Iron in PDB 3dr9: Increased Distal Histidine Conformational Flexibility in the Deoxy Form of Dehaloperoxidase From Amphitrite Ornata

The structure of Increased Distal Histidine Conformational Flexibility in the Deoxy Form of Dehaloperoxidase From Amphitrite Ornata, PDB code: 3dr9 was solved by X.Chen, V.S.De Serrano, L.Betts, S.Franzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	5.00 / 1.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.517, 67.194, 69.094, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 19.6

The binding sites of Iron atom in the Increased Distal Histidine Conformational Flexibility in the Deoxy Form of Dehaloperoxidase From Amphitrite Ornata (pdb code 3dr9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Increased Distal Histidine Conformational Flexibility in the Deoxy Form of Dehaloperoxidase From Amphitrite Ornata, PDB code: 3dr9:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Increased Distal Histidine Conformational Flexibility in the Deoxy Form of Dehaloperoxidase 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 Increased Distal Histidine Conformational Flexibility in the Deoxy Form of Dehaloperoxidase From Amphitrite Ornata within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe139 b:10.2 occ:1.00 FE A:HEM139 0.0 10.2 1.0 ND A:HEM139 2.0 10.5 1.0 NC A:HEM139 2.1 9.3 1.0 NB A:HEM139 2.1 9.0 1.0 NA A:HEM139 2.1 10.1 1.0 NE2 A:HIS89 2.2 10.8 1.0 C1D A:HEM139 3.1 9.8 1.0 C4D A:HEM139 3.1 10.8 1.0 C4C A:HEM139 3.1 9.5 1.0 C4B A:HEM139 3.1 9.1 1.0 C1A A:HEM139 3.1 10.7 1.0 C1C A:HEM139 3.1 9.0 1.0 C1B A:HEM139 3.1 8.8 1.0 C4A A:HEM139 3.1 9.6 1.0 CE1 A:HIS89 3.1 10.6 1.0 CD2 A:HIS89 3.2 11.6 1.0 CHD A:HEM139 3.4 10.7 1.0 CHA A:HEM139 3.4 10.5 1.0 CHC A:HEM139 3.4 8.8 1.0 CHB A:HEM139 3.5 9.1 1.0 ND1 A:HIS89 4.3 11.2 1.0 C2D A:HEM139 4.3 12.0 1.0 C3C A:HEM139 4.3 10.1 1.0 C3D A:HEM139 4.3 12.3 1.0 CG A:HIS89 4.3 11.4 1.0 C2C A:HEM139 4.3 9.5 1.0 C3B A:HEM139 4.3 8.2 1.0 C2B A:HEM139 4.3 8.2 1.0 C2A A:HEM139 4.3 10.7 1.0 C3A A:HEM139 4.3 10.2 1.0 CG2 A:VAL59 4.4 9.0 1.0 CE A:MET86 4.6 16.0 1.0 CG1 A:VAL59 4.7 8.6 1.0

Iron binding site 2 out of 2 in the Increased Distal Histidine Conformational Flexibility in the Deoxy Form of Dehaloperoxidase 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 Increased Distal Histidine Conformational Flexibility in the Deoxy Form of Dehaloperoxidase From Amphitrite Ornata within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe139 b:6.4 occ:0.80 FE B:HEM139 0.0 6.4 0.8 NA B:HEM139 2.0 8.3 1.0 NB B:HEM139 2.1 6.9 1.0 NC B:HEM139 2.1 8.2 1.0 ND B:HEM139 2.1 8.3 1.0 NE2 B:HIS89 2.2 9.0 1.0 C1A B:HEM139 3.1 8.2 1.0 C4A B:HEM139 3.1 7.7 1.0 C4D B:HEM139 3.1 9.3 1.0 C1D B:HEM139 3.1 9.6 1.0 C4C B:HEM139 3.1 8.6 1.0 C1B B:HEM139 3.1 7.0 1.0 C4B B:HEM139 3.1 7.6 1.0 C1C B:HEM139 3.1 7.5 1.0 CE1 B:HIS89 3.1 9.2 1.0 CD2 B:HIS89 3.2 8.7 1.0 CHA B:HEM139 3.4 8.5 1.0 CHD B:HEM139 3.4 9.1 1.0 CHB B:HEM139 3.4 7.3 1.0 CHC B:HEM139 3.5 8.2 1.0 ND1 B:HIS89 4.2 9.6 1.0 CG2 B:VAL59 4.2 8.1 1.0 C2A B:HEM139 4.3 8.4 1.0 CG B:HIS89 4.3 10.2 1.0 C3A B:HEM139 4.3 8.7 1.0 C3B B:HEM139 4.3 7.0 1.0 C2D B:HEM139 4.3 10.0 1.0 C3C B:HEM139 4.3 9.2 1.0 C3D B:HEM139 4.3 10.9 1.0 C2B B:HEM139 4.3 7.2 1.0 C2C B:HEM139 4.3 8.5 1.0 CE B:MET86 4.6 12.0 1.0 CG1 B:VAL59 4.8 7.6 1.0

Z.Chen, V.De Serrano, L.Betts, S.Franzen. Distal Histidine Conformational Flexibility in Dehaloperoxidase From Amphitrite Ornata. Acta Crystallogr.,Sect.D V. 65 34 2009.
ISSN: ISSN 0907-4449
PubMed: 19153464
DOI: 10.1107/S0907444908036548