Iron in PDB 3qnr: Dypb From Rhodococcus Jostii RHA1, Crystal Form 1

The structure of Dypb From Rhodococcus Jostii RHA1, Crystal Form 1, PDB code: 3qnr was solved by R.Singh, J.N.Roberts, J.C.Grigg, 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)	48.41 / 2.25
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.379, 132.379, 160.211, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 21.8

The binding sites of Iron atom in the Dypb From Rhodococcus Jostii RHA1, Crystal Form 1 (pdb code 3qnr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Dypb From Rhodococcus Jostii RHA1, Crystal Form 1, PDB code: 3qnr:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Dypb From Rhodococcus Jostii RHA1, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dypb From Rhodococcus Jostii RHA1, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe400 b:29.7 occ:1.00 FE A:HEM400 0.0 29.7 1.0 NA A:HEM400 2.0 27.1 1.0 NC A:HEM400 2.0 27.9 1.0 NB A:HEM400 2.0 29.2 1.0 NE2 A:HIS226 2.0 27.1 1.0 ND A:HEM400 2.1 27.1 1.0 O A:HOH518 2.2 41.2 1.0 CE1 A:HIS226 2.9 28.9 1.0 C4C A:HEM400 3.0 29.1 1.0 C1C A:HEM400 3.0 29.5 1.0 C1A A:HEM400 3.0 26.9 1.0 C4A A:HEM400 3.0 27.4 1.0 C4B A:HEM400 3.0 30.3 1.0 C1B A:HEM400 3.1 29.3 1.0 C4D A:HEM400 3.1 27.5 1.0 C1D A:HEM400 3.1 29.0 1.0 CD2 A:HIS226 3.1 27.7 1.0 CHA A:HEM400 3.4 25.6 1.0 CHC A:HEM400 3.4 29.1 1.0 CHD A:HEM400 3.4 29.2 1.0 CHB A:HEM400 3.4 26.1 1.0 ND1 A:HIS226 4.1 30.3 1.0 NH1 A:ARG244 4.1 33.6 1.0 CG A:HIS226 4.2 30.9 1.0 C3C A:HEM400 4.2 29.1 1.0 C2C A:HEM400 4.2 28.7 1.0 C3A A:HEM400 4.3 25.8 1.0 C2A A:HEM400 4.3 25.6 1.0 C3B A:HEM400 4.3 30.9 1.0 C2B A:HEM400 4.3 30.2 1.0 OD1 A:ASN230 4.3 36.5 1.0 C2D A:HEM400 4.3 26.7 1.0 C3D A:HEM400 4.3 27.9 1.0 CD A:ARG244 4.7 31.1 1.0 ND2 A:ASN246 4.8 38.7 1.0 CZ A:ARG244 4.9 31.6 1.0

Iron binding site 2 out of 3 in the Dypb From Rhodococcus Jostii RHA1, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dypb From Rhodococcus Jostii RHA1, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe400 b:33.0 occ:1.00 FE B:HEM400 0.0 33.0 1.0 NB B:HEM400 1.9 30.9 1.0 NC B:HEM400 2.0 30.7 1.0 ND B:HEM400 2.0 30.0 1.0 NA B:HEM400 2.1 29.4 1.0 NE2 B:HIS226 2.1 38.8 1.0 O B:HOH394 2.3 44.1 1.0 C1B B:HEM400 3.0 32.5 1.0 C1D B:HEM400 3.0 32.3 1.0 C4C B:HEM400 3.0 29.9 1.0 C4B B:HEM400 3.0 32.5 1.0 C4A B:HEM400 3.0 29.9 1.0 CD2 B:HIS226 3.1 35.8 1.0 C1C B:HEM400 3.1 29.2 1.0 C4D B:HEM400 3.1 31.4 1.0 C1A B:HEM400 3.1 30.1 1.0 CE1 B:HIS226 3.2 37.4 1.0 CHD B:HEM400 3.3 30.5 1.0 CHB B:HEM400 3.4 30.5 1.0 CHC B:HEM400 3.4 30.7 1.0 CHA B:HEM400 3.5 31.2 1.0 NH1 B:ARG244 4.0 32.8 1.0 C2B B:HEM400 4.2 30.7 1.0 C3B B:HEM400 4.2 30.9 1.0 CG B:HIS226 4.2 37.8 1.0 C2D B:HEM400 4.2 30.2 1.0 C3C B:HEM400 4.2 28.6 1.0 ND1 B:HIS226 4.2 36.6 1.0 C2C B:HEM400 4.3 28.9 1.0 C3D B:HEM400 4.3 30.8 1.0 C3A B:HEM400 4.3 30.9 1.0 C2A B:HEM400 4.3 30.9 1.0 OD1 B:ASN230 4.5 37.7 1.0 CD B:ARG244 4.6 32.0 1.0 ND2 B:ASN246 4.7 41.3 1.0 CZ B:ARG244 4.8 33.3 1.0

Iron binding site 3 out of 3 in the Dypb From Rhodococcus Jostii RHA1, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dypb From Rhodococcus Jostii RHA1, Crystal Form 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe400 b:41.0 occ:1.00 FE C:HEM400 0.0 41.0 1.0 NB C:HEM400 2.0 37.2 1.0 ND C:HEM400 2.0 36.8 1.0 NE2 C:HIS226 2.0 44.9 1.0 NA C:HEM400 2.1 37.4 1.0 NC C:HEM400 2.1 40.5 1.0 O C:HOH456 2.1 58.6 1.0 CE1 C:HIS226 2.8 45.8 1.0 C4B C:HEM400 3.0 39.1 1.0 C1B C:HEM400 3.0 37.6 1.0 C1D C:HEM400 3.1 39.9 1.0 C4A C:HEM400 3.1 34.4 1.0 C1A C:HEM400 3.1 35.0 1.0 C4D C:HEM400 3.1 38.7 1.0 C4C C:HEM400 3.1 40.4 1.0 C1C C:HEM400 3.1 39.0 1.0 CD2 C:HIS226 3.2 46.3 1.0 CHB C:HEM400 3.4 35.9 1.0 CHA C:HEM400 3.4 36.5 1.0 CHD C:HEM400 3.4 40.3 1.0 CHC C:HEM400 3.4 39.5 1.0 ND1 C:HIS226 4.0 46.1 1.0 NH1 C:ARG244 4.1 42.2 1.0 CG C:HIS226 4.2 46.3 1.0 C3B C:HEM400 4.2 36.7 1.0 C2B C:HEM400 4.2 35.1 1.0 C3A C:HEM400 4.3 34.2 1.0 C2A C:HEM400 4.3 34.9 1.0 C2D C:HEM400 4.3 38.8 1.0 C3D C:HEM400 4.3 37.1 1.0 C3C C:HEM400 4.3 40.8 1.0 C2C C:HEM400 4.4 41.3 1.0 OD1 C:ASN230 4.4 50.5 1.0 CD C:ARG244 4.6 42.0 1.0 ND2 C:ASN246 4.7 44.7 1.0 CZ C:ARG244 4.8 42.5 1.0

J.N.Roberts, R.Singh, J.C.Grigg, M.E.Murphy, T.D.Bugg, L.D.Eltis. Characterization of Dye-Decolorizing Peroxidases From Rhodococcus Jostii RHA1. Biochemistry V. 50 5108 2011.
ISSN: ISSN 0006-2960
PubMed: 21534572
DOI: 10.1021/BI200427H