Iron in PDB 4dnz: The Crystal Structures of CYP199A4

The structure of The Crystal Structures of CYP199A4, PDB code: 4dnz was solved by W.Zhou, S.G.Bell, W.Yang, A.B.H.Tan, R.Zhou, E.O.D.Johnson, A.Zhang, Z.Rao, L.-L.Wong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.64 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.305, 143.229, 171.596, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.6

The structure of The Crystal Structures of CYP199A4 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Iron atom in the The Crystal Structures of CYP199A4 (pdb code 4dnz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the The Crystal Structures of CYP199A4, PDB code: 4dnz:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the The Crystal Structures of CYP199A4


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structures of CYP199A4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:25.3 occ:1.00 FE A:HEM501 0.0 25.3 1.0 NA A:HEM501 2.0 22.4 1.0 NC A:HEM501 2.0 22.2 1.0 ND A:HEM501 2.0 23.0 1.0 NB A:HEM501 2.1 21.1 1.0 SG A:CYS358 2.3 28.2 1.0 C4C A:HEM501 3.0 22.5 1.0 C1D A:HEM501 3.0 21.0 1.0 C4A A:HEM501 3.0 19.2 1.0 C1A A:HEM501 3.1 23.6 1.0 C1B A:HEM501 3.1 20.9 1.0 C4D A:HEM501 3.1 22.7 1.0 C1C A:HEM501 3.1 23.3 1.0 C4B A:HEM501 3.1 20.6 1.0 CB A:CYS358 3.3 22.6 1.0 CHD A:HEM501 3.3 22.5 1.0 CHA A:HEM501 3.4 23.0 1.0 CHB A:HEM501 3.4 19.5 1.0 CHC A:HEM501 3.5 22.0 1.0 CA A:CYS358 4.0 22.9 1.0 C3C A:HEM501 4.2 21.9 1.0 C2C A:HEM501 4.3 22.4 1.0 C3A A:HEM501 4.3 17.8 1.0 C2D A:HEM501 4.3 16.9 1.0 C2A A:HEM501 4.3 19.9 1.0 C3D A:HEM501 4.3 20.0 1.0 C2B A:HEM501 4.3 21.4 1.0 C3B A:HEM501 4.3 20.9 1.0 CB A:ALA248 4.6 25.3 1.0 C A:CYS358 4.8 23.4 1.0 N A:GLY360 4.8 22.7 1.0 O A:ALA248 5.0 27.5 1.0

Iron binding site 2 out of 4 in the The Crystal Structures of CYP199A4


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structures of CYP199A4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:24.0 occ:1.00 FE B:HEM501 0.0 24.0 1.0 NC B:HEM501 2.0 20.3 1.0 NA B:HEM501 2.0 23.2 1.0 NB B:HEM501 2.1 21.5 1.0 ND B:HEM501 2.1 20.2 1.0 SG B:CYS358 2.2 28.3 1.0 C4C B:HEM501 3.0 19.2 1.0 C1C B:HEM501 3.0 22.7 1.0 C4A B:HEM501 3.0 21.9 1.0 C1D B:HEM501 3.0 21.4 1.0 C1B B:HEM501 3.1 22.1 1.0 C4D B:HEM501 3.1 23.5 1.0 C1A B:HEM501 3.1 22.7 1.0 C4B B:HEM501 3.1 21.0 1.0 CHD B:HEM501 3.3 21.1 1.0 CHB B:HEM501 3.4 22.4 1.0 CB B:CYS358 3.4 23.4 1.0 CHA B:HEM501 3.5 24.1 1.0 CHC B:HEM501 3.5 21.7 1.0 CA B:CYS358 4.1 23.8 1.0 C3C B:HEM501 4.2 21.9 1.0 C2C B:HEM501 4.2 22.0 1.0 C3A B:HEM501 4.3 19.0 1.0 C2A B:HEM501 4.3 22.2 1.0 C2B B:HEM501 4.3 20.4 1.0 C2D B:HEM501 4.3 21.3 1.0 C3D B:HEM501 4.3 21.4 1.0 C3B B:HEM501 4.3 21.2 1.0 CB B:ALA248 4.7 29.0 1.0 O B:ALA248 4.8 29.7 1.0 N B:GLY360 4.8 21.5 1.0 C B:CYS358 4.9 23.8 1.0

Iron binding site 3 out of 4 in the The Crystal Structures of CYP199A4


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structures of CYP199A4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:29.8 occ:1.00 FE C:HEM501 0.0 29.8 1.0 ND C:HEM501 2.0 26.4 1.0 NB C:HEM501 2.0 27.0 1.0 NC C:HEM501 2.0 26.9 1.0 NA C:HEM501 2.1 24.8 1.0 SG C:CYS358 2.2 22.6 1.0 O C:HOH648 2.8 32.6 1.0 C4C C:HEM501 3.0 27.9 1.0 C4D C:HEM501 3.0 28.4 1.0 C1D C:HEM501 3.0 28.5 1.0 C1C C:HEM501 3.0 25.4 1.0 C4B C:HEM501 3.0 27.0 1.0 C1B C:HEM501 3.1 26.3 1.0 C1A C:HEM501 3.1 25.1 1.0 C4A C:HEM501 3.2 24.0 1.0 CHD C:HEM501 3.4 30.3 1.0 CHA C:HEM501 3.4 25.6 1.0 CHC C:HEM501 3.4 23.4 1.0 CB C:CYS358 3.5 25.1 1.0 CHB C:HEM501 3.5 25.2 1.0 C3C C:HEM501 4.2 27.9 1.0 C2C C:HEM501 4.3 26.6 1.0 C3B C:HEM501 4.3 25.1 1.0 CA C:CYS358 4.3 23.9 1.0 C2B C:HEM501 4.3 25.8 1.0 C2D C:HEM501 4.3 27.2 1.0 C3D C:HEM501 4.3 28.0 1.0 O C:ALA248 4.3 39.8 1.0 C2A C:HEM501 4.4 24.9 1.0 C3A C:HEM501 4.4 24.4 1.0 CB C:ALA248 4.7 39.4 1.0 N C:GLY360 4.9 27.1 1.0 C C:CYS358 5.0 23.9 1.0

Iron binding site 4 out of 4 in the The Crystal Structures of CYP199A4


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structures of CYP199A4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:34.7 occ:1.00 FE D:HEM501 0.0 34.7 1.0 NB D:HEM501 1.9 34.8 1.0 NA D:HEM501 2.0 35.4 1.0 NC D:HEM501 2.1 36.3 1.0 ND D:HEM501 2.1 34.9 1.0 SG D:CYS358 2.5 31.3 1.0 O D:HOH613 2.6 29.1 1.0 C1B D:HEM501 2.9 35.6 1.0 C4A D:HEM501 3.0 36.7 1.0 C4C D:HEM501 3.0 36.6 1.0 C4B D:HEM501 3.0 34.6 1.0 C1D D:HEM501 3.0 35.5 1.0 C1C D:HEM501 3.1 35.4 1.0 C1A D:HEM501 3.1 35.1 1.0 C4D D:HEM501 3.2 34.9 1.0 CB D:CYS358 3.2 31.8 1.0 CHB D:HEM501 3.3 37.5 1.0 CHD D:HEM501 3.3 36.0 1.0 CHC D:HEM501 3.5 35.4 1.0 CHA D:HEM501 3.5 33.4 1.0 CA D:CYS358 4.1 31.2 1.0 O D:ALA248 4.1 47.8 1.0 C2B D:HEM501 4.2 34.4 1.0 C3B D:HEM501 4.2 32.3 1.0 C3A D:HEM501 4.2 36.6 1.0 C3C D:HEM501 4.2 37.6 1.0 C2C D:HEM501 4.3 36.8 1.0 C2D D:HEM501 4.3 33.3 1.0 C2A D:HEM501 4.3 36.1 1.0 C3D D:HEM501 4.4 34.2 1.0 CB D:ALA248 4.5 47.6 1.0 C D:CYS358 4.7 31.8 1.0 N D:VAL359 4.9 31.9 1.0 N D:GLY360 4.9 33.5 1.0 C D:ALA248 5.0 47.8 1.0

S.G.Bell, W.Yang, A.B.H.Tan, R.Zhou, E.O.D.Johnson, A.Zhang, W.Zhou, Z.Rao, L.-L.Wong. The Crystal Structures of 4-Methoxybenzoate Bound CYP199A2 and CYP199A4: Structural Changes on Substrate Binding and the Identification of An Anion Binding Site Dalton Trans V. 41 8703 2012.
ISSN: ISSN 1477-9226
PubMed: 22695988
DOI: 10.1039/C2DT30783A