Iron in PDB 5yci: Ancestral Myoglobin Ambwb' of Basilosaurus Relative (Polyphyly)

The structure of Ancestral Myoglobin Ambwb' of Basilosaurus Relative (Polyphyly), PDB code: 5yci 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)	24.98 / 1.97
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.290, 69.320, 108.130, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.7

The binding sites of Iron atom in the Ancestral Myoglobin Ambwb' of Basilosaurus Relative (Polyphyly) (pdb code 5yci). 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), PDB code: 5yci:
Jump to Iron binding site number: 1; 2;

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


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:8.7 occ:1.00 FE A:HEM201 0.0 8.7 1.0 NA A:HEM201 2.0 11.0 1.0 NE2 A:HIS93 2.0 11.4 1.0 ND A:HEM201 2.0 12.3 1.0 NC A:HEM201 2.0 10.6 1.0 NB A:HEM201 2.1 9.5 1.0 O A:HOH326 2.2 9.7 1.0 CE1 A:HIS93 2.9 12.0 1.0 C1A A:HEM201 3.0 12.9 1.0 C4A A:HEM201 3.0 10.9 1.0 C4D A:HEM201 3.0 13.5 1.0 C1C A:HEM201 3.1 11.1 1.0 C1D A:HEM201 3.1 13.0 1.0 C4C A:HEM201 3.1 12.1 1.0 C4B A:HEM201 3.1 9.9 1.0 C1B A:HEM201 3.1 9.3 1.0 CD2 A:HIS93 3.1 11.6 1.0 CHA A:HEM201 3.4 13.9 1.0 CHC A:HEM201 3.4 9.7 1.0 CHD A:HEM201 3.4 12.2 1.0 CHB A:HEM201 3.4 9.8 1.0 ND1 A:HIS93 4.1 12.0 1.0 CG A:HIS93 4.2 12.7 1.0 C2A A:HEM201 4.2 12.7 1.0 C3A A:HEM201 4.3 12.0 1.0 C2C A:HEM201 4.3 11.8 1.0 C3D A:HEM201 4.3 14.5 1.0 C3C A:HEM201 4.3 12.3 1.0 C2D A:HEM201 4.3 14.5 1.0 NE2 A:HIS64 4.3 12.2 1.0 C3B A:HEM201 4.3 9.2 1.0 C2B A:HEM201 4.3 9.1 1.0 CG2 A:VAL68 4.6 9.1 1.0 CE1 A:HIS64 4.8 14.7 1.0

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


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) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:9.5 occ:1.00 FE B:HEM201 0.0 9.5 1.0 NA B:HEM201 2.0 12.9 1.0 NC B:HEM201 2.0 11.1 1.0 NB B:HEM201 2.0 11.1 1.0 ND B:HEM201 2.0 14.0 1.0 NE2 B:HIS93 2.1 13.0 1.0 O B:HOH351 2.2 12.1 1.0 CE1 B:HIS93 3.0 13.1 1.0 C1A B:HEM201 3.0 14.9 1.0 C4B B:HEM201 3.0 10.6 1.0 C1C B:HEM201 3.0 11.1 1.0 C4D B:HEM201 3.0 15.3 1.0 C1D B:HEM201 3.1 14.9 1.0 C4C B:HEM201 3.1 12.4 1.0 C1B B:HEM201 3.1 12.1 1.0 C4A B:HEM201 3.1 13.2 1.0 CD2 B:HIS93 3.1 12.4 1.0 CHA B:HEM201 3.4 16.2 1.0 CHC B:HEM201 3.4 10.0 1.0 CHD B:HEM201 3.4 13.3 1.0 CHB B:HEM201 3.5 12.5 1.0 ND1 B:HIS93 4.2 13.3 1.0 CG B:HIS93 4.2 13.4 1.0 C2C B:HEM201 4.3 10.9 1.0 C3B B:HEM201 4.3 11.2 1.0 C2B B:HEM201 4.3 11.5 1.0 C2A B:HEM201 4.3 14.2 1.0 C3C B:HEM201 4.3 11.3 1.0 C2D B:HEM201 4.3 16.5 1.0 C3D B:HEM201 4.3 16.9 1.0 C3A B:HEM201 4.3 13.6 1.0 NE2 B:HIS64 4.3 15.4 1.0 CG2 B:VAL68 4.7 12.2 1.0 CE1 B:HIS64 4.7 16.8 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