Iron in PDB 3czh: Crystal Structure of CYP2R1 in Complex with Vitamin D2

The structure of Crystal Structure of CYP2R1 in Complex with Vitamin D2, PDB code: 3czh 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 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	137.361, 163.393, 152.289, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 23.1

The binding sites of Iron atom in the Crystal Structure of CYP2R1 in Complex with Vitamin D2 (pdb code 3czh). 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 Vitamin D2, PDB code: 3czh:
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 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 Vitamin D2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:25.9 occ:0.50 FE A:HEM601 0.0 25.9 0.5 FE A:HEM601 0.3 29.9 0.5 NC A:HEM601 2.0 27.7 0.5 NB A:HEM601 2.0 31.4 0.5 NA A:HEM601 2.1 31.2 0.5 NB A:HEM601 2.1 27.6 0.5 NC A:HEM601 2.1 31.5 0.5 NA A:HEM601 2.1 27.1 0.5 ND A:HEM601 2.1 27.2 0.5 ND A:HEM601 2.1 31.3 0.5 SG A:CYS448 2.4 29.6 1.0 C1B A:HEM601 3.0 31.1 0.5 C4C A:HEM601 3.0 27.3 0.5 C1C A:HEM601 3.0 28.1 0.5 C4A A:HEM601 3.1 31.6 0.5 C4B A:HEM601 3.1 31.6 0.5 C4B A:HEM601 3.1 27.5 0.5 C1A A:HEM601 3.1 31.5 0.5 C1D A:HEM601 3.1 27.8 0.5 C1B A:HEM601 3.1 27.0 0.5 C1C A:HEM601 3.1 31.3 0.5 C4A A:HEM601 3.1 26.9 0.5 C4C A:HEM601 3.1 31.0 0.5 C1D A:HEM601 3.1 31.2 0.5 C4D A:HEM601 3.2 31.8 0.5 C1A A:HEM601 3.2 27.6 0.5 C4D A:HEM601 3.2 27.4 0.5 CHB A:HEM601 3.4 31.2 0.5 CHC A:HEM601 3.4 27.9 0.5 CHD A:HEM601 3.4 27.6 0.5 CHC A:HEM601 3.4 31.5 0.5 CHB A:HEM601 3.5 27.1 0.5 CHD A:HEM601 3.5 31.1 0.5 CHA A:HEM601 3.5 31.5 0.5 CB A:CYS448 3.5 30.3 1.0 CHA A:HEM601 3.5 27.3 0.5 CA A:CYS448 4.2 30.7 1.0 C2B A:HEM601 4.2 32.2 0.5 C3B A:HEM601 4.3 32.1 0.5 C2C A:HEM601 4.3 28.7 0.5 C3C A:HEM601 4.3 28.7 0.5 C3A A:HEM601 4.3 32.3 0.5 C2A A:HEM601 4.3 31.7 0.5 C3B A:HEM601 4.3 28.1 0.5 C2B A:HEM601 4.3 27.1 0.5 C2C A:HEM601 4.3 32.0 0.5 C3A A:HEM601 4.4 27.8 0.5 C3C A:HEM601 4.4 31.1 0.5 C2D A:HEM601 4.4 28.4 0.5 C2A A:HEM601 4.4 27.3 0.5 C2D A:HEM601 4.4 32.0 0.5 C3D A:HEM601 4.4 27.7 0.5 C3D A:HEM601 4.4 31.8 0.5 CB A:ALA310 4.6 36.5 1.0 N A:GLY450 4.8 31.1 1.0 O A:ALA310 4.9 45.7 1.0 C A:CYS448 5.0 31.5 1.0 N A:LEU449 5.0 32.7 1.0

Iron binding site 2 out of 4 in the Crystal Structure of CYP2R1 in Complex with 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 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 0.3 25.9 0.5 NC A:HEM601 2.0 27.7 0.5 SG A:CYS448 2.1 29.6 1.0 NB A:HEM601 2.1 31.4 0.5 NB A:HEM601 2.1 27.6 0.5 NA A:HEM601 2.1 31.2 0.5 NC A:HEM601 2.1 31.5 0.5 ND A:HEM601 2.2 31.3 0.5 NA A:HEM601 2.2 27.1 0.5 ND A:HEM601 2.2 27.2 0.5 C1C A:HEM601 3.0 28.1 0.5 C1B A:HEM601 3.1 31.1 0.5 C4B A:HEM601 3.1 31.6 0.5 C4C A:HEM601 3.1 27.3 0.5 C4B A:HEM601 3.1 27.5 0.5 C4A A:HEM601 3.1 31.6 0.5 C1B A:HEM601 3.1 27.0 0.5 C1C A:HEM601 3.1 31.3 0.5 C4C A:HEM601 3.1 31.0 0.5 C4A A:HEM601 3.1 26.9 0.5 C1D A:HEM601 3.1 31.2 0.5 C1A A:HEM601 3.1 31.5 0.5 C1D A:HEM601 3.2 27.8 0.5 C4D A:HEM601 3.2 31.8 0.5 C1A A:HEM601 3.2 27.6 0.5 C4D A:HEM601 3.2 27.4 0.5 CB A:CYS448 3.2 30.3 1.0 CHC A:HEM601 3.4 27.9 0.5 CHB A:HEM601 3.4 31.2 0.5 CHC A:HEM601 3.4 31.5 0.5 CHD A:HEM601 3.5 31.1 0.5 CHD A:HEM601 3.5 27.6 0.5 CHB A:HEM601 3.5 27.1 0.5 CHA A:HEM601 3.5 31.5 0.5 CHA A:HEM601 3.6 27.3 0.5 CA A:CYS448 4.0 30.7 1.0 C2B A:HEM601 4.2 32.2 0.5 C3B A:HEM601 4.2 32.1 0.5 C2C A:HEM601 4.3 28.7 0.5 C3C A:HEM601 4.3 28.7 0.5 C3B A:HEM601 4.3 28.1 0.5 C2B A:HEM601 4.3 27.1 0.5 C3A A:HEM601 4.3 32.3 0.5 C2C A:HEM601 4.3 32.0 0.5 C2A A:HEM601 4.3 31.7 0.5 C3C A:HEM601 4.4 31.1 0.5 C3A A:HEM601 4.4 27.8 0.5 C2D A:HEM601 4.4 32.0 0.5 C2A A:HEM601 4.4 27.3 0.5 C3D A:HEM601 4.4 31.8 0.5 C2D A:HEM601 4.4 28.4 0.5 C3D A:HEM601 4.4 27.7 0.5 N A:GLY450 4.6 31.1 1.0 C A:CYS448 4.7 31.5 1.0 N A:LEU449 4.8 32.7 1.0 CB A:ALA310 4.8 36.5 1.0 CD2 A:PHE441 4.9 28.3 1.0

Iron binding site 3 out of 4 in the Crystal Structure of CYP2R1 in Complex with 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 Vitamin D2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:35.0 occ:0.50 FE B:HEM601 0.0 35.0 0.5 FE B:HEM601 0.2 35.6 0.5 NA B:HEM601 1.9 35.9 0.5 ND B:HEM601 2.0 35.4 0.5 NC B:HEM601 2.0 34.8 0.5 NB B:HEM601 2.0 35.2 0.5 NA B:HEM601 2.1 34.7 0.5 NB B:HEM601 2.1 34.1 0.5 ND B:HEM601 2.2 35.2 0.5 NC B:HEM601 2.2 34.5 0.5 SG B:CYS448 2.4 38.2 1.0 C4A B:HEM601 2.9 36.1 0.5 C1A B:HEM601 2.9 35.9 0.5 C1B B:HEM601 3.0 34.9 0.5 C4D B:HEM601 3.0 35.2 0.5 C1D B:HEM601 3.0 35.5 0.5 C4C B:HEM601 3.0 34.4 0.5 C1C B:HEM601 3.1 34.1 0.5 C4B B:HEM601 3.1 34.3 0.5 C1A B:HEM601 3.1 34.0 0.5 C4D B:HEM601 3.1 34.7 0.5 C4B B:HEM601 3.1 34.2 0.5 C4A B:HEM601 3.2 33.8 0.5 C1B B:HEM601 3.2 33.8 0.5 C1C B:HEM601 3.2 34.3 0.5 C1D B:HEM601 3.3 34.4 0.5 C4C B:HEM601 3.3 34.3 0.5 CHB B:HEM601 3.3 35.5 0.5 CHA B:HEM601 3.4 35.4 0.5 CHD B:HEM601 3.4 34.9 0.5 CHA B:HEM601 3.4 34.8 0.5 CHC B:HEM601 3.5 33.9 0.5 CB B:CYS448 3.5 39.8 1.0 CHC B:HEM601 3.5 34.2 0.5 CHB B:HEM601 3.6 33.6 0.5 CHD B:HEM601 3.6 34.0 0.5 CA B:CYS448 4.1 39.8 1.0 C2A B:HEM601 4.1 36.7 0.5 C3A B:HEM601 4.1 36.5 0.5 C2B B:HEM601 4.2 35.0 0.5 C3B B:HEM601 4.2 34.6 0.5 C3D B:HEM601 4.2 35.8 0.5 C2D B:HEM601 4.2 35.8 0.5 C3C B:HEM601 4.2 34.5 0.5 C2C B:HEM601 4.3 34.4 0.5 C2A B:HEM601 4.4 34.2 0.5 C3B B:HEM601 4.4 33.6 0.5 C3A B:HEM601 4.4 33.4 0.5 C3D B:HEM601 4.4 35.0 0.5 C2B B:HEM601 4.4 32.8 0.5 C2D B:HEM601 4.5 34.0 0.5 C2C B:HEM601 4.5 33.8 0.5 C3C B:HEM601 4.5 33.1 0.5 N B:LEU449 4.7 40.6 1.0 N B:GLY450 4.7 42.1 1.0 C B:CYS448 4.8 41.1 1.0 CB B:ALA310 4.8 39.9 1.0 C1B B:D2V602 4.9 47.4 1.0 O B:ALA310 5.0 46.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of CYP2R1 in Complex with 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 Vitamin D2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:35.6 occ:0.50 FE B:HEM601 0.0 35.6 0.5 FE B:HEM601 0.2 35.0 0.5 NB B:HEM601 2.0 34.1 0.5 NA B:HEM601 2.0 35.9 0.5 NB B:HEM601 2.1 35.2 0.5 NC B:HEM601 2.1 34.8 0.5 NA B:HEM601 2.1 34.7 0.5 NC B:HEM601 2.1 34.5 0.5 ND B:HEM601 2.1 35.4 0.5 ND B:HEM601 2.1 35.2 0.5 SG B:CYS448 2.5 38.2 1.0 C4B B:HEM601 3.0 34.2 0.5 C1B B:HEM601 3.0 33.8 0.5 C1A B:HEM601 3.0 35.9 0.5 C4B B:HEM601 3.0 34.3 0.5 C1B B:HEM601 3.1 34.9 0.5 C1C B:HEM601 3.1 34.1 0.5 C4A B:HEM601 3.1 36.1 0.5 C1C B:HEM601 3.1 34.3 0.5 C4A B:HEM601 3.1 33.8 0.5 C1A B:HEM601 3.1 34.0 0.5 C4D B:HEM601 3.1 35.2 0.5 C4C B:HEM601 3.1 34.4 0.5 C4D B:HEM601 3.1 34.7 0.5 C4C B:HEM601 3.1 34.3 0.5 C1D B:HEM601 3.1 35.5 0.5 C1D B:HEM601 3.2 34.4 0.5 CHC B:HEM601 3.4 33.9 0.5 CHA B:HEM601 3.4 35.4 0.5 CHC B:HEM601 3.4 34.2 0.5 CHB B:HEM601 3.4 33.6 0.5 CHB B:HEM601 3.4 35.5 0.5 CHA B:HEM601 3.5 34.8 0.5 CB B:CYS448 3.5 39.8 1.0 CHD B:HEM601 3.5 34.9 0.5 CHD B:HEM601 3.5 34.0 0.5 CA B:CYS448 4.1 39.8 1.0 C3B B:HEM601 4.2 34.6 0.5 C2B B:HEM601 4.2 35.0 0.5 C3B B:HEM601 4.2 33.6 0.5 C2B B:HEM601 4.3 32.8 0.5 C2A B:HEM601 4.3 36.7 0.5 C3A B:HEM601 4.3 36.5 0.5 C2C B:HEM601 4.3 34.4 0.5 C3A B:HEM601 4.3 33.4 0.5 C3C B:HEM601 4.3 34.5 0.5 C2C B:HEM601 4.3 33.8 0.5 C2A B:HEM601 4.3 34.2 0.5 C3C B:HEM601 4.3 33.1 0.5 C3D B:HEM601 4.3 35.8 0.5 C3D B:HEM601 4.4 35.0 0.5 C2D B:HEM601 4.4 35.8 0.5 C2D B:HEM601 4.4 34.0 0.5 N B:GLY450 4.8 42.1 1.0 N B:LEU449 4.8 40.6 1.0 CB B:ALA310 4.8 39.9 1.0 C1B B:D2V602 4.8 47.4 1.0 C B:CYS448 4.8 41.1 1.0 O B:ALA310 4.9 46.7 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 Vitamin D2. To Be Published.