Iron in PDB 5mns: Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate

The structure of Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate, PDB code: 5mns was solved by G.Parisi, C.Savino, L.C.Montemiglio, B.Vallone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	120.00 / 2.62
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	247.600, 110.800, 159.100, 90.00, 129.60, 90.00
R / Rfree (%)	20.8 / 25.8

The binding sites of Iron atom in the Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate (pdb code 5mns). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate, PDB code: 5mns:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:28.7 occ:1.00 FE A:HEM501 0.0 28.7 1.0 SG A:CYS356 1.3 42.0 1.0 ND A:HEM501 1.9 26.5 1.0 NA A:HEM501 2.0 26.5 1.0 NC A:HEM501 2.1 28.2 1.0 NB A:HEM501 2.1 27.5 1.0 CB A:CYS356 2.8 39.4 1.0 C4D A:HEM501 2.9 26.5 1.0 C1D A:HEM501 2.9 25.4 1.0 C1A A:HEM501 3.0 26.2 1.0 C4B A:HEM501 3.0 27.8 1.0 C4C A:HEM501 3.0 28.2 1.0 C4A A:HEM501 3.1 26.7 1.0 C1B A:HEM501 3.1 28.2 1.0 C1C A:HEM501 3.1 28.5 1.0 CHA A:HEM501 3.4 26.2 1.0 CHD A:HEM501 3.4 26.6 1.0 CHC A:HEM501 3.4 27.7 1.0 CHB A:HEM501 3.5 27.5 1.0 C23 A:DEB502 4.0 28.2 1.0 CA A:CYS356 4.1 38.6 1.0 C2D A:HEM501 4.2 24.7 1.0 C3D A:HEM501 4.2 25.6 1.0 C3A A:HEM501 4.2 26.2 1.0 C2A A:HEM501 4.2 26.3 1.0 C3C A:HEM501 4.3 28.7 1.0 C3B A:HEM501 4.3 29.3 1.0 C2B A:HEM501 4.3 28.6 1.0 C2C A:HEM501 4.3 28.7 1.0 CG2 A:THR248 4.3 37.4 1.0 C8 A:DEB502 4.5 27.6 1.0 C9 A:DEB502 4.8 28.4 1.0 C A:CYS356 4.9 40.4 1.0 O24 A:DEB502 4.9 27.5 1.0 CB A:ALA244 5.0 32.0 1.0

Iron binding site 2 out of 6 in the Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:21.9 occ:1.00 FE B:HEM501 0.0 21.9 1.0 ND B:HEM501 1.9 21.2 1.0 NA B:HEM501 2.0 20.6 1.0 NB B:HEM501 2.1 20.6 1.0 NC B:HEM501 2.1 21.4 1.0 SG B:CYS356 2.3 30.1 1.0 C4D B:HEM501 2.9 21.6 1.0 C1D B:HEM501 2.9 21.3 1.0 C4B B:HEM501 3.0 22.0 1.0 C1A B:HEM501 3.0 21.0 1.0 C4C B:HEM501 3.0 21.8 1.0 C1B B:HEM501 3.1 21.4 1.0 C4A B:HEM501 3.1 20.9 1.0 C1C B:HEM501 3.1 22.1 1.0 CHD B:HEM501 3.4 21.7 1.0 CHA B:HEM501 3.4 21.4 1.0 CB B:CYS356 3.4 32.2 1.0 CHC B:HEM501 3.4 22.1 1.0 CHB B:HEM501 3.5 20.9 1.0 C23 B:DEB502 3.9 31.1 1.0 CA B:CYS356 4.1 32.1 1.0 C3D B:HEM501 4.1 22.2 1.0 C2D B:HEM501 4.1 21.6 1.0 C2A B:HEM501 4.2 21.6 1.0 C3A B:HEM501 4.3 21.3 1.0 C3C B:HEM501 4.3 22.8 1.0 C3B B:HEM501 4.3 22.9 1.0 C2B B:HEM501 4.3 22.2 1.0 C2C B:HEM501 4.3 22.6 1.0 CG2 B:THR248 4.5 34.6 1.0 C8 B:DEB502 4.6 31.4 1.0 CB B:ALA244 4.9 30.1 1.0 C B:CYS356 4.9 32.8 1.0

Iron binding site 3 out of 6 in the Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:27.4 occ:1.00 FE C:HEM501 0.0 27.4 1.0 ND C:HEM501 1.9 25.3 1.0 NA C:HEM501 2.0 25.0 1.0 SG C:CYS356 2.1 29.4 1.0 NC C:HEM501 2.1 26.2 1.0 NB C:HEM501 2.1 27.1 1.0 C1D C:HEM501 2.9 25.1 1.0 C4D C:HEM501 2.9 25.3 1.0 C1A C:HEM501 3.0 24.7 1.0 C4B C:HEM501 3.0 27.8 1.0 C4C C:HEM501 3.1 26.4 1.0 C4A C:HEM501 3.1 25.0 1.0 C1B C:HEM501 3.1 27.4 1.0 C1C C:HEM501 3.1 26.7 1.0 CHA C:HEM501 3.4 24.5 1.0 CHD C:HEM501 3.4 26.3 1.0 CB C:CYS356 3.4 28.9 1.0 CHC C:HEM501 3.4 26.7 1.0 CHB C:HEM501 3.5 25.8 1.0 C23 C:DEB502 3.8 27.2 1.0 CA C:CYS356 4.1 29.2 1.0 C2D C:HEM501 4.2 24.8 1.0 C3D C:HEM501 4.2 24.9 1.0 C3A C:HEM501 4.2 24.2 1.0 C2A C:HEM501 4.2 24.6 1.0 C3C C:HEM501 4.3 26.9 1.0 C2B C:HEM501 4.3 29.4 1.0 C3B C:HEM501 4.3 30.4 1.0 C2C C:HEM501 4.3 27.4 1.0 CG2 C:THR248 4.5 27.8 1.0 C8 C:DEB502 4.6 27.1 1.0 CB C:ALA244 4.9 31.0 1.0 C C:CYS356 4.9 28.9 1.0

Iron binding site 4 out of 6 in the Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:27.0 occ:1.00 FE D:HEM501 0.0 27.0 1.0 ND D:HEM501 1.9 23.6 1.0 NA D:HEM501 2.0 23.8 1.0 NC D:HEM501 2.1 23.6 1.0 NB D:HEM501 2.1 22.1 1.0 SG D:CYS356 2.5 42.4 1.0 C1D D:HEM501 2.9 23.7 1.0 C4D D:HEM501 2.9 24.3 1.0 C4C D:HEM501 3.0 24.4 1.0 C1A D:HEM501 3.0 24.3 1.0 C4A D:HEM501 3.0 24.0 1.0 C4B D:HEM501 3.0 23.4 1.0 C1B D:HEM501 3.1 22.6 1.0 C1C D:HEM501 3.1 23.2 1.0 CHD D:HEM501 3.3 23.8 1.0 CHA D:HEM501 3.4 23.9 1.0 CHB D:HEM501 3.4 23.2 1.0 CHC D:HEM501 3.5 23.3 1.0 CB D:CYS356 3.6 41.7 1.0 C23 D:DEB502 4.1 42.7 1.0 C2D D:HEM501 4.1 24.3 1.0 C3D D:HEM501 4.1 26.4 1.0 CA D:CYS356 4.2 42.1 1.0 C3A D:HEM501 4.2 24.8 1.0 C2A D:HEM501 4.2 25.7 1.0 C3C D:HEM501 4.3 24.5 1.0 C2B D:HEM501 4.3 23.5 1.0 C2C D:HEM501 4.3 23.6 1.0 C3B D:HEM501 4.3 23.9 1.0 CG2 D:THR248 4.4 38.9 1.0 C8 D:DEB502 4.6 43.0 1.0 CB D:ALA244 4.8 42.3 1.0 C D:CYS356 4.9 41.6 1.0 C9 D:DEB502 4.9 42.3 1.0 N D:ILE357 5.0 39.2 1.0

Iron binding site 5 out of 6 in the Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe501 b:45.8 occ:1.00 FE E:HEM501 0.0 45.8 1.0 SG E:CYS356 1.0 47.0 1.0 ND E:HEM501 1.8 44.0 1.0 NA E:HEM501 1.9 44.0 1.0 NC E:HEM501 2.0 43.5 1.0 NB E:HEM501 2.1 44.9 1.0 CB E:CYS356 2.8 49.6 1.0 C4D E:HEM501 2.8 44.0 1.0 C1D E:HEM501 2.8 43.2 1.0 C1A E:HEM501 2.9 45.7 1.0 C4C E:HEM501 3.0 41.9 1.0 C4A E:HEM501 3.0 44.6 1.0 C1B E:HEM501 3.0 46.3 1.0 C4B E:HEM501 3.0 44.5 1.0 C1C E:HEM501 3.1 42.4 1.0 CHA E:HEM501 3.3 45.2 1.0 CHD E:HEM501 3.3 42.3 1.0 CHB E:HEM501 3.4 45.4 1.0 CHC E:HEM501 3.5 43.8 1.0 CA E:CYS356 3.7 49.6 1.0 C23 E:DEB502 4.0 42.9 1.0 C3D E:HEM501 4.1 42.9 1.0 C2D E:HEM501 4.1 42.7 1.0 C2A E:HEM501 4.1 46.9 1.0 C3A E:HEM501 4.1 44.6 1.0 C3C E:HEM501 4.2 40.1 1.0 C2C E:HEM501 4.2 40.1 1.0 C2B E:HEM501 4.2 46.4 1.0 C3B E:HEM501 4.3 46.8 1.0 CG2 E:THR248 4.5 46.8 1.0 C8 E:DEB502 4.6 43.4 1.0 C E:CYS356 4.6 47.3 1.0 N E:CYS356 4.8 50.1 1.0 N E:ILE357 4.9 44.5 1.0 CB E:ALA244 4.9 42.7 1.0 C9 E:DEB502 4.9 42.7 1.0

Iron binding site 6 out of 6 in the Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structural and Functional Characterization of Olep in Complex with 6DEB in Sodium Formate within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe501 b:73.3 occ:1.00 FE F:HEM501 0.0 73.3 1.0 ND F:HEM501 1.9 73.7 1.0 NA F:HEM501 2.0 69.5 1.0 NC F:HEM501 2.1 75.4 1.0 NB F:HEM501 2.1 74.7 1.0 SG F:CYS356 2.5 66.2 1.0 C1D F:HEM501 2.9 74.1 1.0 C4D F:HEM501 2.9 70.8 1.0 C1A F:HEM501 3.0 69.0 1.0 C4A F:HEM501 3.1 66.4 1.0 C4C F:HEM501 3.1 75.3 1.0 C4B F:HEM501 3.1 75.9 1.0 C1B F:HEM501 3.1 72.8 1.0 C1C F:HEM501 3.1 74.4 1.0 CHD F:HEM501 3.4 76.5 1.0 CHA F:HEM501 3.4 70.6 1.0 CHB F:HEM501 3.5 69.5 1.0 CHC F:HEM501 3.5 75.3 1.0 CB F:CYS356 3.7 65.0 1.0 C23 F:DEB502 4.1 60.6 1.0 C3D F:HEM501 4.2 69.4 1.0 C2D F:HEM501 4.2 72.5 1.0 C2A F:HEM501 4.2 63.0 1.0 C3A F:HEM501 4.3 62.3 1.0 C3C F:HEM501 4.3 73.4 1.0 C2C F:HEM501 4.3 72.4 1.0 C2B F:HEM501 4.4 75.2 1.0 CA F:CYS356 4.4 64.4 1.0 C3B F:HEM501 4.4 77.2 1.0 C8 F:DEB502 4.4 60.6 1.0 CG2 F:THR248 4.5 67.2 1.0 CB F:ALA244 4.6 61.3 1.0 C9 F:DEB502 4.8 60.3 1.0 O24 F:DEB502 4.8 60.9 1.0

G.Parisi, L.C.Montemiglio, A.Giuffre, A.Macone, A.Scaglione, G.Cerutti, C.Exertier, C.Savino, B.Vallone. Substrate-Induced Conformational Change in Cytochrome P450 Olep. Faseb J. V. 33 1787 2019.
ISSN: ESSN 1530-6860
PubMed: 30207799
DOI: 10.1096/FJ.201800450RR