Iron in PDB 6ra6: Ferric Murine Neuroglobin Gly-LOOP44-47/F106A Mutant

The structure of Ferric Murine Neuroglobin Gly-LOOP44-47/F106A Mutant, PDB code: 6ra6 was solved by C.Exertier, I.Freda, L.C.Montemiglio, C.Savino, B.Vallone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.32 / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.587, 74.587, 77.091, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 21.9

The binding sites of Iron atom in the Ferric Murine Neuroglobin Gly-LOOP44-47/F106A Mutant (pdb code 6ra6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Ferric Murine Neuroglobin Gly-LOOP44-47/F106A Mutant, PDB code: 6ra6:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Ferric Murine Neuroglobin Gly-LOOP44-47/F106A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ferric Murine Neuroglobin Gly-LOOP44-47/F106A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:35.3 occ:0.54 FE A:HEM201 0.0 35.3 0.5 FE A:HEM201 0.4 41.1 0.5 NA A:HEM201 1.7 46.2 0.5 ND A:HEM201 1.7 45.4 0.5 ND A:HEM201 1.9 35.9 0.5 NE2 A:HIS63 2.0 36.7 0.5 NA A:HEM201 2.0 36.4 0.5 NE2 A:HIS95 2.0 34.4 0.5 NE2 A:HIS63 2.0 35.9 0.5 NC A:HEM201 2.1 34.9 0.5 NB A:HEM201 2.1 35.4 0.5 NE2 A:HIS95 2.1 38.9 0.5 NB A:HEM201 2.3 43.3 0.5 NC A:HEM201 2.4 42.5 0.5 C1A A:HEM201 2.6 48.7 0.5 C4D A:HEM201 2.6 47.2 0.5 C4A A:HEM201 2.8 49.7 0.5 C4D A:HEM201 2.9 36.2 0.5 C1D A:HEM201 2.9 38.9 0.5 C1D A:HEM201 2.9 46.8 0.5 CD2 A:HIS63 2.9 37.1 0.5 CD2 A:HIS63 3.0 37.6 0.5 CE1 A:HIS95 3.0 35.2 0.5 CE1 A:HIS95 3.0 40.9 0.5 C1A A:HEM201 3.0 36.9 0.5 C4C A:HEM201 3.0 36.3 0.5 CE1 A:HIS63 3.0 37.8 0.5 CHA A:HEM201 3.0 47.5 0.5 CD2 A:HIS95 3.0 35.0 0.5 C4A A:HEM201 3.1 38.1 0.5 C4B A:HEM201 3.1 38.8 0.5 C1B A:HEM201 3.1 35.4 0.5 C1B A:HEM201 3.1 45.6 0.5 C1C A:HEM201 3.1 37.5 0.5 CE1 A:HIS63 3.1 37.6 0.5 CD2 A:HIS95 3.2 39.7 0.5 C4C A:HEM201 3.3 40.3 0.5 CHD A:HEM201 3.3 36.4 0.5 C4B A:HEM201 3.3 46.0 0.5 CHB A:HEM201 3.3 45.4 0.5 CHA A:HEM201 3.4 34.7 0.5 CHC A:HEM201 3.5 39.3 0.5 CHB A:HEM201 3.5 34.5 0.5 C1C A:HEM201 3.5 44.0 0.5 CHD A:HEM201 3.5 41.8 0.5 C2A A:HEM201 3.8 47.3 0.5 CHC A:HEM201 3.9 45.7 0.5 C3A A:HEM201 3.9 49.0 0.5 C3D A:HEM201 3.9 49.4 0.5 C2D A:HEM201 4.1 50.9 0.5 ND1 A:HIS95 4.1 35.2 0.5 C3D A:HEM201 4.1 34.5 0.5 CG A:HIS63 4.1 37.8 0.5 CG A:HIS63 4.1 37.4 0.5 ND1 A:HIS63 4.1 38.6 0.5 C2D A:HEM201 4.1 35.8 0.5 ND1 A:HIS95 4.1 39.4 0.5 CG A:HIS95 4.2 38.7 0.5 ND1 A:HIS63 4.2 37.3 0.5 C2A A:HEM201 4.2 38.6 0.5 C3A A:HEM201 4.2 39.3 0.5 C3C A:HEM201 4.2 37.6 0.5 C2C A:HEM201 4.3 36.2 0.5 CG A:HIS95 4.3 41.6 0.5 C2B A:HEM201 4.3 37.8 0.5 C3B A:HEM201 4.3 35.7 0.5 C2B A:HEM201 4.4 46.2 0.5 C3B A:HEM201 4.5 45.8 0.5 C3C A:HEM201 4.5 39.5 0.5 C2C A:HEM201 4.6 39.5 0.5 CG2 A:VAL67 4.8 40.6 1.0

Iron binding site 2 out of 2 in the Ferric Murine Neuroglobin Gly-LOOP44-47/F106A Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ferric Murine Neuroglobin Gly-LOOP44-47/F106A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:41.1 occ:0.46 FE A:HEM201 0.0 41.1 0.5 FE A:HEM201 0.4 35.3 0.5 NB A:HEM201 1.7 35.4 0.5 ND A:HEM201 1.9 45.4 0.5 NC A:HEM201 1.9 34.9 0.5 NE2 A:HIS95 1.9 34.4 0.5 NE2 A:HIS95 2.0 38.9 0.5 NA A:HEM201 2.0 46.2 0.5 NC A:HEM201 2.1 42.5 0.5 NB A:HEM201 2.1 43.3 0.5 NE2 A:HIS63 2.1 36.7 0.5 NE2 A:HIS63 2.1 35.9 0.5 NA A:HEM201 2.2 36.4 0.5 ND A:HEM201 2.2 35.9 0.5 C4B A:HEM201 2.7 38.8 0.5 C1C A:HEM201 2.8 37.5 0.5 C1B A:HEM201 2.8 35.4 0.5 CD2 A:HIS95 2.9 35.0 0.5 C1D A:HEM201 2.9 46.8 0.5 C4D A:HEM201 2.9 47.2 0.5 CE1 A:HIS95 2.9 40.9 0.5 C1A A:HEM201 3.0 48.7 0.5 CE1 A:HIS63 3.0 37.8 0.5 C4C A:HEM201 3.0 36.3 0.5 CD2 A:HIS95 3.0 39.7 0.5 CE1 A:HIS95 3.0 35.2 0.5 C4C A:HEM201 3.0 40.3 0.5 C1B A:HEM201 3.0 45.6 0.5 C4A A:HEM201 3.1 49.7 0.5 C4B A:HEM201 3.1 46.0 0.5 C4A A:HEM201 3.1 38.1 0.5 CHC A:HEM201 3.1 39.3 0.5 CE1 A:HIS63 3.1 37.6 0.5 C1C A:HEM201 3.1 44.0 0.5 CD2 A:HIS63 3.2 37.1 0.5 C1D A:HEM201 3.2 38.9 0.5 CD2 A:HIS63 3.2 37.6 0.5 C4D A:HEM201 3.2 36.2 0.5 C1A A:HEM201 3.3 36.9 0.5 CHD A:HEM201 3.4 41.8 0.5 CHB A:HEM201 3.4 34.5 0.5 CHA A:HEM201 3.4 47.5 0.5 CHB A:HEM201 3.5 45.4 0.5 CHD A:HEM201 3.5 36.4 0.5 CHC A:HEM201 3.5 45.7 0.5 CHA A:HEM201 3.7 34.7 0.5 C3B A:HEM201 4.0 35.7 0.5 C2B A:HEM201 4.0 37.8 0.5 CG A:HIS95 4.0 38.7 0.5 ND1 A:HIS95 4.0 39.4 0.5 C2C A:HEM201 4.0 36.2 0.5 ND1 A:HIS95 4.1 35.2 0.5 CG A:HIS95 4.1 41.6 0.5 C3C A:HEM201 4.1 37.6 0.5 C2D A:HEM201 4.1 50.9 0.5 C3D A:HEM201 4.1 49.4 0.5 ND1 A:HIS63 4.2 38.6 0.5 C2A A:HEM201 4.2 47.3 0.5 C3A A:HEM201 4.2 49.0 0.5 C3C A:HEM201 4.2 39.5 0.5 ND1 A:HIS63 4.2 37.3 0.5 C2C A:HEM201 4.2 39.5 0.5 C2B A:HEM201 4.3 46.2 0.5 CG A:HIS63 4.3 37.8 0.5 CG A:HIS63 4.3 37.4 0.5 C3B A:HEM201 4.3 45.8 0.5 C3A A:HEM201 4.3 39.3 0.5 C2A A:HEM201 4.4 38.6 0.5 C2D A:HEM201 4.5 35.8 0.5 C3D A:HEM201 4.5 34.5 0.5 CG2 A:VAL67 4.8 40.6 1.0

L.Milazzo, C.Exertier, M.Becucci, I.Freda, L.C.Montemiglio, C.Savino, B.Vallone, G.Smulevich. Lack of Orientation Selectivity of the Heme Insertion in Murine Neuroglobin Revealed By Resonance Raman Spectroscopy. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 32034988
DOI: 10.1111/FEBS.15241