Iron in PDB 6zhz: Olep-Oleandolide(Deo) in High Salt Crystallization Conditions

The structure of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions, PDB code: 6zhz was solved by L.C.Montemiglio, C.Savino, B.Vallone, G.Parisi, C.Cecchetti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.73 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	247.469, 111.215, 159.203, 90.00, 129.39, 90.00
R / Rfree (%)	18.7 / 24.3

The structure of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions also contains other interesting chemical elements:

Sodium

(Na)

5 atoms

The binding sites of Iron atom in the Olep-Oleandolide(Deo) in High Salt Crystallization Conditions (pdb code 6zhz). 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-Oleandolide(Deo) in High Salt Crystallization Conditions, PDB code: 6zhz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Olep-Oleandolide(Deo) in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:38.2 occ:1.00 FE A:HEM501 0.0 38.2 1.0 ND A:HEM501 1.9 37.4 1.0 NA A:HEM501 2.0 34.3 1.0 NB A:HEM501 2.0 36.5 1.0 NC A:HEM501 2.0 38.4 1.0 SG A:CYS356 2.4 42.6 1.0 C1D A:HEM501 2.9 37.5 1.0 C4D A:HEM501 3.0 36.5 1.0 C4B A:HEM501 3.0 38.5 1.0 C4A A:HEM501 3.0 35.4 1.0 C4C A:HEM501 3.0 39.9 1.0 C1A A:HEM501 3.0 34.0 1.0 C1B A:HEM501 3.0 36.7 1.0 C1C A:HEM501 3.1 40.8 1.0 CB A:CYS356 3.2 39.4 1.0 CHD A:HEM501 3.3 39.2 1.0 CHB A:HEM501 3.4 37.4 1.0 CHC A:HEM501 3.4 40.2 1.0 CHA A:HEM501 3.4 34.0 1.0 C33 A:QR8502 3.6 54.8 1.0 CA A:CYS356 4.1 41.0 1.0 C2D A:HEM501 4.2 36.8 1.0 C3A A:HEM501 4.2 32.7 1.0 C3D A:HEM501 4.2 36.6 1.0 C3B A:HEM501 4.2 37.9 1.0 C2A A:HEM501 4.2 33.2 1.0 C3C A:HEM501 4.2 40.7 1.0 C2B A:HEM501 4.2 36.5 1.0 C2C A:HEM501 4.3 40.9 1.0 CG2 A:THR248 4.6 43.5 1.0 C A:CYS356 4.9 42.4 1.0 N A:GLY358 4.9 44.2 1.0 CB A:ALA244 4.9 46.1 1.0 C8 A:QR8502 5.0 52.1 1.0

Iron binding site 2 out of 6 in the Olep-Oleandolide(Deo) in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:33.3 occ:1.00 FE B:HEM501 0.0 33.3 1.0 ND B:HEM501 1.8 32.3 1.0 NA B:HEM501 2.0 32.2 1.0 NB B:HEM501 2.0 32.4 1.0 NC B:HEM501 2.1 32.3 1.0 SG B:CYS356 2.3 36.9 1.0 C4D B:HEM501 2.8 33.8 1.0 C1D B:HEM501 2.9 33.8 1.0 C4B B:HEM501 2.9 32.8 1.0 C1A B:HEM501 3.0 31.0 1.0 C1C B:HEM501 3.0 32.1 1.0 C4C B:HEM501 3.0 32.5 1.0 C1B B:HEM501 3.0 34.3 1.0 C4A B:HEM501 3.1 32.7 1.0 CHA B:HEM501 3.3 31.8 1.0 CHC B:HEM501 3.3 32.3 1.0 CB B:CYS356 3.4 39.6 1.0 CHD B:HEM501 3.4 33.0 1.0 CHB B:HEM501 3.5 34.2 1.0 C33 B:QR8502 3.9 42.5 1.0 CA B:CYS356 4.0 35.4 1.0 C2D B:HEM501 4.1 31.4 1.0 C3D B:HEM501 4.1 34.5 1.0 C3B B:HEM501 4.2 34.7 1.0 C2B B:HEM501 4.2 32.6 1.0 C2C B:HEM501 4.2 34.6 1.0 C3C B:HEM501 4.2 34.0 1.0 C2A B:HEM501 4.3 32.1 1.0 C3A B:HEM501 4.3 33.2 1.0 CG2 B:THR248 4.7 37.0 1.0 C B:CYS356 4.8 34.7 1.0 N B:GLY358 4.8 37.5 1.0 N B:ILE357 4.9 36.2 1.0 CB B:ALA244 5.0 41.1 1.0

Iron binding site 3 out of 6 in the Olep-Oleandolide(Deo) in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:32.2 occ:1.00 FE C:HEM501 0.0 32.2 1.0 ND C:HEM501 1.9 32.0 1.0 NB C:HEM501 2.0 28.8 1.0 NA C:HEM501 2.0 29.9 1.0 NC C:HEM501 2.0 32.0 1.0 SG C:CYS356 2.4 32.7 1.0 C4B C:HEM501 2.9 31.7 1.0 C1B C:HEM501 2.9 30.6 1.0 C4D C:HEM501 2.9 32.6 1.0 C1D C:HEM501 2.9 32.2 1.0 C1A C:HEM501 3.0 31.9 1.0 C4C C:HEM501 3.0 33.0 1.0 C4A C:HEM501 3.0 29.6 1.0 C1C C:HEM501 3.0 33.3 1.0 CB C:CYS356 3.2 32.1 1.0 CHC C:HEM501 3.4 31.4 1.0 CHB C:HEM501 3.4 31.7 1.0 CHA C:HEM501 3.4 32.6 1.0 CHD C:HEM501 3.4 32.4 1.0 C33 C:QR8502 3.6 45.0 1.0 CA C:CYS356 4.1 34.7 1.0 C3B C:HEM501 4.1 32.6 1.0 C2B C:HEM501 4.1 32.0 1.0 C2D C:HEM501 4.2 30.7 1.0 C3D C:HEM501 4.2 31.8 1.0 C3A C:HEM501 4.2 30.1 1.0 C3C C:HEM501 4.2 33.2 1.0 C2C C:HEM501 4.2 32.9 1.0 C2A C:HEM501 4.2 32.1 1.0 CG2 C:THR248 4.5 38.4 1.0 C C:CYS356 4.9 35.6 1.0 N C:GLY358 5.0 35.8 1.0 CB C:ALA244 5.0 40.5 1.0 C8 C:QR8502 5.0 45.2 1.0

Iron binding site 4 out of 6 in the Olep-Oleandolide(Deo) in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:45.0 occ:1.00 FE D:HEM501 0.0 45.0 1.0 ND D:HEM501 1.8 43.6 1.0 NC D:HEM501 2.0 43.9 1.0 NA D:HEM501 2.0 45.3 1.0 NB D:HEM501 2.1 41.3 1.0 SG D:CYS356 2.4 49.6 1.0 C1D D:HEM501 2.8 44.8 1.0 C4D D:HEM501 2.9 45.7 1.0 C4C D:HEM501 2.9 45.7 1.0 C4B D:HEM501 2.9 42.3 1.0 C1C D:HEM501 3.0 42.8 1.0 C1A D:HEM501 3.1 44.2 1.0 C1B D:HEM501 3.1 42.8 1.0 C4A D:HEM501 3.1 45.3 1.0 CHD D:HEM501 3.2 45.8 1.0 CHC D:HEM501 3.3 42.9 1.0 CHA D:HEM501 3.4 44.4 1.0 CB D:CYS356 3.4 50.0 1.0 CHB D:HEM501 3.5 46.1 1.0 C33 D:QR8502 3.7 55.6 1.0 C2D D:HEM501 4.0 44.4 1.0 C3C D:HEM501 4.1 45.2 1.0 C3D D:HEM501 4.1 46.2 1.0 CA D:CYS356 4.1 49.0 1.0 C2C D:HEM501 4.2 43.5 1.0 C3B D:HEM501 4.2 42.6 1.0 C3A D:HEM501 4.2 45.9 1.0 C2A D:HEM501 4.2 46.6 1.0 C2B D:HEM501 4.3 42.0 1.0 CG2 D:THR248 4.6 46.0 1.0 N D:GLY358 4.8 48.6 1.0 CB D:ALA244 4.8 53.1 1.0 C D:CYS356 4.9 47.8 1.0

Iron binding site 5 out of 6 in the Olep-Oleandolide(Deo) in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe501 b:48.4 occ:1.00 FE E:HEM501 0.0 48.4 1.0 ND E:HEM501 1.9 48.3 1.0 NA E:HEM501 2.0 48.9 1.0 NB E:HEM501 2.1 47.2 1.0 NC E:HEM501 2.1 45.7 1.0 SG E:CYS356 2.5 52.3 1.0 C4D E:HEM501 2.9 49.6 1.0 C1D E:HEM501 2.9 48.3 1.0 C1A E:HEM501 2.9 49.7 1.0 C4B E:HEM501 3.0 46.6 1.0 C4C E:HEM501 3.1 44.7 1.0 C4A E:HEM501 3.1 50.1 1.0 C1B E:HEM501 3.1 51.0 1.0 C1C E:HEM501 3.2 47.6 1.0 CHA E:HEM501 3.3 49.7 1.0 CB E:CYS356 3.4 53.6 1.0 CHD E:HEM501 3.4 45.1 1.0 CHC E:HEM501 3.5 48.1 1.0 CHB E:HEM501 3.5 51.0 1.0 C33 E:QR8502 3.7 57.1 1.0 CA E:CYS356 4.1 55.3 1.0 C3D E:HEM501 4.2 50.3 1.0 C2A E:HEM501 4.2 51.5 1.0 C2D E:HEM501 4.2 50.2 1.0 C3A E:HEM501 4.2 50.4 1.0 C3B E:HEM501 4.3 48.1 1.0 C2B E:HEM501 4.3 48.9 1.0 C3C E:HEM501 4.3 45.3 1.0 C2C E:HEM501 4.4 45.0 1.0 CG2 E:THR248 4.4 49.6 1.0 C E:CYS356 4.9 53.1 1.0 CB E:ALA244 4.9 48.9 1.0 N E:GLY358 5.0 50.5 1.0

Iron binding site 6 out of 6 in the Olep-Oleandolide(Deo) in High Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Olep-Oleandolide(Deo) in High Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:64.9 occ:1.00 FE F:HEM501 0.0 64.9 1.0 ND F:HEM501 1.9 65.2 1.0 NA F:HEM501 2.0 62.1 1.0 NB F:HEM501 2.1 69.4 1.0 NC F:HEM501 2.1 70.0 1.0 SG F:CYS356 2.5 69.2 1.0 C4D F:HEM501 2.9 60.9 1.0 C1D F:HEM501 2.9 61.6 1.0 C1A F:HEM501 3.0 60.5 1.0 C4A F:HEM501 3.0 65.5 1.0 C1B F:HEM501 3.0 72.5 1.0 C4C F:HEM501 3.1 69.0 1.0 C4B F:HEM501 3.1 71.6 1.0 C1C F:HEM501 3.2 72.2 1.0 CB F:CYS356 3.3 64.8 1.0 CHA F:HEM501 3.4 60.4 1.0 CHB F:HEM501 3.4 69.9 1.0 CHD F:HEM501 3.4 64.9 1.0 CHC F:HEM501 3.6 71.2 1.0 C33 F:QR8502 3.8 77.1 1.0 CA F:CYS356 4.1 62.6 1.0 C3A F:HEM501 4.1 64.2 1.0 C2A F:HEM501 4.2 65.2 1.0 C3D F:HEM501 4.2 59.8 1.0 C2D F:HEM501 4.2 62.4 1.0 C2B F:HEM501 4.3 77.0 1.0 C3C F:HEM501 4.3 72.0 1.0 C3B F:HEM501 4.3 79.6 1.0 C2C F:HEM501 4.3 72.8 1.0 CG2 F:THR248 4.6 68.7 1.0 CB F:ALA244 4.8 61.1 1.0 O11 F:QR8502 5.0 79.4 1.0

G.Parisi, I.Freda, C.Exertier, C.Cecchetti, E.Gugole, G.Cerutti, L.D'auria, A.Macone, B.Vallone, C.Savino, L.C.Montemiglio. Dissecting the Cytochrome P450 Olep Substrate Specificity: Evidence For A Preferential Substrate. Biomolecules V. 10 2020.
ISSN: ESSN 2218-273X
PubMed: 33036250
DOI: 10.3390/BIOM10101411