Zinc in PDB 2x7y: P450 BM3 F87A in Complex with Dmso

All present enzymatic activity of P450 BM3 F87A in Complex with Dmso:
1.14.14.1;

The structure of P450 BM3 F87A in Complex with Dmso, PDB code: 2x7y was solved by J.Kuper, T.S.Wong, D.Roccatano, M.Wilmanns, U.Schwaneberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.54 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.976, 87.880, 159.592, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.3

The structure of P450 BM3 F87A in Complex with Dmso also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the P450 BM3 F87A in Complex with Dmso (pdb code 2x7y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the P450 BM3 F87A in Complex with Dmso, PDB code: 2x7y:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the P450 BM3 F87A in Complex with Dmso


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of P450 BM3 F87A in Complex with Dmso within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1457 b:23.8 occ:1.00 OD1 A:ASP231 2.0 23.9 1.0 NE2 A:HIS236 2.0 23.9 1.0 O A:HOH2278 2.2 17.0 1.0 CG A:ASP231 2.8 25.5 1.0 CD2 A:HIS236 3.0 24.4 1.0 OD2 A:ASP231 3.0 26.6 1.0 CE1 A:HIS236 3.0 24.0 1.0 ND1 A:HIS236 4.1 23.7 1.0 CG A:HIS236 4.1 22.3 1.0 O A:HOH2141 4.1 34.5 1.0 CB A:ASP231 4.3 24.6 1.0 O A:HOH2142 4.5 39.1 1.0 O A:HOH2083 4.7 32.0 1.0 C A:ASP231 4.8 24.0 1.0 O A:ASP231 4.8 23.9 1.0 CA A:ASP231 4.8 24.2 1.0

Zinc binding site 2 out of 4 in the P450 BM3 F87A in Complex with Dmso


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of P450 BM3 F87A in Complex with Dmso within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1458 b:67.7 occ:1.00 NE2 A:HIS92 2.3 28.5 1.0 CD2 A:HIS92 3.2 24.8 1.0 CE1 A:HIS92 3.3 27.4 1.0 NZ A:LYS336 3.7 32.0 1.0 CE A:LYS336 4.0 28.1 1.0 OD2 A:ASP68 4.0 34.2 1.0 ND1 A:HIS92 4.4 25.2 1.0 CG A:HIS92 4.4 22.4 1.0 CG A:ASP68 4.5 28.2 1.0 CB A:ASP68 4.9 20.6 1.0 CD A:LYS336 5.0 25.6 1.0

Zinc binding site 3 out of 4 in the P450 BM3 F87A in Complex with Dmso


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of P450 BM3 F87A in Complex with Dmso within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1459 b:23.4 occ:1.00 OD2 A:ASP338 2.0 16.2 1.0 OE1 A:GLU348 2.1 23.5 1.0 OD1 A:ASP338 2.5 20.2 1.0 CG A:ASP338 2.5 20.1 1.0 OE2 A:GLU348 2.5 23.0 1.0 CD A:GLU348 2.6 22.8 1.0 CB A:ASP338 4.0 20.1 1.0 CG A:GLU348 4.1 24.7 1.0 O A:HOH2189 4.3 24.5 1.0 CB A:GLU348 4.5 23.1 1.0 N A:LYS349 4.6 22.3 1.0 CA A:GLU348 4.7 23.1 1.0 CA A:ASP338 5.0 20.6 1.0

Zinc binding site 4 out of 4 in the P450 BM3 F87A in Complex with Dmso


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of P450 BM3 F87A in Complex with Dmso within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1457 b:21.1 occ:1.00 OD2 B:ASP231 2.0 22.9 1.0 NE2 B:HIS236 2.1 23.1 1.0 CG B:ASP231 2.7 24.1 1.0 OD1 B:ASP231 2.8 24.9 1.0 CE1 B:HIS236 3.0 22.9 1.0 CD2 B:HIS236 3.1 24.2 1.0 NE2 B:GLN110 4.2 25.9 1.0 ND1 B:HIS236 4.2 21.4 1.0 CB B:ASP231 4.2 22.7 1.0 CG B:HIS236 4.3 24.1 1.0 OE1 B:GLN110 4.3 29.5 1.0 CD B:GLN110 4.7 28.0 1.0 C B:ASP231 4.7 22.1 1.0 O B:ASP231 4.7 22.2 1.0 CA B:ASP231 4.7 22.6 1.0

J.Kuper, K.L.Tee, M.Wilmanns, D.Roccatano, U.Schwaneberg, T.S.Wong. The Role of Active-Site PHE87 in Modulating the Organic Co-Solvent Tolerance of Cytochrome P450 BM3 Monooxygenase. Acta Crystallogr.,Sect.F V. 68 1013 2012.
ISSN: ESSN 1744-3091
PubMed: 22949185
DOI: 10.1107/S1744309112031570