Iron in PDB 6zi7: Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose

The structure of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose, PDB code: 6zi7 was solved by L.C.Montemiglio, C.Savino, B.Vallone, G.Parisi, I.Freda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.92 / 2.28
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	247.531, 110.683, 159.285, 90.00, 129.46, 90.00
R / Rfree (%)	18.4 / 24.7

The structure of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose also contains other interesting chemical elements:

Sodium

(Na)

6 atoms

The binding sites of Iron atom in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose (pdb code 6zi7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose, PDB code: 6zi7:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:35.9 occ:1.00 FE A:HEM501 0.0 35.9 1.0 ND A:HEM501 1.8 32.2 1.0 NA A:HEM501 2.0 31.7 1.0 NC A:HEM501 2.0 31.6 1.0 NB A:HEM501 2.0 32.3 1.0 SG A:CYS356 2.3 42.5 1.0 C1D A:HEM501 2.8 31.6 1.0 C4D A:HEM501 2.9 33.2 1.0 C4C A:HEM501 2.9 31.9 1.0 C4B A:HEM501 3.0 33.8 1.0 C1A A:HEM501 3.0 32.3 1.0 C1B A:HEM501 3.0 31.1 1.0 C1C A:HEM501 3.1 33.9 1.0 C4A A:HEM501 3.1 31.2 1.0 CHD A:HEM501 3.2 31.2 1.0 CB A:CYS356 3.3 38.8 1.0 CHA A:HEM501 3.4 32.3 1.0 CHC A:HEM501 3.4 32.9 1.0 CHB A:HEM501 3.4 32.3 1.0 C33 A:QR8502 3.7 35.2 1.0 CA A:CYS356 4.1 37.3 1.0 C2D A:HEM501 4.1 31.7 1.0 C3C A:HEM501 4.1 34.6 1.0 C3D A:HEM501 4.2 32.4 1.0 C3A A:HEM501 4.2 29.9 1.0 C2C A:HEM501 4.2 33.7 1.0 C3B A:HEM501 4.2 32.8 1.0 C2A A:HEM501 4.2 30.4 1.0 C2B A:HEM501 4.2 31.7 1.0 CG2 A:THR248 4.6 34.0 1.0 CB A:ALA244 4.8 40.1 1.0 C A:CYS356 4.8 40.3 1.0 N A:GLY358 4.9 45.4 1.0 N A:ILE357 4.9 40.2 1.0 C8 A:QR8502 5.0 35.4 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:38.0 occ:1.00 FE B:HEM501 0.0 38.0 1.0 ND B:HEM501 1.9 33.1 1.0 NB B:HEM501 2.0 36.3 1.0 NA B:HEM501 2.1 34.1 1.0 NC B:HEM501 2.1 35.2 1.0 SG B:CYS356 2.3 36.6 1.0 C1D B:HEM501 2.9 35.1 1.0 C4B B:HEM501 2.9 36.8 1.0 C4D B:HEM501 3.0 35.9 1.0 C1B B:HEM501 3.0 38.6 1.0 C1C B:HEM501 3.0 36.1 1.0 C4C B:HEM501 3.1 34.9 1.0 C4A B:HEM501 3.1 35.2 1.0 C1A B:HEM501 3.1 33.2 1.0 CHC B:HEM501 3.3 35.4 1.0 CB B:CYS356 3.4 42.2 1.0 CHD B:HEM501 3.4 35.2 1.0 CHB B:HEM501 3.5 36.4 1.0 CHA B:HEM501 3.5 33.3 1.0 C33 B:QR8502 4.0 40.4 1.0 CA B:CYS356 4.1 38.1 1.0 C2D B:HEM501 4.2 33.8 1.0 C3B B:HEM501 4.2 39.1 1.0 C3D B:HEM501 4.2 35.5 1.0 C2B B:HEM501 4.2 37.6 1.0 C3C B:HEM501 4.2 36.3 1.0 C2C B:HEM501 4.3 37.1 1.0 C3A B:HEM501 4.3 36.0 1.0 C2A B:HEM501 4.3 34.4 1.0 CG2 B:THR248 4.5 39.2 1.0 N B:GLY358 4.9 36.4 1.0 C B:CYS356 4.9 36.1 1.0 CB B:ALA244 4.9 41.9 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:32.7 occ:1.00 FE C:HEM501 0.0 32.7 1.0 ND C:HEM501 1.8 29.6 1.0 NA C:HEM501 2.0 28.7 1.0 NB C:HEM501 2.0 29.4 1.0 NC C:HEM501 2.0 29.8 1.0 SG C:CYS356 2.4 35.9 1.0 C1D C:HEM501 2.8 29.5 1.0 C4D C:HEM501 2.9 30.6 1.0 C4B C:HEM501 2.9 30.8 1.0 C1A C:HEM501 2.9 29.1 1.0 C4C C:HEM501 3.0 29.8 1.0 C1B C:HEM501 3.0 29.8 1.0 C4A C:HEM501 3.0 28.6 1.0 C1C C:HEM501 3.1 30.5 1.0 CHD C:HEM501 3.3 28.9 1.0 CB C:CYS356 3.3 34.0 1.0 CHA C:HEM501 3.3 30.0 1.0 CHC C:HEM501 3.3 30.2 1.0 CHB C:HEM501 3.4 30.3 1.0 C33 C:QR8502 3.7 36.5 1.0 CA C:CYS356 4.0 34.1 1.0 C2D C:HEM501 4.1 28.9 1.0 C3D C:HEM501 4.1 29.5 1.0 C3C C:HEM501 4.2 31.4 1.0 C3B C:HEM501 4.2 30.5 1.0 C2A C:HEM501 4.2 28.6 1.0 C3A C:HEM501 4.2 27.9 1.0 C2C C:HEM501 4.2 31.2 1.0 C2B C:HEM501 4.2 30.9 1.0 CG2 C:THR248 4.6 30.6 1.0 CB C:ALA244 4.7 35.4 1.0 C C:CYS356 4.9 35.1 1.0 N C:GLY358 4.9 40.1 1.0 CD1 C:PHE349 4.9 30.7 0.5

Iron binding site 4 out of 6 in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:41.3 occ:1.00 FE D:HEM501 0.0 41.3 1.0 ND D:HEM501 1.9 36.9 1.0 NB D:HEM501 2.0 38.5 1.0 NA D:HEM501 2.0 38.7 1.0 NC D:HEM501 2.1 38.7 1.0 SG D:CYS356 2.4 41.0 1.0 C1D D:HEM501 2.8 38.2 1.0 C4B D:HEM501 2.9 40.5 1.0 C4D D:HEM501 2.9 39.3 1.0 C4C D:HEM501 3.0 39.2 1.0 C1A D:HEM501 3.0 38.0 1.0 C1C D:HEM501 3.0 37.6 1.0 C1B D:HEM501 3.1 40.3 1.0 C4A D:HEM501 3.1 40.5 1.0 CHD D:HEM501 3.2 39.6 1.0 CHC D:HEM501 3.3 38.1 1.0 CB D:CYS356 3.4 43.9 1.0 CHA D:HEM501 3.4 37.4 1.0 CHB D:HEM501 3.6 41.3 1.0 C33 D:QR8502 3.9 45.7 1.0 CA D:CYS356 4.1 42.8 1.0 C2D D:HEM501 4.1 36.9 1.0 C3B D:HEM501 4.2 40.7 1.0 C3C D:HEM501 4.2 41.0 1.0 C3D D:HEM501 4.2 39.2 1.0 C2C D:HEM501 4.2 40.1 1.0 C2B D:HEM501 4.3 41.2 1.0 C2A D:HEM501 4.3 41.4 1.0 C3A D:HEM501 4.3 41.3 1.0 CG2 D:THR248 4.6 43.4 1.0 C D:CYS356 4.8 40.5 1.0 CB D:ALA244 4.8 45.8 1.0 N D:GLY358 4.9 44.2 1.0 N D:ILE357 5.0 41.4 1.0

Iron binding site 5 out of 6 in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe502 b:46.3 occ:1.00 FE E:HEM502 0.0 46.3 1.0 ND E:HEM502 1.9 45.7 1.0 NA E:HEM502 2.0 46.4 1.0 NC E:HEM502 2.1 42.8 1.0 NB E:HEM502 2.1 48.1 1.0 SG E:CYS356 2.4 48.1 1.0 C4D E:HEM502 2.9 46.1 1.0 C1D E:HEM502 3.0 45.2 1.0 C1A E:HEM502 3.0 49.5 1.0 C1C E:HEM502 3.1 47.5 1.0 C4B E:HEM502 3.1 46.3 1.0 C4C E:HEM502 3.1 45.1 1.0 C4A E:HEM502 3.1 52.5 1.0 C1B E:HEM502 3.1 50.9 1.0 CB E:CYS356 3.3 47.7 1.0 CHA E:HEM502 3.4 47.7 1.0 CHC E:HEM502 3.4 47.2 1.0 CHD E:HEM502 3.4 43.1 1.0 CHB E:HEM502 3.6 50.1 1.0 C33 E:QR8503 4.0 55.8 1.0 CA E:CYS356 4.1 50.4 1.0 C3D E:HEM502 4.2 48.0 1.0 C2A E:HEM502 4.2 52.0 1.0 C2D E:HEM502 4.2 47.2 1.0 C2C E:HEM502 4.3 45.8 1.0 C3C E:HEM502 4.3 46.0 1.0 C3A E:HEM502 4.3 49.1 1.0 C3B E:HEM502 4.3 48.2 1.0 C2B E:HEM502 4.4 49.8 1.0 CG2 E:THR248 4.4 44.5 1.0 C E:CYS356 4.8 50.8 1.0 CB E:ALA244 4.8 48.0 1.0 N E:GLY358 4.9 51.3 1.0 N E:ILE357 4.9 47.8 1.0 CD1 E:PHE349 5.0 51.5 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Olep-Oleandolide(Deo) Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe502 b:65.2 occ:1.00 FE F:HEM502 0.0 65.2 1.0 ND F:HEM502 1.9 70.4 1.0 NA F:HEM502 2.0 64.6 1.0 NB F:HEM502 2.1 70.3 1.0 NC F:HEM502 2.1 67.9 1.0 SG F:CYS356 2.4 60.6 1.0 C4D F:HEM502 2.9 64.0 1.0 C1D F:HEM502 3.0 62.7 1.0 C1A F:HEM502 3.0 62.8 1.0 C4B F:HEM502 3.0 74.9 1.0 C4C F:HEM502 3.1 67.5 1.0 C1B F:HEM502 3.1 72.3 1.0 C4A F:HEM502 3.1 63.9 1.0 C1C F:HEM502 3.1 71.2 1.0 CHA F:HEM502 3.4 61.1 1.0 CHD F:HEM502 3.4 64.1 1.0 CB F:CYS356 3.4 60.2 1.0 CHC F:HEM502 3.5 69.9 1.0 CHB F:HEM502 3.5 66.9 1.0 C33 F:QR8503 3.6 66.5 1.0 C3D F:HEM502 4.2 58.5 1.0 C2D F:HEM502 4.2 59.8 1.0 CA F:CYS356 4.2 61.7 1.0 C2A F:HEM502 4.2 59.2 1.0 C3A F:HEM502 4.2 59.4 1.0 C3C F:HEM502 4.3 70.0 1.0 C2C F:HEM502 4.3 73.4 1.0 C3B F:HEM502 4.3 77.6 1.0 C2B F:HEM502 4.3 75.1 1.0 CG2 F:THR248 4.6 52.4 1.0 CB F:ALA244 4.7 56.5 1.0 C8 F:QR8503 4.9 62.6 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