Iron in PDB 5yce: Sperm Whale Myoglobin Swmb

The structure of Sperm Whale Myoglobin Swmb, PDB code: 5yce 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)	9.95 / 0.77
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.180, 30.660, 63.570, 90.00, 105.49, 90.00
R / Rfree (%)	14.4 / 16.2

The binding sites of Iron atom in the Sperm Whale Myoglobin Swmb (pdb code 5yce). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total only one binding site of Iron was determined in the Sperm Whale Myoglobin Swmb, PDB code: 5yce:

Iron binding site 1 out of 1 in the Sperm Whale Myoglobin Swmb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Sperm Whale Myoglobin Swmb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:4.8 occ:1.00 FE A:HEM201 0.0 4.8 1.0 NA A:HEM201 2.0 5.4 1.0 ND A:HEM201 2.0 5.1 1.0 NC A:HEM201 2.0 4.9 1.0 NB A:HEM201 2.1 5.2 1.0 O A:HOH365 2.1 6.0 1.0 NE2 A:HIS93 2.1 5.4 1.0 C1D A:HEM201 3.0 5.9 1.0 C4C A:HEM201 3.0 5.3 1.0 C1A A:HEM201 3.1 6.3 1.0 C4A A:HEM201 3.1 5.9 1.0 C4D A:HEM201 3.1 5.8 1.0 C1C A:HEM201 3.1 4.9 1.0 CE1 A:HIS93 3.1 6.6 1.0 C4B A:HEM201 3.1 4.9 1.0 C1B A:HEM201 3.1 5.3 1.0 CD2 A:HIS93 3.2 5.1 1.0 CHD A:HEM201 3.4 5.5 1.0 CHB A:HEM201 3.4 5.8 1.0 CHA A:HEM201 3.4 6.7 1.0 CHC A:HEM201 3.4 5.3 1.0 ND1 A:HIS93 4.2 6.9 1.0 NE2 A:HIS64 4.3 7.1 1.0 C3C A:HEM201 4.3 5.5 1.0 C2C A:HEM201 4.3 5.5 1.0 C3A A:HEM201 4.3 6.7 1.0 C2A A:HEM201 4.3 6.5 1.0 CG A:HIS93 4.3 5.9 1.0 C2D A:HEM201 4.3 6.2 1.0 C3D A:HEM201 4.3 6.8 1.0 C3B A:HEM201 4.3 5.6 1.0 C2B A:HEM201 4.3 5.5 1.0 CG2 A:VAL68 4.8 5.3 1.0 CE1 A:HIS64 4.8 7.2 1.0 CZ A:PHE43 4.9 8.0 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