Iron in PDB 3dl9: Crystal Structure of CYP2R1 in Complex with 1-Alpha-Hydroxy-Vitamin D2

The structure of Crystal Structure of CYP2R1 in Complex with 1-Alpha-Hydroxy-Vitamin D2, PDB code: 3dl9 was solved by N.V.Strushkevich, W.Tempel, A.A.Gilep, P.Loppnau, C.H.Arrowsmith, A.M.Edwards, C.Bountra, M.Wilkstrom, A.Bochkarev, H.Park, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.72
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	137.303, 163.040, 152.588, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.8

The binding sites of Iron atom in the Crystal Structure of CYP2R1 in Complex with 1-Alpha-Hydroxy-Vitamin D2 (pdb code 3dl9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of CYP2R1 in Complex with 1-Alpha-Hydroxy-Vitamin D2, PDB code: 3dl9:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of CYP2R1 in Complex with 1-Alpha-Hydroxy-Vitamin D2


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 CYP2R1 in Complex with 1-Alpha-Hydroxy-Vitamin D2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:29.9 occ:0.50 FE A:HEM601 0.0 29.9 0.5 FE A:HEM601 0.5 26.5 0.5 ND A:HEM601 2.0 27.0 0.5 NC A:HEM601 2.0 30.3 0.5 NA A:HEM601 2.0 27.2 0.5 NA A:HEM601 2.0 30.2 0.5 NB A:HEM601 2.1 30.4 0.5 ND A:HEM601 2.1 30.4 0.5 NC A:HEM601 2.1 27.3 0.5 NB A:HEM601 2.1 27.0 0.5 SG A:CYS448 2.5 28.9 1.0 C4D A:HEM601 3.0 27.4 0.5 C1D A:HEM601 3.0 27.4 0.5 C1A A:HEM601 3.0 27.0 0.5 C1C A:HEM601 3.0 30.7 0.5 C4C A:HEM601 3.0 30.3 0.5 C4B A:HEM601 3.0 30.4 0.5 C4A A:HEM601 3.1 30.6 0.5 C1A A:HEM601 3.1 30.2 0.5 C1D A:HEM601 3.1 30.3 0.5 C4D A:HEM601 3.1 30.1 0.5 C4A A:HEM601 3.1 27.1 0.5 C4C A:HEM601 3.1 27.2 0.5 C1B A:HEM601 3.1 30.1 0.5 C1C A:HEM601 3.1 27.3 0.5 C1B A:HEM601 3.1 27.2 0.5 C4B A:HEM601 3.1 27.5 0.5 CHA A:HEM601 3.3 27.2 0.5 CHC A:HEM601 3.4 30.4 0.5 CHD A:HEM601 3.4 27.3 0.5 CHD A:HEM601 3.4 30.2 0.5 CHA A:HEM601 3.4 30.2 0.5 CHB A:HEM601 3.4 30.2 0.5 CHB A:HEM601 3.5 26.9 0.5 CB A:CYS448 3.5 28.4 1.0 CHC A:HEM601 3.5 27.3 0.5 CA A:CYS448 4.1 29.8 1.0 C3D A:HEM601 4.2 27.7 0.5 C3C A:HEM601 4.2 30.6 0.5 C2C A:HEM601 4.2 30.6 0.5 C2D A:HEM601 4.2 27.7 0.5 C2A A:HEM601 4.2 26.5 0.5 C3A A:HEM601 4.3 27.2 0.5 C3A A:HEM601 4.3 30.7 0.5 C2A A:HEM601 4.3 30.3 0.5 C3B A:HEM601 4.3 30.5 0.5 C3D A:HEM601 4.3 29.6 0.5 C2D A:HEM601 4.3 30.0 0.5 C3C A:HEM601 4.3 27.2 0.5 C2B A:HEM601 4.3 30.1 0.5 C2C A:HEM601 4.3 27.5 0.5 C2B A:HEM601 4.4 27.4 0.5 C3B A:HEM601 4.4 27.4 0.5 CB A:ALA310 4.6 34.7 1.0 O A:ALA310 4.7 41.0 1.0 N A:LEU449 4.9 32.6 1.0 OG1 A:THR314 5.0 34.6 1.0 C A:CYS448 5.0 31.1 1.0

Iron binding site 2 out of 4 in the Crystal Structure of CYP2R1 in Complex with 1-Alpha-Hydroxy-Vitamin D2


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 CYP2R1 in Complex with 1-Alpha-Hydroxy-Vitamin D2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:26.5 occ:0.50 FE A:HEM601 0.0 26.5 0.5 FE A:HEM601 0.5 29.9 0.5 SG A:CYS448 2.0 28.9 1.0 NC A:HEM601 2.0 30.3 0.5 NA A:HEM601 2.0 27.2 0.5 NB A:HEM601 2.0 27.0 0.5 ND A:HEM601 2.1 27.0 0.5 NC A:HEM601 2.1 27.3 0.5 NB A:HEM601 2.1 30.4 0.5 ND A:HEM601 2.2 30.4 0.5 NA A:HEM601 2.2 30.2 0.5 C1C A:HEM601 2.9 30.7 0.5 C4C A:HEM601 3.0 30.3 0.5 C1B A:HEM601 3.0 27.2 0.5 C4B A:HEM601 3.0 30.4 0.5 C4A A:HEM601 3.0 27.1 0.5 C4B A:HEM601 3.0 27.5 0.5 C1A A:HEM601 3.1 27.0 0.5 CB A:CYS448 3.1 28.4 1.0 C1D A:HEM601 3.1 27.4 0.5 C4D A:HEM601 3.1 27.4 0.5 C4C A:HEM601 3.1 27.2 0.5 C1C A:HEM601 3.1 27.3 0.5 C1D A:HEM601 3.1 30.3 0.5 C4D A:HEM601 3.2 30.1 0.5 C1A A:HEM601 3.2 30.2 0.5 C1B A:HEM601 3.2 30.1 0.5 C4A A:HEM601 3.2 30.6 0.5 CHC A:HEM601 3.3 30.4 0.5 CHB A:HEM601 3.4 26.9 0.5 CHD A:HEM601 3.4 30.2 0.5 CHD A:HEM601 3.4 27.3 0.5 CHA A:HEM601 3.4 27.2 0.5 CHC A:HEM601 3.5 27.3 0.5 CHA A:HEM601 3.5 30.2 0.5 CHB A:HEM601 3.6 30.2 0.5 CA A:CYS448 3.7 29.8 1.0 C2C A:HEM601 4.1 30.6 0.5 C3C A:HEM601 4.1 30.6 0.5 C2B A:HEM601 4.2 27.4 0.5 C3B A:HEM601 4.2 27.4 0.5 C3A A:HEM601 4.3 27.2 0.5 C2A A:HEM601 4.3 26.5 0.5 C3B A:HEM601 4.3 30.5 0.5 C3D A:HEM601 4.3 27.7 0.5 C2D A:HEM601 4.3 27.7 0.5 C2C A:HEM601 4.4 27.5 0.5 C3C A:HEM601 4.4 27.2 0.5 C2B A:HEM601 4.4 30.1 0.5 C3D A:HEM601 4.4 29.6 0.5 C2D A:HEM601 4.4 30.0 0.5 C2A A:HEM601 4.4 30.3 0.5 C3A A:HEM601 4.4 30.7 0.5 N A:LEU449 4.5 32.6 1.0 C A:CYS448 4.5 31.1 1.0 N A:GLY450 4.6 31.3 1.0 CD2 A:PHE441 4.8 25.9 1.0 N A:CYS448 4.9 31.0 1.0 CB A:ALA310 5.0 34.7 1.0

Iron binding site 3 out of 4 in the Crystal Structure of CYP2R1 in Complex with 1-Alpha-Hydroxy-Vitamin D2


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 CYP2R1 in Complex with 1-Alpha-Hydroxy-Vitamin D2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:27.8 occ:0.50 FE B:HEM601 0.0 27.8 0.5 FE B:HEM601 0.6 32.4 0.5 NA B:HEM601 1.7 31.1 0.5 ND B:HEM601 1.9 26.6 0.5 NC B:HEM601 2.0 26.4 0.5 NB B:HEM601 2.1 31.1 0.5 NA B:HEM601 2.2 25.9 0.5 ND B:HEM601 2.2 30.8 0.5 NB B:HEM601 2.2 25.6 0.5 SG B:CYS448 2.2 37.1 1.0 NC B:HEM601 2.4 30.3 0.5 C1A B:HEM601 2.8 32.1 0.5 C4A B:HEM601 2.8 31.7 0.5 C1B B:HEM601 2.9 31.3 0.5 C1D B:HEM601 3.0 27.3 0.5 C4C B:HEM601 3.0 26.8 0.5 C4D B:HEM601 3.0 27.6 0.5 C1C B:HEM601 3.0 26.3 0.5 C4D B:HEM601 3.0 31.2 0.5 C1A B:HEM601 3.1 26.2 0.5 C4B B:HEM601 3.1 30.9 0.5 CB B:CYS448 3.1 38.2 1.0 C4B B:HEM601 3.2 25.8 0.5 C4A B:HEM601 3.2 25.7 0.5 CHB B:HEM601 3.2 31.6 0.5 CHA B:HEM601 3.2 31.4 0.5 C1B B:HEM601 3.2 25.5 0.5 C1D B:HEM601 3.3 30.8 0.5 CHD B:HEM601 3.3 27.0 0.5 C1C B:HEM601 3.4 30.3 0.5 CHA B:HEM601 3.4 26.6 0.5 C4C B:HEM601 3.4 30.3 0.5 CHC B:HEM601 3.4 25.9 0.5 CHB B:HEM601 3.6 25.8 0.5 CHC B:HEM601 3.6 30.5 0.5 CA B:CYS448 3.7 39.2 1.0 CHD B:HEM601 3.8 30.6 0.5 C2A B:HEM601 4.0 32.2 0.5 C3A B:HEM601 4.0 31.9 0.5 C2B B:HEM601 4.2 31.1 0.5 C3D B:HEM601 4.2 27.8 0.5 C3C B:HEM601 4.2 26.4 0.5 C2D B:HEM601 4.2 27.4 0.5 C2C B:HEM601 4.2 26.4 0.5 N B:LEU449 4.2 39.5 1.0 C3B B:HEM601 4.3 31.1 0.5 C3D B:HEM601 4.3 31.7 0.5 C2A B:HEM601 4.4 26.3 0.5 C B:CYS448 4.4 39.8 1.0 C3A B:HEM601 4.4 25.6 0.5 C3B B:HEM601 4.4 25.1 0.5 C2B B:HEM601 4.4 24.8 0.5 C2D B:HEM601 4.5 31.0 0.5 N B:GLY450 4.5 37.2 1.0 C2C B:HEM601 4.6 29.5 0.5 C3C B:HEM601 4.7 29.5 0.5 N B:CYS448 4.9 39.6 1.0 CB B:ALA310 5.0 37.4 1.0 CD2 B:PHE441 5.0 36.3 1.0

Iron binding site 4 out of 4 in the Crystal Structure of CYP2R1 in Complex with 1-Alpha-Hydroxy-Vitamin D2


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 CYP2R1 in Complex with 1-Alpha-Hydroxy-Vitamin D2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:32.4 occ:0.50 FE B:HEM601 0.0 32.4 0.5 FE B:HEM601 0.6 27.8 0.5 NB B:HEM601 1.8 25.6 0.5 NC B:HEM601 2.0 26.4 0.5 NB B:HEM601 2.0 31.1 0.5 NC B:HEM601 2.0 30.3 0.5 NA B:HEM601 2.0 31.1 0.5 NA B:HEM601 2.1 25.9 0.5 ND B:HEM601 2.1 30.8 0.5 ND B:HEM601 2.3 26.6 0.5 SG B:CYS448 2.6 37.1 1.0 C4B B:HEM601 2.8 25.8 0.5 C1B B:HEM601 2.9 25.5 0.5 C1C B:HEM601 2.9 26.3 0.5 C4B B:HEM601 3.0 30.9 0.5 C1C B:HEM601 3.0 30.3 0.5 C1B B:HEM601 3.0 31.3 0.5 C4A B:HEM601 3.0 25.7 0.5 C4C B:HEM601 3.1 30.3 0.5 C1A B:HEM601 3.1 32.1 0.5 C4A B:HEM601 3.1 31.7 0.5 C4C B:HEM601 3.1 26.8 0.5 C4D B:HEM601 3.1 31.2 0.5 C1D B:HEM601 3.1 30.8 0.5 C1A B:HEM601 3.2 26.2 0.5 CHC B:HEM601 3.2 25.9 0.5 C1D B:HEM601 3.3 27.3 0.5 C4D B:HEM601 3.3 27.6 0.5 CHB B:HEM601 3.3 25.8 0.5 CHC B:HEM601 3.4 30.5 0.5 CHB B:HEM601 3.4 31.6 0.5 CHA B:HEM601 3.5 31.4 0.5 CHD B:HEM601 3.5 30.6 0.5 CHD B:HEM601 3.6 27.0 0.5 CB B:CYS448 3.6 38.2 1.0 CHA B:HEM601 3.6 26.6 0.5 C3B B:HEM601 4.0 25.1 0.5 C2B B:HEM601 4.1 24.8 0.5 C2C B:HEM601 4.2 26.4 0.5 C3B B:HEM601 4.2 31.1 0.5 C2B B:HEM601 4.2 31.1 0.5 CA B:CYS448 4.2 39.2 1.0 C2C B:HEM601 4.2 29.5 0.5 C3C B:HEM601 4.3 26.4 0.5 C3C B:HEM601 4.3 29.5 0.5 C2A B:HEM601 4.3 32.2 0.5 C3A B:HEM601 4.3 31.9 0.5 C3A B:HEM601 4.3 25.6 0.5 C3D B:HEM601 4.3 31.7 0.5 C2D B:HEM601 4.3 31.0 0.5 C2A B:HEM601 4.4 26.3 0.5 C3D B:HEM601 4.5 27.8 0.5 C2D B:HEM601 4.5 27.4 0.5 O B:ALA310 4.7 41.6 1.0 CB B:ALA310 4.7 37.4 1.0 CAB B:V2H602 4.8 42.8 1.0 CG2 B:THR314 4.8 38.0 1.0 N B:LEU449 4.8 39.5 1.0 OG1 B:THR314 4.9 40.2 1.0 C B:CYS448 5.0 39.8 1.0 N B:GLY450 5.0 37.2 1.0

N.V.Strushkevich, W.Tempel, A.A.Gilep, P.Loppnau, C.H.Arrowsmith, A.M.Edwards, C.Bountra, M.Wilkstrom, A.Bochkarev, H.Park. Crystal Structure of CYP2R1 in Complex with 1-Alpha-Hydroxy-Vitamin D2. To Be Published.