Iron in PDB 6zi3: Crystal Structure of Olep-6DEB Bound to L-Rhamnose

The structure of Crystal Structure of Olep-6DEB Bound to L-Rhamnose, PDB code: 6zi3 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)	48.09 / 2.08
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	247.379, 111.149, 159.144, 90.00, 129.40, 90.00
R / Rfree (%)	17.2 / 22.5

The structure of Crystal Structure of Olep-6DEB Bound to L-Rhamnose also contains other interesting chemical elements:

Sodium

(Na)

7 atoms

The binding sites of Iron atom in the Crystal Structure of Olep-6DEB Bound to L-Rhamnose (pdb code 6zi3). 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-6DEB Bound to L-Rhamnose, PDB code: 6zi3:
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-6DEB 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-6DEB Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:37.5 occ:1.00 FE A:HEM501 0.0 37.5 1.0 ND A:HEM501 1.8 34.4 1.0 NA A:HEM501 2.0 34.0 1.0 NC A:HEM501 2.0 36.6 1.0 NB A:HEM501 2.0 35.5 1.0 SG A:CYS356 2.4 41.8 1.0 C1D A:HEM501 2.8 36.0 1.0 C4D A:HEM501 2.9 34.5 1.0 C1A A:HEM501 2.9 34.0 1.0 C4B A:HEM501 3.0 37.3 1.0 C4C A:HEM501 3.0 37.6 1.0 C1B A:HEM501 3.0 35.3 1.0 C4A A:HEM501 3.0 35.1 1.0 C1C A:HEM501 3.1 37.6 1.0 CHA A:HEM501 3.3 33.1 1.0 CHD A:HEM501 3.3 36.6 1.0 CB A:CYS356 3.4 39.0 1.0 CHB A:HEM501 3.4 36.5 1.0 CHC A:HEM501 3.4 36.9 1.0 CA A:CYS356 4.0 37.9 1.0 C2D A:HEM501 4.1 35.2 1.0 C3D A:HEM501 4.1 34.7 1.0 C23 A:DEB502 4.1 42.9 1.0 C2A A:HEM501 4.1 32.5 1.0 C3A A:HEM501 4.2 32.5 1.0 C3C A:HEM501 4.2 39.8 1.0 C3B A:HEM501 4.2 38.8 1.0 C2B A:HEM501 4.2 35.8 1.0 C2C A:HEM501 4.2 37.2 1.0 CG2 A:THR248 4.5 40.0 1.0 C8 A:DEB502 4.6 42.1 1.0 C A:CYS356 4.8 41.5 1.0 N A:GLY358 4.8 42.1 1.0 N A:ILE357 4.9 41.1 1.0 C9 A:DEB502 5.0 42.1 1.0 CB A:ALA244 5.0 41.5 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Olep-6DEB 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-6DEB Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:35.5 occ:1.00 FE B:HEM501 0.0 35.5 1.0 ND B:HEM501 1.8 33.1 1.0 NA B:HEM501 2.0 35.1 1.0 NB B:HEM501 2.0 33.6 1.0 NC B:HEM501 2.1 34.1 1.0 SG B:CYS356 2.3 36.9 1.0 C4D B:HEM501 2.8 34.6 1.0 C1D B:HEM501 2.8 34.5 1.0 C1A B:HEM501 3.0 32.5 1.0 C4B B:HEM501 3.0 34.0 1.0 C4C B:HEM501 3.0 32.5 1.0 C1B B:HEM501 3.0 36.2 1.0 C4A B:HEM501 3.0 35.5 1.0 C1C B:HEM501 3.1 34.0 1.0 CHA B:HEM501 3.3 32.9 1.0 CB B:CYS356 3.3 36.9 1.0 CHD B:HEM501 3.3 33.1 1.0 CHB B:HEM501 3.4 35.5 1.0 CHC B:HEM501 3.4 33.7 1.0 C23 B:DEB502 4.0 39.8 1.0 CA B:CYS356 4.0 35.9 1.0 C2D B:HEM501 4.1 33.7 1.0 C3D B:HEM501 4.1 35.1 1.0 C3A B:HEM501 4.2 36.0 1.0 C2A B:HEM501 4.2 33.4 1.0 C3C B:HEM501 4.2 34.9 1.0 C2B B:HEM501 4.2 36.1 1.0 C3B B:HEM501 4.2 37.4 1.0 C2C B:HEM501 4.2 35.0 1.0 CG2 B:THR248 4.6 34.6 1.0 C8 B:DEB502 4.7 38.6 1.0 N B:GLY358 4.8 36.1 1.0 C B:CYS356 4.8 36.1 1.0 N B:ILE357 5.0 37.6 1.0 CD1 B:PHE349 5.0 35.8 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Olep-6DEB 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-6DEB Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:33.9 occ:1.00 FE C:HEM501 0.0 33.9 1.0 ND C:HEM501 1.9 32.5 1.0 NA C:HEM501 2.0 30.9 1.0 NB C:HEM501 2.1 32.4 1.0 NC C:HEM501 2.1 32.4 1.0 SG C:CYS356 2.4 35.3 1.0 C4D C:HEM501 2.9 31.2 1.0 C1D C:HEM501 2.9 32.1 1.0 C1A C:HEM501 2.9 31.5 1.0 C4B C:HEM501 3.0 32.0 1.0 C4C C:HEM501 3.0 32.9 1.0 C4A C:HEM501 3.0 33.4 1.0 C1B C:HEM501 3.0 34.5 1.0 C1C C:HEM501 3.1 32.6 1.0 CHA C:HEM501 3.3 33.7 1.0 CHD C:HEM501 3.3 30.9 1.0 CB C:CYS356 3.3 34.3 1.0 CHC C:HEM501 3.4 31.8 1.0 CHB C:HEM501 3.4 33.5 1.0 C23 C:DEB502 4.0 36.6 1.0 C2D C:HEM501 4.1 31.2 1.0 CA C:CYS356 4.1 33.0 1.0 C3D C:HEM501 4.1 32.5 1.0 C2A C:HEM501 4.1 32.4 1.0 C3A C:HEM501 4.1 31.1 1.0 C3C C:HEM501 4.2 32.8 1.0 C3B C:HEM501 4.2 33.5 1.0 C2C C:HEM501 4.2 31.3 1.0 C2B C:HEM501 4.2 34.3 1.0 CG2 C:THR248 4.5 33.4 1.0 C8 C:DEB502 4.7 36.2 1.0 C C:CYS356 4.8 35.0 1.0 CB C:ALA244 4.9 38.1 1.0 N C:GLY358 4.9 36.1 1.0 CD1 C:PHE349 5.0 32.6 0.5

Iron binding site 4 out of 6 in the Crystal Structure of Olep-6DEB 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-6DEB Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:44.9 occ:1.00 FE D:HEM501 0.0 44.9 1.0 ND D:HEM501 1.8 38.4 1.0 NA D:HEM501 2.0 42.2 1.0 NB D:HEM501 2.0 40.2 1.0 NC D:HEM501 2.1 41.4 1.0 SG D:CYS356 2.4 47.3 1.0 C1D D:HEM501 2.8 42.1 1.0 C4D D:HEM501 2.8 42.2 1.0 C1A D:HEM501 3.0 42.0 1.0 C4B D:HEM501 3.0 42.8 1.0 C1B D:HEM501 3.0 41.7 1.0 C4C D:HEM501 3.0 41.0 1.0 C4A D:HEM501 3.0 43.6 1.0 C1C D:HEM501 3.1 42.8 1.0 CHA D:HEM501 3.3 42.5 1.0 CHD D:HEM501 3.3 41.7 1.0 CB D:CYS356 3.4 45.7 1.0 CHB D:HEM501 3.4 44.3 1.0 CHC D:HEM501 3.4 42.0 1.0 C23 D:DEB502 3.8 52.0 1.0 C2D D:HEM501 4.0 41.6 1.0 C3D D:HEM501 4.0 41.3 1.0 CA D:CYS356 4.1 47.4 1.0 C2A D:HEM501 4.1 42.8 1.0 C3A D:HEM501 4.2 44.7 1.0 C3B D:HEM501 4.2 43.5 1.0 C2B D:HEM501 4.2 41.5 1.0 C3C D:HEM501 4.2 47.1 1.0 C2C D:HEM501 4.2 44.5 1.0 CG2 D:THR248 4.4 46.4 1.0 C8 D:DEB502 4.5 54.7 1.0 C D:CYS356 4.9 47.5 1.0 N D:GLY358 4.9 45.5 1.0 CB D:ALA244 4.9 49.5 1.0 C9 D:DEB502 5.0 51.6 1.0

Iron binding site 5 out of 6 in the Crystal Structure of Olep-6DEB 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-6DEB Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe501 b:42.0 occ:1.00 FE E:HEM501 0.0 42.0 1.0 ND E:HEM501 1.9 43.7 1.0 NA E:HEM501 2.0 41.8 1.0 NC E:HEM501 2.1 39.7 1.0 NB E:HEM501 2.1 39.8 1.0 SG E:CYS356 2.5 44.5 1.0 C4D E:HEM501 2.9 43.5 1.0 C1D E:HEM501 2.9 41.5 1.0 C1A E:HEM501 2.9 46.1 1.0 C4C E:HEM501 3.0 40.8 1.0 C1B E:HEM501 3.0 45.2 1.0 C4A E:HEM501 3.0 46.9 1.0 C4B E:HEM501 3.0 41.0 1.0 C1C E:HEM501 3.1 40.5 1.0 CHA E:HEM501 3.3 44.1 1.0 CB E:CYS356 3.3 44.9 1.0 CHD E:HEM501 3.3 42.5 1.0 CHB E:HEM501 3.4 48.4 1.0 CHC E:HEM501 3.4 41.5 1.0 C23 E:DEB502 4.1 44.4 1.0 CA E:CYS356 4.1 45.8 1.0 C2D E:HEM501 4.1 44.4 1.0 C3D E:HEM501 4.1 44.2 1.0 C2A E:HEM501 4.2 45.1 1.0 C3A E:HEM501 4.2 44.2 1.0 C3C E:HEM501 4.2 41.7 1.0 C2B E:HEM501 4.2 47.0 1.0 C2C E:HEM501 4.2 41.6 1.0 C3B E:HEM501 4.3 44.3 1.0 CG2 E:THR248 4.4 45.0 1.0 C8 E:DEB502 4.7 44.6 1.0 C E:CYS356 4.8 48.0 1.0 N E:GLY358 4.9 49.8 1.0 N E:ILE357 5.0 46.7 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Olep-6DEB 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-6DEB Bound to L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe702 b:56.0 occ:1.00 FE F:HEM702 0.0 56.0 1.0 ND F:HEM702 1.9 59.1 1.0 NA F:HEM702 2.0 56.3 1.0 NC F:HEM702 2.1 58.0 1.0 NB F:HEM702 2.1 62.4 1.0 SG F:CYS356 2.3 56.7 1.0 C4D F:HEM702 2.9 56.3 1.0 C1D F:HEM702 2.9 53.4 1.0 C1A F:HEM702 2.9 54.9 1.0 C4C F:HEM702 3.0 57.0 1.0 C4A F:HEM702 3.0 56.4 1.0 C1B F:HEM702 3.0 65.0 1.0 C4B F:HEM702 3.0 65.4 1.0 C1C F:HEM702 3.1 59.6 1.0 CB F:CYS356 3.3 56.4 1.0 CHA F:HEM702 3.3 55.2 1.0 CHD F:HEM702 3.3 53.3 1.0 CHB F:HEM702 3.4 59.9 1.0 CHC F:HEM702 3.5 61.1 1.0 CA F:CYS356 4.0 55.9 1.0 C23 F:DEB703 4.0 58.0 1.0 C2D F:HEM702 4.1 53.3 1.0 C3D F:HEM702 4.1 55.3 1.0 C2A F:HEM702 4.1 57.9 1.0 C3A F:HEM702 4.1 59.6 1.0 C3C F:HEM702 4.2 58.7 1.0 C2C F:HEM702 4.2 62.4 1.0 C2B F:HEM702 4.2 69.5 1.0 C3B F:HEM702 4.3 73.1 1.0 C8 F:DEB703 4.6 56.0 1.0 CG2 F:THR248 4.7 57.1 1.0 C F:CYS356 4.8 55.4 1.0 N F:GLY358 4.9 56.6 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