Iron in PDB 7q89: Olep Mutant G92W in Complex with 6DEB

The structure of Olep Mutant G92W in Complex with 6DEB, PDB code: 7q89 was solved by C.Savino, L.C.Montemiglio, B.Vallone, C.Exertier, I.Freda, E.Gugole, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.03 / 2.08
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	247.758, 110.489, 159.818, 90, 129.66, 90
R / Rfree (%)	17 / 22.8

The structure of Olep Mutant G92W in Complex with 6DEB also contains other interesting chemical elements:

Sodium

(Na)

8 atoms

The binding sites of Iron atom in the Olep Mutant G92W in Complex with 6DEB (pdb code 7q89). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Olep Mutant G92W in Complex with 6DEB, PDB code: 7q89:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Olep Mutant G92W in Complex with 6DEB


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:36.0 occ:1.00 FE A:HEM501 0.0 36.0 1.0 ND A:HEM501 1.9 38.1 1.0 NB A:HEM501 2.0 35.1 1.0 NA A:HEM501 2.1 32.9 1.0 NC A:HEM501 2.1 38.0 1.0 SG A:CYS356 2.4 36.7 1.0 C1D A:HEM501 3.0 34.8 1.0 C4B A:HEM501 3.0 35.8 1.0 C4D A:HEM501 3.0 33.5 1.0 C1A A:HEM501 3.0 33.9 1.0 C4C A:HEM501 3.1 38.4 1.0 C1B A:HEM501 3.1 32.9 1.0 C1C A:HEM501 3.1 39.4 1.0 C4A A:HEM501 3.1 30.9 1.0 CHC A:HEM501 3.4 39.0 1.0 CHA A:HEM501 3.4 29.7 1.0 CHD A:HEM501 3.4 34.5 1.0 CB A:CYS356 3.5 29.0 1.0 CHB A:HEM501 3.5 35.7 1.0 C23 A:DEB502 4.0 37.0 1.0 CA A:CYS356 4.0 31.2 1.0 C2D A:HEM501 4.2 33.8 1.0 C3D A:HEM501 4.2 34.4 1.0 C3B A:HEM501 4.3 38.4 1.0 C3C A:HEM501 4.3 38.3 1.0 C2B A:HEM501 4.3 37.4 1.0 C3A A:HEM501 4.3 33.0 1.0 C2A A:HEM501 4.3 30.2 1.0 C2C A:HEM501 4.3 35.7 1.0 C8 A:DEB502 4.6 35.6 1.0 CG2 A:THR248 4.7 37.9 1.0 C A:CYS356 4.8 43.8 1.0 N A:GLY358 4.8 37.6 1.0 N A:ILE357 4.8 37.3 1.0 CB A:ALA244 5.0 37.5 1.0

Iron binding site 2 out of 6 in the Olep Mutant G92W in Complex with 6DEB


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:35.0 occ:1.00 FE B:HEM501 0.0 35.0 1.0 ND B:HEM501 1.9 30.3 1.0 NB B:HEM501 2.0 29.4 1.0 NA B:HEM501 2.1 33.1 1.0 NC B:HEM501 2.1 36.2 1.0 SG B:CYS356 2.4 36.5 1.0 C1D B:HEM501 2.9 35.7 1.0 C4B B:HEM501 2.9 34.2 1.0 C4D B:HEM501 3.0 33.1 1.0 C4C B:HEM501 3.0 31.5 1.0 C1B B:HEM501 3.0 37.1 1.0 C4A B:HEM501 3.1 29.7 1.0 C1C B:HEM501 3.1 31.7 1.0 C1A B:HEM501 3.1 33.2 1.0 CB B:CYS356 3.2 36.5 1.0 CHC B:HEM501 3.4 33.0 1.0 CHD B:HEM501 3.4 31.6 1.0 CHB B:HEM501 3.4 31.8 1.0 CHA B:HEM501 3.5 33.3 1.0 CA B:CYS356 4.0 39.0 1.0 C23 B:DEB502 4.1 39.0 1.0 C3B B:HEM501 4.2 30.7 1.0 C2D B:HEM501 4.2 30.7 1.0 C3D B:HEM501 4.2 34.9 1.0 C2B B:HEM501 4.2 33.6 1.0 C3C B:HEM501 4.3 35.1 1.0 C3A B:HEM501 4.3 35.5 1.0 C2A B:HEM501 4.3 32.3 1.0 C2C B:HEM501 4.3 33.8 1.0 CG2 B:THR248 4.6 38.8 1.0 C B:CYS356 4.7 38.7 1.0 C8 B:DEB502 4.7 36.8 1.0 N B:GLY358 4.8 35.2 1.0 N B:ILE357 4.9 37.4 1.0 CB B:ALA244 4.9 41.1 1.0

Iron binding site 3 out of 6 in the Olep Mutant G92W in Complex with 6DEB


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:37.4 occ:1.00 FE C:HEM501 0.0 37.4 1.0 ND C:HEM501 1.9 35.6 1.0 NA C:HEM501 2.0 33.3 1.0 NC C:HEM501 2.0 38.4 1.0 NB C:HEM501 2.1 35.8 1.0 SG C:CYS356 2.4 37.3 1.0 C1D C:HEM501 2.9 37.5 1.0 C4D C:HEM501 3.0 36.0 1.0 C4C C:HEM501 3.0 38.2 1.0 C1A C:HEM501 3.0 33.8 1.0 C4B C:HEM501 3.0 32.3 1.0 C4A C:HEM501 3.1 34.9 1.0 C1C C:HEM501 3.1 35.2 1.0 C1B C:HEM501 3.1 38.5 1.0 CB C:CYS356 3.3 34.0 1.0 CHD C:HEM501 3.4 35.1 1.0 CHC C:HEM501 3.4 39.9 1.0 CHA C:HEM501 3.5 36.9 1.0 CHB C:HEM501 3.5 36.5 1.0 C23 C:DEB533 3.9 37.0 1.0 CA C:CYS356 4.1 36.0 1.0 C2D C:HEM501 4.2 36.0 1.0 C3A C:HEM501 4.2 32.7 1.0 C2A C:HEM501 4.2 31.7 1.0 C3C C:HEM501 4.2 34.7 1.0 C3D C:HEM501 4.2 34.3 1.0 C2C C:HEM501 4.3 34.0 1.0 C3B C:HEM501 4.3 40.8 1.0 C2B C:HEM501 4.4 37.1 1.0 CG2 C:THR248 4.5 42.5 1.0 C8 C:DEB533 4.7 35.6 1.0 C C:CYS356 4.8 41.7 1.0 N C:GLY358 4.9 36.7 1.0 CB C:ALA244 4.9 48.0 1.0 N C:ILE357 4.9 39.5 1.0

Iron binding site 4 out of 6 in the Olep Mutant G92W in Complex with 6DEB


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:37.6 occ:1.00 FE D:HEM501 0.0 37.6 1.0 ND D:HEM501 1.8 25.8 1.0 NB D:HEM501 1.9 26.1 1.0 NA D:HEM501 2.0 33.1 1.0 NC D:HEM501 2.0 32.8 1.0 SG D:CYS356 2.4 40.8 1.0 C1D D:HEM501 2.8 35.4 1.0 C4B D:HEM501 2.8 37.8 1.0 C4D D:HEM501 2.8 35.4 1.0 C1B D:HEM501 3.0 37.9 1.0 C4C D:HEM501 3.0 29.1 1.0 C1A D:HEM501 3.0 30.2 1.0 C1C D:HEM501 3.1 32.4 1.0 C4A D:HEM501 3.1 28.4 1.0 CHD D:HEM501 3.3 35.9 1.0 CB D:CYS356 3.3 39.1 1.0 CHA D:HEM501 3.4 40.9 1.0 CHC D:HEM501 3.4 35.0 1.0 CHB D:HEM501 3.5 38.5 1.0 C2D D:HEM501 4.0 28.0 1.0 C3B D:HEM501 4.0 31.9 1.0 CA D:CYS356 4.1 43.8 1.0 C3D D:HEM501 4.1 31.1 1.0 C2B D:HEM501 4.1 31.3 1.0 C23 D:DEB502 4.2 47.2 1.0 C3C D:HEM501 4.2 40.8 1.0 C2A D:HEM501 4.3 34.1 1.0 C3A D:HEM501 4.3 35.2 1.0 C2C D:HEM501 4.3 35.5 1.0 CG2 D:THR248 4.5 43.5 1.0 C8 D:DEB502 4.8 44.6 1.0 C D:CYS356 4.8 41.5 1.0 CB D:ALA244 4.9 46.1 1.0 N D:GLY358 4.9 42.6 1.0

Iron binding site 5 out of 6 in the Olep Mutant G92W in Complex with 6DEB


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe501 b:44.2 occ:1.00 FE E:HEM501 0.0 44.2 1.0 ND E:HEM501 1.9 48.4 1.0 NA E:HEM501 2.0 42.3 1.0 NC E:HEM501 2.1 40.1 1.0 NB E:HEM501 2.1 46.7 1.0 SG E:CYS356 2.5 48.2 1.0 C4D E:HEM501 3.0 41.3 1.0 C1A E:HEM501 3.0 43.0 1.0 C1D E:HEM501 3.0 42.4 1.0 C4C E:HEM501 3.0 44.4 1.0 C4A E:HEM501 3.0 41.3 1.0 C4B E:HEM501 3.1 45.5 1.0 C1B E:HEM501 3.1 46.1 1.0 C1C E:HEM501 3.1 45.2 1.0 CB E:CYS356 3.2 47.4 1.0 CHA E:HEM501 3.3 41.9 1.0 CHD E:HEM501 3.4 41.4 1.0 CHC E:HEM501 3.4 44.6 1.0 CHB E:HEM501 3.5 48.4 1.0 CA E:CYS356 4.0 45.7 1.0 C23 E:DEB502 4.1 47.3 1.0 C3A E:HEM501 4.2 40.9 1.0 C2A E:HEM501 4.2 42.5 1.0 C3C E:HEM501 4.2 39.7 1.0 C3D E:HEM501 4.3 47.8 1.0 C2C E:HEM501 4.3 41.9 1.0 C2D E:HEM501 4.3 44.0 1.0 C2B E:HEM501 4.3 47.9 1.0 C3B E:HEM501 4.3 48.5 1.0 CG2 E:THR248 4.5 53.8 1.0 C8 E:DEB502 4.7 48.0 1.0 C E:CYS356 4.7 48.7 1.0 N E:GLY358 4.9 50.2 1.0 CB E:ALA244 4.9 46.0 1.0 N E:ILE357 4.9 44.0 1.0

Iron binding site 6 out of 6 in the Olep Mutant G92W in Complex with 6DEB


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Olep Mutant G92W in Complex with 6DEB within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:53.8 occ:1.00 FE F:HEM501 0.0 53.8 1.0 ND F:HEM501 1.9 54.5 1.0 NA F:HEM501 2.0 53.6 1.0 NB F:HEM501 2.1 55.3 1.0 NC F:HEM501 2.1 54.1 1.0 SG F:CYS356 2.3 57.6 1.0 C1D F:HEM501 2.9 50.6 1.0 C4D F:HEM501 3.0 53.2 1.0 C1A F:HEM501 3.0 55.1 1.0 C4C F:HEM501 3.0 52.9 1.0 C4B F:HEM501 3.0 59.3 1.0 C1B F:HEM501 3.0 54.6 1.0 C4A F:HEM501 3.1 53.2 1.0 C1C F:HEM501 3.2 56.2 1.0 CB F:CYS356 3.3 56.5 1.0 CHD F:HEM501 3.4 49.1 1.0 CHA F:HEM501 3.4 47.4 1.0 CHB F:HEM501 3.5 52.7 1.0 CHC F:HEM501 3.5 56.7 1.0 CA F:CYS356 4.0 56.2 1.0 C23 F:DEB502 4.1 64.9 1.0 C2D F:HEM501 4.2 49.0 1.0 C2A F:HEM501 4.2 53.1 1.0 C3D F:HEM501 4.2 50.3 1.0 C3A F:HEM501 4.2 51.8 1.0 C3C F:HEM501 4.3 54.1 1.0 C2B F:HEM501 4.3 61.0 1.0 C3B F:HEM501 4.3 68.7 1.0 C2C F:HEM501 4.3 61.1 1.0 CG2 F:THR248 4.6 49.9 1.0 C8 F:DEB502 4.7 60.9 1.0 CB F:ALA244 4.8 51.5 1.0 C F:CYS356 4.8 51.7 1.0 N F:GLY358 5.0 52.8 1.0

L.C.Montemiglio, E.Gugole, I.Freda, C.Exertier, L.D'auria, C.G.Chen, A.N.Nardi, G.Cerutti, G.Parisi, M.D'abramo, C.Savino, B.Vallone. Point Mutations at A Key Site Alter the Cytochrome P450 Olep Structural Dynamics. Biomolecules V. 12 2021.
ISSN: ESSN 2218-273X
PubMed: 35053203
DOI: 10.3390/BIOM12010055