Iron in PDB 3wyo: Heterodimeric Myoglobin Formed By Domain Swapping

The structure of Heterodimeric Myoglobin Formed By Domain Swapping, PDB code: 3wyo was solved by Y.W.Lin, S.Nagao, M.Zhang, Y.Shomura, Y.Higuchi, S.Hirota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.702, 72.168, 161.520, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 26.6

The binding sites of Iron atom in the Heterodimeric Myoglobin Formed By Domain Swapping (pdb code 3wyo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Heterodimeric Myoglobin Formed By Domain Swapping, PDB code: 3wyo:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Heterodimeric Myoglobin Formed By Domain Swapping


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Heterodimeric Myoglobin Formed By Domain Swapping within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:26.8 occ:1.00 FE A:HEM201 0.0 26.8 1.0 ND A:HEM201 1.9 29.0 1.0 O B:HOH301 1.9 30.3 1.0 NA A:HEM201 2.0 24.0 1.0 NB A:HEM201 2.1 24.7 1.0 NC A:HEM201 2.1 24.4 1.0 NE2 A:HIS93 2.1 32.8 1.0 C1D A:HEM201 2.9 27.3 1.0 C4D A:HEM201 2.9 28.4 1.0 CE1 A:HIS93 3.0 33.1 1.0 C4A A:HEM201 3.0 25.0 1.0 C1A A:HEM201 3.0 28.4 1.0 C1B A:HEM201 3.0 25.2 1.0 C4B A:HEM201 3.0 25.3 1.0 C4C A:HEM201 3.1 27.0 1.0 C1C A:HEM201 3.1 26.6 1.0 CD2 A:HIS93 3.2 33.9 1.0 CHD A:HEM201 3.4 29.0 1.0 CHB A:HEM201 3.4 24.0 1.0 CHA A:HEM201 3.4 29.0 1.0 CHC A:HEM201 3.5 25.4 1.0 ND1 A:HIS93 4.1 34.2 1.0 C2D A:HEM201 4.2 33.1 1.0 NE2 B:HIS64 4.2 38.6 1.0 C3D A:HEM201 4.2 31.7 1.0 C2A A:HEM201 4.2 26.1 1.0 C3A A:HEM201 4.2 23.4 1.0 C2B A:HEM201 4.3 23.1 1.0 CG A:HIS93 4.3 34.6 1.0 C3B A:HEM201 4.3 21.5 1.0 C3C A:HEM201 4.3 26.6 1.0 CG2 B:VAL68 4.3 21.6 1.0 C2C A:HEM201 4.3 23.5 1.0 CE1 B:HIS64 4.6 39.8 1.0 CD2 A:HIS97 5.0 47.4 1.0

Iron binding site 2 out of 4 in the Heterodimeric Myoglobin Formed By Domain Swapping


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Heterodimeric Myoglobin Formed By Domain Swapping within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:15.4 occ:1.00 FE B:HEM201 0.0 15.4 1.0 ND B:HEM201 1.9 14.1 1.0 NA B:HEM201 2.0 14.5 1.0 NB B:HEM201 2.1 14.8 1.0 NC B:HEM201 2.1 11.9 1.0 NE2 B:HIS93 2.1 17.1 1.0 NE2 A:HIS68 2.3 26.6 1.0 C4D B:HEM201 2.9 16.6 1.0 C1D B:HEM201 2.9 14.2 1.0 C1A B:HEM201 3.0 15.1 1.0 C4B B:HEM201 3.0 14.2 1.0 C4A B:HEM201 3.0 15.1 1.0 C1B B:HEM201 3.0 15.0 1.0 C4C B:HEM201 3.1 12.1 1.0 C1C B:HEM201 3.1 12.1 1.0 CE1 B:HIS93 3.1 17.6 1.0 CD2 B:HIS93 3.1 16.9 1.0 CD2 A:HIS68 3.1 24.6 1.0 CE1 A:HIS68 3.2 26.6 1.0 CHA B:HEM201 3.4 16.3 1.0 CHC B:HEM201 3.4 13.2 1.0 CHD B:HEM201 3.4 12.6 1.0 CHB B:HEM201 3.4 14.8 1.0 C3D B:HEM201 4.2 18.2 1.0 C2D B:HEM201 4.2 15.8 1.0 ND1 B:HIS93 4.2 17.7 1.0 C3A B:HEM201 4.2 16.1 1.0 ND1 A:HIS68 4.2 24.1 1.0 CG A:HIS68 4.2 22.5 1.0 C2A B:HEM201 4.2 15.4 1.0 CG B:HIS93 4.3 17.3 1.0 C2B B:HEM201 4.3 14.9 1.0 C2C B:HEM201 4.3 11.9 1.0 C3B B:HEM201 4.3 15.0 1.0 C3C B:HEM201 4.3 12.0 1.0 CD2 B:HIS97 5.0 18.6 1.0

Iron binding site 3 out of 4 in the Heterodimeric Myoglobin Formed By Domain Swapping


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Heterodimeric Myoglobin Formed By Domain Swapping within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:19.0 occ:1.00 FE C:HEM201 0.0 19.0 1.0 ND C:HEM201 1.9 18.5 1.0 NA C:HEM201 2.0 17.1 1.0 O D:HOH301 2.0 28.3 1.0 NB C:HEM201 2.1 20.7 1.0 NE2 C:HIS93 2.1 23.5 1.0 NC C:HEM201 2.1 18.2 1.0 C1D C:HEM201 2.9 20.2 1.0 C4D C:HEM201 2.9 20.1 1.0 CE1 C:HIS93 3.0 23.3 1.0 C4A C:HEM201 3.0 17.6 1.0 C1A C:HEM201 3.0 17.2 1.0 C4B C:HEM201 3.0 21.5 1.0 C1B C:HEM201 3.0 20.7 1.0 C4C C:HEM201 3.1 18.0 1.0 C1C C:HEM201 3.1 18.8 1.0 CD2 C:HIS93 3.1 23.9 1.0 CHA C:HEM201 3.4 18.5 1.0 CHB C:HEM201 3.4 20.5 1.0 CHD C:HEM201 3.4 18.6 1.0 CHC C:HEM201 3.5 20.2 1.0 ND1 C:HIS93 4.1 22.9 1.0 C3A C:HEM201 4.2 18.5 1.0 C2D C:HEM201 4.2 20.7 1.0 C3D C:HEM201 4.2 22.6 1.0 C2A C:HEM201 4.2 18.1 1.0 CG C:HIS93 4.2 23.5 1.0 C2B C:HEM201 4.2 20.3 1.0 NE2 D:HIS64 4.2 29.5 1.0 C3B C:HEM201 4.3 20.9 1.0 C3C C:HEM201 4.3 19.2 1.0 C2C C:HEM201 4.3 18.9 1.0 CG2 D:VAL68 4.3 20.3 1.0 CE1 D:HIS64 4.7 29.7 1.0 CD2 C:HIS97 5.0 25.9 1.0

Iron binding site 4 out of 4 in the Heterodimeric Myoglobin Formed By Domain Swapping


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Heterodimeric Myoglobin Formed By Domain Swapping within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:29.4 occ:1.00 FE D:HEM201 0.0 29.4 1.0 ND D:HEM201 1.9 34.8 1.0 NA D:HEM201 2.0 31.5 1.0 NC D:HEM201 2.1 32.5 1.0 NB D:HEM201 2.1 30.4 1.0 NE2 D:HIS93 2.2 32.7 1.0 NE2 C:HIS68 2.2 42.0 1.0 C4D D:HEM201 2.9 35.3 1.0 C1D D:HEM201 2.9 36.0 1.0 C1A D:HEM201 3.0 32.0 1.0 C4A D:HEM201 3.0 32.8 1.0 C4B D:HEM201 3.0 30.3 1.0 C4C D:HEM201 3.1 33.2 1.0 C1C D:HEM201 3.1 29.6 1.0 CD2 C:HIS68 3.1 38.8 1.0 C1B D:HEM201 3.1 29.8 1.0 CE1 D:HIS93 3.1 34.7 1.0 CE1 C:HIS68 3.1 41.6 1.0 CD2 D:HIS93 3.3 32.6 1.0 CHA D:HEM201 3.4 32.6 1.0 CHD D:HEM201 3.4 33.3 1.0 CHC D:HEM201 3.4 28.4 1.0 CHB D:HEM201 3.5 32.1 1.0 ND1 C:HIS68 4.1 38.0 1.0 CG C:HIS68 4.1 35.6 1.0 C2A D:HEM201 4.2 33.3 1.0 C3A D:HEM201 4.2 31.5 1.0 C2D D:HEM201 4.2 36.6 1.0 C3D D:HEM201 4.2 37.1 1.0 ND1 D:HIS93 4.3 34.9 1.0 C2C D:HEM201 4.3 29.2 1.0 C3C D:HEM201 4.3 30.6 1.0 C3B D:HEM201 4.3 29.7 1.0 C2B D:HEM201 4.3 29.0 1.0 CG D:HIS93 4.4 33.0 1.0

Y.W.Lin, S.Nagao, M.Zhang, Y.Shomura, Y.Higuchi, S.Hirota. Rational Design of Heterodimeric Protein Using Domain Swapping For Myoglobin Angew.Chem.Int.Ed.Engl. 2014.
ISSN: ESSN 1521-3773
PubMed: 25370865
DOI: 10.1002/ANIE.201409267