Iron in PDB 6zi2: Olep-Oleandolide(Deo) in Low Salt Crystallization Conditions

The structure of Olep-Oleandolide(Deo) in Low Salt Crystallization Conditions, PDB code: 6zi2 was solved by C.Savino, L.C.Montemiglio, 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)	39.89 / 2.93
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	112.066, 116.642, 125.170, 104.43, 104.25, 113.91
R / Rfree (%)	23.9 / 29.1

The binding sites of Iron atom in the Olep-Oleandolide(Deo) in Low Salt Crystallization Conditions (pdb code 6zi2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the Olep-Oleandolide(Deo) in Low Salt Crystallization Conditions, PDB code: 6zi2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iron binding site 1 out of 9 in the Olep-Oleandolide(Deo) in Low 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 Low Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:8.6 occ:1.00 FE A:HEM501 0.0 8.6 1.0 ND A:HEM501 1.9 9.0 1.0 NA A:HEM501 2.0 8.3 1.0 NB A:HEM501 2.0 8.3 1.0 NC A:HEM501 2.1 8.4 1.0 SG A:CYS356 2.1 17.3 1.0 O A:HOH604 2.6 12.9 1.0 CB A:CYS356 2.9 19.2 1.0 C1D A:HEM501 2.9 9.1 1.0 C4A A:HEM501 3.0 8.2 1.0 C1B A:HEM501 3.0 8.2 1.0 C4D A:HEM501 3.0 9.2 1.0 C1A A:HEM501 3.0 8.4 1.0 C4B A:HEM501 3.0 8.1 1.0 C4C A:HEM501 3.0 8.6 1.0 C1C A:HEM501 3.1 8.1 1.0 CHB A:HEM501 3.3 8.3 1.0 CHD A:HEM501 3.3 9.0 1.0 CHA A:HEM501 3.4 8.8 1.0 CHC A:HEM501 3.5 7.9 1.0 O7 A:QR8502 3.9 28.9 1.0 CA A:CYS356 4.0 21.3 1.0 C3A A:HEM501 4.2 8.2 1.0 C2A A:HEM501 4.2 8.2 1.0 C2D A:HEM501 4.2 9.1 1.0 C2B A:HEM501 4.2 8.0 1.0 C3D A:HEM501 4.3 9.2 1.0 C3B A:HEM501 4.3 7.9 1.0 C3C A:HEM501 4.3 8.0 1.0 C2C A:HEM501 4.3 7.8 1.0 C31 A:QR8502 4.6 37.2 1.0 O A:ALA244 4.6 30.3 1.0 CB A:ALA244 4.7 33.2 1.0 OG1 A:THR248 4.7 31.0 1.0 C5 A:QR8502 4.7 30.7 1.0 C A:CYS356 4.8 23.5 1.0 C A:ALA244 4.9 31.7 1.0 CG2 A:THR248 5.0 26.7 1.0

Iron binding site 2 out of 9 in the Olep-Oleandolide(Deo) in Low 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 Low Salt Crystallization Conditions 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 38.2 1.0 NA B:HEM501 2.0 30.9 1.0 SG B:CYS356 2.0 41.7 1.0 NB B:HEM501 2.1 33.8 1.0 NC B:HEM501 2.1 31.3 1.0 C4D B:HEM501 2.9 38.1 1.0 C1D B:HEM501 2.9 36.7 1.0 C1A B:HEM501 2.9 32.9 1.0 C4A B:HEM501 3.0 30.6 1.0 C1B B:HEM501 3.0 30.7 1.0 C4B B:HEM501 3.0 34.3 1.0 C4C B:HEM501 3.1 30.8 1.0 C1C B:HEM501 3.2 28.9 1.0 CB B:CYS356 3.2 44.7 1.0 CHA B:HEM501 3.3 35.7 1.0 CHB B:HEM501 3.3 30.9 1.0 CHD B:HEM501 3.4 32.6 1.0 CHC B:HEM501 3.5 30.2 1.0 CA B:CYS356 3.9 49.9 1.0 C33 B:QR8502 3.9 34.1 1.0 C3A B:HEM501 4.2 31.6 1.0 C2D B:HEM501 4.2 38.3 1.0 C2A B:HEM501 4.2 34.7 1.0 C3D B:HEM501 4.2 36.5 1.0 C2B B:HEM501 4.2 31.3 1.0 C3C B:HEM501 4.3 28.4 1.0 C3B B:HEM501 4.3 33.9 1.0 C2C B:HEM501 4.3 28.2 1.0 CB B:ALA244 4.4 35.6 1.0 CG2 B:THR248 4.7 37.3 1.0 C B:CYS356 4.8 51.1 1.0 OG1 B:THR248 4.9 28.9 1.0 O11 B:QR8502 5.0 29.6 1.0 N B:CYS356 5.0 49.0 1.0

Iron binding site 3 out of 9 in the Olep-Oleandolide(Deo) in Low 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 Low Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:26.5 occ:1.00 FE C:HEM501 0.0 26.5 1.0 ND C:HEM501 1.9 24.8 1.0 SG C:CYS356 1.9 32.9 1.0 NA C:HEM501 2.0 23.7 1.0 NC C:HEM501 2.1 22.5 1.0 NB C:HEM501 2.1 23.8 1.0 C1D C:HEM501 2.9 23.4 1.0 C4D C:HEM501 2.9 24.2 1.0 C1A C:HEM501 3.0 22.7 1.0 C4A C:HEM501 3.0 23.9 1.0 C4B C:HEM501 3.0 24.3 1.0 C4C C:HEM501 3.0 21.8 1.0 C1B C:HEM501 3.1 24.0 1.0 C1C C:HEM501 3.1 22.2 1.0 CB C:CYS356 3.2 32.2 1.0 CHA C:HEM501 3.4 22.8 1.0 CHD C:HEM501 3.4 22.5 1.0 CHC C:HEM501 3.4 23.1 1.0 CHB C:HEM501 3.4 23.8 1.0 C33 C:QR8502 3.8 18.3 1.0 CA C:CYS356 3.9 34.0 1.0 C2A C:HEM501 4.1 23.7 1.0 C3A C:HEM501 4.2 24.0 1.0 C2D C:HEM501 4.2 22.6 1.0 C3D C:HEM501 4.2 23.7 1.0 C3C C:HEM501 4.2 21.9 1.0 C2C C:HEM501 4.3 22.9 1.0 C2B C:HEM501 4.3 24.6 1.0 C3B C:HEM501 4.3 25.5 1.0 CB C:ALA244 4.6 30.9 1.0 CG2 C:THR248 4.7 32.8 1.0 C C:CYS356 4.8 34.1 1.0 C8 C:QR8502 4.9 18.5 1.0 N C:CYS356 5.0 33.0 1.0

Iron binding site 4 out of 9 in the Olep-Oleandolide(Deo) in Low 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 Low Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:23.2 occ:1.00 FE D:HEM501 0.0 23.2 1.0 SG D:CYS356 1.9 23.3 1.0 ND D:HEM501 1.9 28.9 1.0 NA D:HEM501 2.0 25.3 1.0 O D:HOH603 2.0 15.0 1.0 NB D:HEM501 2.1 24.4 1.0 NC D:HEM501 2.1 24.8 1.0 C4D D:HEM501 2.9 30.5 1.0 C1D D:HEM501 2.9 30.5 1.0 C1A D:HEM501 2.9 27.1 1.0 C4B D:HEM501 3.0 23.5 1.0 C4A D:HEM501 3.0 25.3 1.0 C1B D:HEM501 3.1 24.3 1.0 C4C D:HEM501 3.1 24.9 1.0 C1C D:HEM501 3.1 24.0 1.0 CB D:CYS356 3.2 27.1 1.0 CHA D:HEM501 3.3 29.1 1.0 CHC D:HEM501 3.4 24.1 1.0 CHD D:HEM501 3.4 27.5 1.0 CHB D:HEM501 3.4 25.2 1.0 CA D:CYS356 4.0 29.2 1.0 C2A D:HEM501 4.1 26.1 1.0 C3A D:HEM501 4.2 25.4 1.0 C3D D:HEM501 4.2 33.5 1.0 C2D D:HEM501 4.2 31.4 1.0 O1 D:QR8502 4.2 40.6 1.0 C2C D:HEM501 4.3 23.1 1.0 C3C D:HEM501 4.3 23.4 1.0 C3B D:HEM501 4.3 22.6 1.0 C2B D:HEM501 4.3 23.0 1.0 O D:ALA244 4.4 38.7 1.0 OG1 D:THR248 4.8 40.9 1.0 C D:CYS356 4.9 32.5 1.0 CG2 D:THR248 5.0 32.3 1.0

Iron binding site 5 out of 9 in the Olep-Oleandolide(Deo) in Low 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 Low Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe501 b:40.1 occ:1.00 FE E:HEM501 0.0 40.1 1.0 SG E:CYS356 1.7 38.4 1.0 ND E:HEM501 1.9 38.6 1.0 NA E:HEM501 2.0 37.3 1.0 NC E:HEM501 2.1 39.5 1.0 NB E:HEM501 2.1 36.6 1.0 C4D E:HEM501 2.9 38.7 1.0 C1D E:HEM501 2.9 36.3 1.0 C1A E:HEM501 3.0 38.3 1.0 C4A E:HEM501 3.0 39.1 1.0 C4C E:HEM501 3.0 41.2 1.0 C4B E:HEM501 3.0 39.6 1.0 CB E:CYS356 3.0 43.3 1.0 C1B E:HEM501 3.1 36.1 1.0 C1C E:HEM501 3.1 38.4 1.0 CHA E:HEM501 3.3 37.1 1.0 CHD E:HEM501 3.4 39.4 1.0 CHB E:HEM501 3.4 38.5 1.0 CHC E:HEM501 3.5 39.3 1.0 CA E:CYS356 3.9 42.8 1.0 C2D E:HEM501 4.2 35.2 1.0 C3D E:HEM501 4.2 39.7 1.0 C3A E:HEM501 4.2 40.5 1.0 C2A E:HEM501 4.2 42.1 1.0 C3C E:HEM501 4.2 38.9 1.0 C2C E:HEM501 4.3 37.1 1.0 C2B E:HEM501 4.3 34.7 1.0 C3B E:HEM501 4.3 40.2 1.0 O E:ALA244 4.6 51.7 1.0 O7 E:QR8502 4.7 61.5 1.0 C E:CYS356 4.8 43.1 1.0 N E:CYS356 5.0 43.4 1.0

Iron binding site 6 out of 9 in the Olep-Oleandolide(Deo) in Low 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 Low Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:57.8 occ:1.00 FE F:HEM501 0.0 57.8 1.0 SG F:CYS356 1.9 22.2 1.0 ND F:HEM501 1.9 77.6 1.0 NA F:HEM501 2.0 69.7 1.0 O F:HOH603 2.1 21.4 1.0 NC F:HEM501 2.1 77.3 1.0 NB F:HEM501 2.1 73.5 1.0 C1D F:HEM501 2.9 80.1 1.0 C4D F:HEM501 2.9 71.9 1.0 C1A F:HEM501 3.0 67.2 1.0 C4A F:HEM501 3.0 73.3 1.0 C4C F:HEM501 3.1 73.8 1.0 C4B F:HEM501 3.1 71.5 1.0 C1B F:HEM501 3.1 69.8 1.0 C1C F:HEM501 3.1 81.6 1.0 CB F:CYS356 3.2 34.7 1.0 CHA F:HEM501 3.4 66.6 1.0 CHD F:HEM501 3.4 77.1 1.0 CHB F:HEM501 3.5 71.2 1.0 CHC F:HEM501 3.5 80.7 1.0 CA F:CYS356 4.0 41.8 1.0 C2D F:HEM501 4.2 73.3 1.0 C3D F:HEM501 4.2 69.9 1.0 C2A F:HEM501 4.2 66.1 1.0 C3A F:HEM501 4.2 72.1 1.0 O3 F:QR8502 4.3 57.3 1.0 C3C F:HEM501 4.3 73.7 1.0 C2C F:HEM501 4.3 73.4 1.0 C2B F:HEM501 4.4 62.6 1.0 C3B F:HEM501 4.4 62.8 1.0 O F:ALA244 4.5 51.1 1.0 CB F:ALA244 4.7 46.6 1.0 OG1 F:THR248 4.8 57.7 1.0 C F:ALA244 4.8 51.5 1.0 C F:CYS356 4.9 44.3 1.0

Iron binding site 7 out of 9 in the Olep-Oleandolide(Deo) in Low Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Olep-Oleandolide(Deo) in Low Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe501 b:52.2 occ:1.00 FE G:HEM501 0.0 52.2 1.0 ND G:HEM501 1.9 52.4 1.0 SG G:CYS356 1.9 64.8 1.0 NA G:HEM501 2.0 53.9 1.0 NC G:HEM501 2.1 51.4 1.0 NB G:HEM501 2.1 52.5 1.0 C1D G:HEM501 2.8 53.7 1.0 C4D G:HEM501 2.9 51.5 1.0 C4C G:HEM501 3.0 54.5 1.0 C1A G:HEM501 3.0 51.3 1.0 C4B G:HEM501 3.1 52.7 1.0 C4A G:HEM501 3.1 51.8 1.0 C1C G:HEM501 3.1 51.7 1.0 C1B G:HEM501 3.1 47.3 1.0 CHD G:HEM501 3.3 56.6 1.0 CB G:CYS356 3.3 72.3 1.0 CHA G:HEM501 3.4 48.2 1.0 CHC G:HEM501 3.5 49.9 1.0 CHB G:HEM501 3.5 47.7 1.0 C31 G:QR8502 4.0 66.9 1.0 CA G:CYS356 4.0 72.8 1.0 C2D G:HEM501 4.1 55.9 1.0 C3D G:HEM501 4.1 52.5 1.0 C3C G:HEM501 4.2 55.0 1.0 C2A G:HEM501 4.2 56.3 1.0 C3A G:HEM501 4.2 52.6 1.0 C2C G:HEM501 4.2 54.3 1.0 C3B G:HEM501 4.3 53.2 1.0 C2B G:HEM501 4.3 48.6 1.0 O G:ALA244 4.6 66.3 1.0 CB G:ALA244 4.8 64.4 1.0 CG2 G:THR248 4.9 66.2 1.0 OG1 G:THR248 4.9 69.3 1.0 C G:CYS356 4.9 72.2 1.0

Iron binding site 8 out of 9 in the Olep-Oleandolide(Deo) in Low Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Olep-Oleandolide(Deo) in Low Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe501 b:55.7 occ:1.00 FE H:HEM501 0.0 55.7 1.0 ND H:HEM501 1.9 66.7 1.0 SG H:CYS356 1.9 33.7 1.0 O H:HOH603 2.0 10.0 1.0 NA H:HEM501 2.0 55.2 1.0 NC H:HEM501 2.1 59.5 1.0 NB H:HEM501 2.1 68.8 1.0 C4D H:HEM501 2.9 60.4 1.0 C1D H:HEM501 2.9 65.9 1.0 C1A H:HEM501 3.0 57.2 1.0 C4A H:HEM501 3.0 59.3 1.0 C4C H:HEM501 3.1 55.8 1.0 C4B H:HEM501 3.1 71.3 1.0 C1B H:HEM501 3.1 69.1 1.0 C1C H:HEM501 3.1 65.4 1.0 CB H:CYS356 3.1 37.8 1.0 CHA H:HEM501 3.3 59.7 1.0 CHD H:HEM501 3.4 62.5 1.0 CHB H:HEM501 3.5 65.4 1.0 CHC H:HEM501 3.5 76.0 1.0 CA H:CYS356 3.8 43.3 1.0 O7 H:QR8502 4.1 40.4 1.0 C3D H:HEM501 4.2 54.2 1.0 C2D H:HEM501 4.2 56.3 1.0 C2A H:HEM501 4.2 50.8 1.0 C3A H:HEM501 4.2 55.3 1.0 C3C H:HEM501 4.3 57.4 1.0 C2C H:HEM501 4.3 57.2 1.0 O H:ALA244 4.4 48.5 1.0 C2B H:HEM501 4.4 65.9 1.0 C3B H:HEM501 4.4 65.3 1.0 OG1 H:THR248 4.8 64.8 1.0 C H:CYS356 4.8 46.1 1.0 CB H:ALA244 4.8 46.9 1.0 C31 H:QR8502 4.8 56.6 1.0 C H:ALA244 4.9 48.3 1.0 N H:CYS356 4.9 46.4 1.0

Iron binding site 9 out of 9 in the Olep-Oleandolide(Deo) in Low Salt Crystallization Conditions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Olep-Oleandolide(Deo) in Low Salt Crystallization Conditions within 5.0Å range: probe atom residue distance (Å) B Occ I:Fe501 b:0.4 occ:1.00 FE I:HEM501 0.0 0.4 1.0 ND I:HEM501 1.9 0.5 1.0 NA I:HEM501 2.0 0.6 1.0 NC I:HEM501 2.1 0.8 1.0 NB I:HEM501 2.1 0.1 1.0 SG I:CYS356 2.2 0.8 1.0 C4D I:HEM501 2.9 0.5 1.0 C1D I:HEM501 2.9 0.8 1.0 C1A I:HEM501 3.0 0.8 1.0 C4A I:HEM501 3.0 0.4 1.0 C1B I:HEM501 3.1 0.6 1.0 C4C I:HEM501 3.1 0.5 1.0 C4B I:HEM501 3.1 0.8 1.0 C1C I:HEM501 3.2 0.6 1.0 CHA I:HEM501 3.4 0.0 1.0 CHD I:HEM501 3.4 0.8 1.0 CHB I:HEM501 3.4 0.7 1.0 CB I:CYS356 3.6 0.6 1.0 CHC I:HEM501 3.6 0.1 1.0 C34 I:QR8502 4.0 0.2 1.0 C3D I:HEM501 4.2 0.9 1.0 C2D I:HEM501 4.2 0.6 1.0 CA I:CYS356 4.2 0.7 1.0 C3A I:HEM501 4.2 0.0 1.0 C2A I:HEM501 4.3 0.3 1.0 C2B I:HEM501 4.3 0.5 1.0 C3C I:HEM501 4.3 0.5 1.0 C3B I:HEM501 4.4 0.7 1.0 C2C I:HEM501 4.4 0.5 1.0 O11 I:QR8502 4.7 0.2 1.0 CG2 I:THR248 4.8 0.1 1.0 CB I:ALA244 4.9 0.6 1.0 OG1 I:THR248 4.9 0.4 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