Iron in PDB 3ixf: Crystal Structure of Dehaloperoxidase B at 1.58 and Structural Characterization of the Ab Dimer From Amphitrite Ornata

The structure of Crystal Structure of Dehaloperoxidase B at 1.58 and Structural Characterization of the Ab Dimer From Amphitrite Ornata, PDB code: 3ixf was solved by V.S.De Serrano, J.D'antonio, M.K.Thompson, S.Franzen, R.A.Ghiladi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.17 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.650, 67.416, 67.484, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.9

The binding sites of Iron atom in the Crystal Structure of Dehaloperoxidase B at 1.58 and Structural Characterization of the Ab Dimer From Amphitrite Ornata (pdb code 3ixf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Dehaloperoxidase B at 1.58 and Structural Characterization of the Ab Dimer From Amphitrite Ornata, PDB code: 3ixf:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Dehaloperoxidase B at 1.58 and Structural Characterization of the Ab Dimer From Amphitrite Ornata


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 Dehaloperoxidase B at 1.58 and Structural Characterization of the Ab Dimer From Amphitrite Ornata within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe139 b:11.8 occ:1.00 FE A:HEM139 0.0 11.8 1.0 NC A:HEM139 2.0 13.0 1.0 NB A:HEM139 2.1 12.1 1.0 ND A:HEM139 2.1 13.0 1.0 NA A:HEM139 2.1 10.8 1.0 O A:HOH429 2.1 13.1 0.3 NE2 A:HIS89 2.2 11.9 1.0 O1 A:OXY186 3.0 3.6 0.1 C1D A:HEM139 3.1 14.0 1.0 C4A A:HEM139 3.1 11.4 1.0 C1C A:HEM139 3.1 13.1 1.0 C1B A:HEM139 3.1 10.1 1.0 C4C A:HEM139 3.1 12.9 1.0 C1A A:HEM139 3.1 12.7 1.0 C4B A:HEM139 3.1 11.1 1.0 CE1 A:HIS89 3.1 10.9 1.0 C4D A:HEM139 3.2 14.3 1.0 CD2 A:HIS89 3.2 10.4 1.0 CHD A:HEM139 3.4 10.8 1.0 CHC A:HEM139 3.5 13.8 1.0 CHB A:HEM139 3.5 11.2 1.0 CHA A:HEM139 3.6 7.3 1.0 O2 A:OXY186 4.2 2.0 0.1 C2C A:HEM139 4.3 12.6 1.0 ND1 A:HIS89 4.3 12.2 1.0 C3A A:HEM139 4.3 13.3 1.0 C2A A:HEM139 4.3 11.1 1.0 C3C A:HEM139 4.3 12.1 1.0 C2D A:HEM139 4.3 11.8 1.0 C3B A:HEM139 4.3 13.3 1.0 C2B A:HEM139 4.3 10.7 1.0 CG A:HIS89 4.3 11.1 1.0 C3D A:HEM139 4.3 11.9 1.0 CG2 A:VAL59 4.4 9.6 1.0 CE A:MET86 4.6 8.0 0.5 CG1 A:VAL59 4.8 8.4 1.0 CE1 A:HIS55 4.9 10.5 0.1 CE1 A:HIS55 4.9 2.0 0.3 CE A:MET86 4.9 6.0 0.3

Iron binding site 2 out of 2 in the Crystal Structure of Dehaloperoxidase B at 1.58 and Structural Characterization of the Ab Dimer From Amphitrite Ornata


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 Dehaloperoxidase B at 1.58 and Structural Characterization of the Ab Dimer From Amphitrite Ornata within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe139 b:10.8 occ:1.00 FE B:HEM139 0.0 10.8 1.0 NC B:HEM139 2.0 11.4 1.0 NA B:HEM139 2.0 11.1 1.0 NB B:HEM139 2.1 8.6 1.0 ND B:HEM139 2.1 11.3 1.0 NE2 B:HIS89 2.2 8.4 1.0 O B:HOH608 2.2 2.0 0.1 C4A B:HEM139 3.0 10.1 1.0 C4C B:HEM139 3.0 12.6 1.0 C1D B:HEM139 3.1 12.5 1.0 C1B B:HEM139 3.1 5.8 1.0 C1A B:HEM139 3.1 13.3 1.0 C1C B:HEM139 3.1 10.9 1.0 C4D B:HEM139 3.1 12.3 1.0 C4B B:HEM139 3.1 7.5 1.0 CE1 B:HIS89 3.1 12.6 1.0 CD2 B:HIS89 3.2 12.4 1.0 CHB B:HEM139 3.4 9.3 1.0 CHD B:HEM139 3.4 12.2 1.0 CHC B:HEM139 3.5 9.3 1.0 CHA B:HEM139 3.5 12.6 1.0 CG2 B:VAL59 4.2 9.8 1.0 ND1 B:HIS89 4.3 10.8 1.0 C3A B:HEM139 4.3 12.1 1.0 C3C B:HEM139 4.3 14.9 1.0 CG B:HIS89 4.3 12.3 1.0 C2C B:HEM139 4.3 14.6 1.0 C3B B:HEM139 4.3 10.7 1.0 C2D B:HEM139 4.3 13.4 1.0 C2A B:HEM139 4.3 11.0 1.0 C2B B:HEM139 4.3 8.8 1.0 C3D B:HEM139 4.3 12.8 1.0 CG1 B:VAL59 4.9 10.1 1.0 O B:HOH602 4.9 23.5 1.0 CE B:MET86 4.9 8.6 0.5

V.De Serrano, J.D'antonio, S.Franzen, R.A.Ghiladi. Structure of Dehaloperoxidase B at 1.58 A Resolution and Structural Characterization of the Ab Dimer From Amphitrite Ornata. Acta Crystallogr.,Sect.D V. 66 529 2010.
ISSN: ISSN 0907-4449
PubMed: 20445228
DOI: 10.1107/S0907444910004580