Iron in PDB 5utd: Sperm Whale Myoglobin V68A/I107Y with Nitrite

The structure of Sperm Whale Myoglobin V68A/I107Y with Nitrite, PDB code: 5utd was solved by B.Wang, L.M.Thomas, G.B.Richter-Addo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.60 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.840, 29.260, 64.060, 90.00, 105.76, 90.00
R / Rfree (%)	17.5 / 24.7

The binding sites of Iron atom in the Sperm Whale Myoglobin V68A/I107Y with Nitrite (pdb code 5utd). 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 V68A/I107Y with Nitrite, PDB code: 5utd:

Iron binding site 1 out of 1 in the Sperm Whale Myoglobin V68A/I107Y with Nitrite


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 V68A/I107Y with Nitrite within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:12.3 occ:1.00 FE A:HEM201 0.0 12.3 1.0 ND A:HEM201 2.0 10.5 1.0 O1 A:NO2203 2.0 18.3 1.0 NA A:HEM201 2.0 11.0 1.0 NC A:HEM201 2.1 11.7 1.0 NE2 A:HIS93 2.1 11.8 1.0 NB A:HEM201 2.1 12.9 1.0 N A:NO2203 2.8 17.3 1.0 CD2 A:HIS93 3.0 10.2 1.0 C4D A:HEM201 3.0 10.5 1.0 C1A A:HEM201 3.0 11.1 1.0 C1D A:HEM201 3.0 11.5 1.0 C4B A:HEM201 3.0 15.0 1.0 C4C A:HEM201 3.1 11.6 1.0 C1B A:HEM201 3.1 14.2 1.0 C1C A:HEM201 3.1 12.3 1.0 C4A A:HEM201 3.1 12.0 1.0 CE1 A:HIS93 3.1 11.6 1.0 CHC A:HEM201 3.4 12.4 1.0 CHA A:HEM201 3.4 10.6 1.0 CHB A:HEM201 3.5 11.6 1.0 CHD A:HEM201 3.5 11.5 1.0 O2 A:NO2203 4.0 19.1 1.0 CG A:HIS93 4.2 10.8 1.0 ND1 A:HIS93 4.2 10.9 1.0 C2A A:HEM201 4.2 11.3 1.0 C2C A:HEM201 4.3 12.7 1.0 C3C A:HEM201 4.3 12.6 1.0 C3D A:HEM201 4.3 10.6 1.0 C3A A:HEM201 4.3 11.7 1.0 C2D A:HEM201 4.3 11.0 1.0 C3B A:HEM201 4.3 16.8 1.0 C2B A:HEM201 4.3 15.6 1.0 NE2 A:HIS64 4.5 11.2 1.0 CE1 A:HIS64 4.9 11.9 1.0

B.Wang, Y.Shi, J.Tejero, S.M.Powell, L.M.Thomas, M.T.Gladwin, S.Shiva, Y.Zhang, G.B.Richter-Addo. Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -No Ligand Orientations in Myoglobin Distal Pockets. Biochemistry V. 57 4788 2018.
ISSN: ISSN 1520-4995
PubMed: 29999305
DOI: 10.1021/ACS.BIOCHEM.8B00542