0 CD2 A:HIS138 3.6 62.1 1.0 NZ A:LYS447 4.0 61.9 1.0 CG A:HIS138 4.2 59.2 1.0 CG A:HIS426 4.3 63.7 1.0 ND1 A:HIS426 4.4 64.5 1.0

Nickel binding site 3 out of 4 in the Cytochrome P450 Pentamutant From BM3 Bound to Palmitic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Cytochrome P450 Pentamutant From BM3 Bound to Palmitic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni506 b:65.9 occ:1.00 OD1 A:ASP214 2.6 54.3 1.0 CG A:ASP214 3.0 54.1 1.0 OD2 A:ASP214 3.1 53.7 1.0 NZ A:LYS210 3.8 59.4 1.0 OD2 A:ASP217 3.8 50.5 1.0 O A:HOH641 3.9 41.8 1.0 O A:LYS210 4.1 53.1 1.0 CB A:ASP214 4.1 50.3 1.0 CA A:ASP214 4.2 48.5 1.0 CG A:LYS210 4.4 61.6 1.0 N A:ASP214 4.4 47.6 1.0 C A:ASN213 4.9 46.9 1.0 CE A:LYS210 4.9 66.4 1.0

Nickel binding site 4 out of 4 in the Cytochrome P450 Pentamutant From BM3 Bound to Palmitic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Cytochrome P450 Pentamutant From BM3 Bound to Palmitic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni507 b:91.4 occ:1.00 CE1 A:HIS236 2.2 71.8 1.0 NE2 A:HIS236 2.6 69.5 1.0 OD1 A:ASP231 2.8 72.6 1.0 OD2 A:ASP231 2.9 71.0 1.0 CG A:ASP231 3.2 74.2 1.0 ND1 A:HIS236 3.4 64.4 1.0 CD2 A:HIS236 4.0 61.2 1.0 CG A:HIS236 4.3 54.8 1.0 CB A:ASP231 4.7 71.6 1.0

I.Geronimo, C.A.Denning, W.E.Rogers, T.Othman, T.Huxford, D.K.Heidary, E.C.Glazer, C.M.Payne. Effect of Mutation and Substrate Binding on the Stability of Cytochrome P450BM3 Variants. Biochemistry V. 55 3594 2016.
ISSN: ISSN 0006-2960
PubMed: 27267136
DOI: 10.1021/ACS.BIOCHEM.6B00183