Iron in PDB 3ved: Rhodococcus Jostii RHA1 Dypb D153H Variant in Complex with Heme

The structure of Rhodococcus Jostii RHA1 Dypb D153H Variant in Complex with Heme, PDB code: 3ved was solved by J.C.Grigg, R.Singh, Z.Armstrong, L.D.Eltis, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.50
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.642, 132.642, 159.610, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 21.8

The structure of Rhodococcus Jostii RHA1 Dypb D153H Variant in Complex with Heme also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Iron atom in the Rhodococcus Jostii RHA1 Dypb D153H Variant in Complex with Heme (pdb code 3ved). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Rhodococcus Jostii RHA1 Dypb D153H Variant in Complex with Heme, PDB code: 3ved:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Rhodococcus Jostii RHA1 Dypb D153H Variant in Complex with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Rhodococcus Jostii RHA1 Dypb D153H Variant in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:33.4 occ:1.00 FE A:HEM401 0.0 33.4 1.0 NC A:HEM401 2.0 33.3 1.0 NE2 A:HIS226 2.0 34.6 1.0 NB A:HEM401 2.0 36.7 1.0 ND A:HEM401 2.0 32.9 1.0 NA A:HEM401 2.1 35.0 1.0 CL A:CL404 2.7 51.0 1.0 CE1 A:HIS226 2.8 36.2 1.0 C4C A:HEM401 3.0 34.0 1.0 C1C A:HEM401 3.0 34.9 1.0 C4B A:HEM401 3.0 36.6 1.0 C1D A:HEM401 3.1 31.7 1.0 C1A A:HEM401 3.1 33.7 1.0 C4D A:HEM401 3.1 32.5 1.0 C1B A:HEM401 3.1 36.9 1.0 C4A A:HEM401 3.1 34.5 1.0 CD2 A:HIS226 3.1 36.3 1.0 CHD A:HEM401 3.4 34.2 1.0 CHC A:HEM401 3.4 36.2 1.0 CHA A:HEM401 3.4 32.2 1.0 CHB A:HEM401 3.5 36.2 1.0 ND1 A:HIS226 4.0 36.4 1.0 NH1 A:ARG244 4.1 31.4 1.0 CG A:HIS226 4.2 36.7 1.0 C3C A:HEM401 4.2 35.8 1.0 C2C A:HEM401 4.2 35.9 1.0 NE2 A:HIS153 4.2 46.8 1.0 C3B A:HEM401 4.3 37.5 1.0 C2B A:HEM401 4.3 36.9 1.0 C2A A:HEM401 4.3 32.1 1.0 C2D A:HEM401 4.3 31.2 1.0 C3D A:HEM401 4.3 32.4 1.0 C3A A:HEM401 4.3 33.5 1.0 OD1 A:ASN230 4.5 43.1 1.0 CD A:ARG244 4.8 35.5 1.0 CE1 A:HIS153 4.8 45.5 1.0 ND2 A:ASN246 4.9 29.6 0.5 CZ A:ARG244 5.0 33.4 1.0

Iron binding site 2 out of 3 in the Rhodococcus Jostii RHA1 Dypb D153H Variant in Complex with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Rhodococcus Jostii RHA1 Dypb D153H Variant in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:37.0 occ:1.00 FE B:HEM401 0.0 37.0 1.0 NB B:HEM401 1.9 34.9 1.0 NC B:HEM401 2.0 32.6 1.0 ND B:HEM401 2.0 30.4 1.0 NA B:HEM401 2.0 32.1 1.0 NE2 B:HIS226 2.0 47.2 1.0 CL B:CL403 2.7 56.6 1.0 CD2 B:HIS226 2.9 45.7 1.0 C1D B:HEM401 3.0 32.8 1.0 C1B B:HEM401 3.0 37.6 1.0 C4C B:HEM401 3.0 31.3 1.0 C4B B:HEM401 3.0 36.0 1.0 C4A B:HEM401 3.0 35.0 1.0 C4D B:HEM401 3.0 32.1 1.0 C1C B:HEM401 3.0 33.4 1.0 CE1 B:HIS226 3.1 45.5 1.0 C1A B:HEM401 3.1 32.7 1.0 CHD B:HEM401 3.3 31.6 1.0 CHB B:HEM401 3.4 37.0 1.0 CHC B:HEM401 3.4 33.8 1.0 CHA B:HEM401 3.5 32.3 1.0 NH1 B:ARG244 3.9 32.6 1.0 CG B:HIS226 4.1 46.4 1.0 ND1 B:HIS226 4.1 45.8 1.0 C3B B:HEM401 4.2 34.9 1.0 C2B B:HEM401 4.2 36.4 1.0 C3C B:HEM401 4.2 31.2 1.0 C2D B:HEM401 4.2 33.3 1.0 C2C B:HEM401 4.3 31.2 1.0 C3D B:HEM401 4.3 33.5 1.0 C3A B:HEM401 4.3 34.1 1.0 C2A B:HEM401 4.3 32.4 1.0 NE2 B:HIS153 4.4 51.9 1.0 ND2 B:ASN230 4.6 46.5 1.0 CD B:ARG244 4.8 36.2 1.0 CZ B:ARG244 4.8 35.2 1.0 ND2 B:ASN246 4.9 34.8 0.5

Iron binding site 3 out of 3 in the Rhodococcus Jostii RHA1 Dypb D153H Variant in Complex with Heme


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Rhodococcus Jostii RHA1 Dypb D153H Variant in Complex with Heme within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:46.7 occ:1.00 FE C:HEM401 0.0 46.7 1.0 NB C:HEM401 1.9 43.9 1.0 ND C:HEM401 2.0 42.0 1.0 NA C:HEM401 2.1 44.2 1.0 NE2 C:HIS226 2.1 57.4 1.0 NC C:HEM401 2.1 46.6 1.0 CL C:CL403 2.8 64.8 1.0 CE1 C:HIS226 2.9 58.5 1.0 C1B C:HEM401 3.0 45.6 1.0 C4B C:HEM401 3.0 46.5 1.0 C1D C:HEM401 3.0 44.4 1.0 C4A C:HEM401 3.1 43.5 1.0 C4D C:HEM401 3.1 43.3 1.0 C1A C:HEM401 3.1 42.3 1.0 C4C C:HEM401 3.1 46.2 1.0 C1C C:HEM401 3.1 47.0 1.0 CD2 C:HIS226 3.2 57.3 1.0 CHB C:HEM401 3.4 44.3 1.0 CHC C:HEM401 3.4 46.3 1.0 CHD C:HEM401 3.4 46.1 1.0 CHA C:HEM401 3.4 41.1 1.0 NH1 C:ARG244 4.0 44.9 1.0 ND1 C:HIS226 4.0 58.1 1.0 C3B C:HEM401 4.2 44.9 1.0 C2B C:HEM401 4.2 44.7 1.0 CG C:HIS226 4.2 57.6 1.0 C2D C:HEM401 4.3 43.4 1.0 NE2 C:HIS153 4.3 58.3 1.0 C3A C:HEM401 4.3 42.7 1.0 C3D C:HEM401 4.3 43.2 1.0 C2A C:HEM401 4.3 42.1 1.0 C3C C:HEM401 4.3 47.6 1.0 C2C C:HEM401 4.4 47.6 1.0 OD1 C:ASN230 4.5 60.9 1.0 ND2 C:ASN246 4.9 38.7 0.5 CZ C:ARG244 4.9 47.5 1.0 CD C:ARG244 4.9 48.7 1.0

R.Singh, J.C.Grigg, Z.Armstrong, M.E.Murphy, L.D.Eltis. Distal Heme Pocket Residues of B-Type Dye-Decolorizing Peroxidase: Arginine But Not Aspartate Is Essential For Peroxidase Activity. J.Biol.Chem. V. 287 10623 2012.
ISSN: ISSN 0021-9258
PubMed: 22308037
DOI: 10.1074/JBC.M111.332171