Iron in PDB 5ycj: Ancestral Myoglobin Ambwb' of Basilosaurus Relative (Polyphyly) Imidazole-Ligand

The structure of Ancestral Myoglobin Ambwb' of Basilosaurus Relative (Polyphyly) Imidazole-Ligand, PDB code: 5ycj was solved by Y.Isogai, H.Imamura, S.Nakae, T.Sumi, K.Takahashi, T.Nakagawa, A.Tsuneshige, T.Shirai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.97 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.200, 69.120, 108.380, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 18.3

The binding sites of Iron atom in the Ancestral Myoglobin Ambwb' of Basilosaurus Relative (Polyphyly) Imidazole-Ligand (pdb code 5ycj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Ancestral Myoglobin Ambwb' of Basilosaurus Relative (Polyphyly) Imidazole-Ligand, PDB code: 5ycj:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Ancestral Myoglobin Ambwb' of Basilosaurus Relative (Polyphyly) Imidazole-Ligand


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ancestral Myoglobin Ambwb' of Basilosaurus Relative (Polyphyly) Imidazole-Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:7.1 occ:1.00 FE A:HEM201 0.0 7.1 1.0 NA A:HEM201 2.0 7.4 1.0 NC A:HEM201 2.0 5.4 1.0 ND A:HEM201 2.1 8.4 1.0 NB A:HEM201 2.1 8.6 1.0 NE2 A:HIS93 2.1 6.1 1.0 N1 A:IMD202 2.2 7.8 1.0 C4C A:HEM201 3.0 6.1 1.0 CE1 A:HIS93 3.0 10.0 1.0 C1D A:HEM201 3.0 9.4 1.0 C1A A:HEM201 3.0 8.8 1.0 C4A A:HEM201 3.1 8.1 1.0 C4B A:HEM201 3.1 7.6 1.0 C1C A:HEM201 3.1 6.1 1.0 C4D A:HEM201 3.1 7.8 1.0 C2 A:IMD202 3.1 13.3 1.0 CD2 A:HIS93 3.1 6.2 1.0 C1B A:HEM201 3.1 7.4 1.0 C5 A:IMD202 3.1 9.8 1.0 CHD A:HEM201 3.4 7.5 1.0 CHC A:HEM201 3.5 6.7 1.0 CHA A:HEM201 3.5 10.5 1.0 CHB A:HEM201 3.5 8.3 1.0 ND1 A:HIS93 4.2 8.4 1.0 CG A:HIS93 4.2 6.8 1.0 N3 A:IMD202 4.2 10.8 1.0 C4 A:IMD202 4.3 9.0 1.0 C3C A:HEM201 4.3 5.9 1.0 C3A A:HEM201 4.3 7.7 1.0 C2A A:HEM201 4.3 6.3 1.0 C2C A:HEM201 4.4 6.8 1.0 C2D A:HEM201 4.4 8.1 1.0 C3D A:HEM201 4.4 7.9 1.0 C3B A:HEM201 4.4 6.5 1.0 C2B A:HEM201 4.4 6.7 1.0 CG2 A:VAL68 4.7 10.4 1.0

Iron binding site 2 out of 2 in the Ancestral Myoglobin Ambwb' of Basilosaurus Relative (Polyphyly) Imidazole-Ligand


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ancestral Myoglobin Ambwb' of Basilosaurus Relative (Polyphyly) Imidazole-Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:8.7 occ:1.00 FE B:HEM201 0.0 8.7 1.0 NC B:HEM201 2.0 9.4 1.0 NA B:HEM201 2.0 11.9 1.0 NE2 B:HIS93 2.1 7.0 1.0 NB B:HEM201 2.1 9.8 1.0 ND B:HEM201 2.1 11.8 1.0 N1 B:IMD202 2.2 10.2 1.0 CE1 B:HIS93 3.0 10.3 1.0 C4C B:HEM201 3.1 8.5 1.0 C1D B:HEM201 3.1 10.4 1.0 C4B B:HEM201 3.1 9.1 1.0 C4A B:HEM201 3.1 8.3 1.0 C1C B:HEM201 3.1 6.0 1.0 CD2 B:HIS93 3.1 11.2 1.0 C1A B:HEM201 3.1 10.1 1.0 C2 B:IMD202 3.1 18.9 1.0 C1B B:HEM201 3.1 8.8 1.0 C4D B:HEM201 3.2 12.7 1.0 C5 B:IMD202 3.2 15.4 1.0 CHD B:HEM201 3.4 8.6 1.0 CHC B:HEM201 3.4 6.8 1.0 CHB B:HEM201 3.5 9.6 1.0 CHA B:HEM201 3.6 10.3 1.0 ND1 B:HIS93 4.1 9.2 1.0 CG B:HIS93 4.2 9.6 1.0 N3 B:IMD202 4.2 15.7 1.0 C3C B:HEM201 4.3 8.9 1.0 C4 B:IMD202 4.3 15.6 1.0 C2C B:HEM201 4.3 6.0 1.0 C3B B:HEM201 4.4 8.8 1.0 C3A B:HEM201 4.4 10.6 1.0 C2A B:HEM201 4.4 10.1 1.0 C2D B:HEM201 4.4 11.4 1.0 C2B B:HEM201 4.4 7.3 1.0 C3D B:HEM201 4.4 15.0 1.0 CG2 B:VAL68 4.8 14.0 0.6 CD2 B:HIS97 5.0 11.6 1.0

Y.Isogai, H.Imamura, S.Nakae, T.Sumi, K.I.Takahashi, T.Nakagawa, A.Tsuneshige, T.Shirai. Tracing Whale Myoglobin Evolution By Resurrecting Ancient Proteins. Sci Rep V. 8 16883 2018.
ISSN: ESSN 2045-2322
PubMed: 30442991
DOI: 10.1038/S41598-018-34984-6