Iron in PDB 7ohd: Crystal Structure of Ferric Murine Neuroglobin Cdless Mutant

The structure of Crystal Structure of Ferric Murine Neuroglobin Cdless Mutant, PDB code: 7ohd was solved by C.Exertier, I.Freda, L.C.Montemiglio, C.Savino, G.Cerutti, E.Gugole, B.Vallone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.02 / 1.80
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	95.941, 95.941, 58.56, 90, 90, 120
R / Rfree (%)	18.2 / 21.1

The binding sites of Iron atom in the Crystal Structure of Ferric Murine Neuroglobin Cdless Mutant (pdb code 7ohd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Ferric Murine Neuroglobin Cdless Mutant, PDB code: 7ohd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Ferric Murine Neuroglobin Cdless Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Ferric Murine Neuroglobin Cdless Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:34.4 occ:0.71 FE A:HEM201 0.0 34.4 0.7 FE A:HEM201 0.8 31.4 0.3 NB A:HEM201 1.3 29.2 0.3 NE2 A:HIS83 1.9 39.0 0.3 ND A:HEM201 1.9 33.2 0.7 NE2 A:HIS83 2.0 37.9 0.7 NA A:HEM201 2.0 36.6 0.7 NE2 A:HIS51 2.0 26.6 0.7 NB A:HEM201 2.1 34.7 0.7 NC A:HEM201 2.1 34.9 0.7 NA A:HEM201 2.1 31.3 0.3 NC A:HEM201 2.1 30.0 0.3 NE2 A:HIS51 2.2 42.6 0.3 C4B A:HEM201 2.4 30.2 0.3 C1B A:HEM201 2.4 31.7 0.3 ND A:HEM201 2.6 33.7 0.3 CE1 A:HIS83 2.8 41.0 0.3 C4A A:HEM201 2.9 32.9 0.3 C1C A:HEM201 2.9 31.2 0.3 C4D A:HEM201 2.9 31.8 0.7 CE1 A:HIS51 2.9 27.4 0.7 C1D A:HEM201 3.0 31.6 0.7 CD2 A:HIS83 3.0 40.0 0.3 CE1 A:HIS83 3.0 39.9 0.7 CHB A:HEM201 3.0 30.9 0.3 C4B A:HEM201 3.0 34.0 0.7 CD2 A:HIS83 3.0 39.1 0.7 C1A A:HEM201 3.0 35.2 0.7 CHC A:HEM201 3.0 28.0 0.3 C1B A:HEM201 3.0 34.4 0.7 C4A A:HEM201 3.0 35.4 0.7 C1C A:HEM201 3.1 35.1 0.7 C4C A:HEM201 3.1 34.2 0.7 CD2 A:HIS51 3.1 40.4 0.3 CD2 A:HIS51 3.1 26.4 0.7 CE1 A:HIS51 3.3 40.4 0.3 C4C A:HEM201 3.3 29.8 0.3 C1A A:HEM201 3.3 34.1 0.3 CHA A:HEM201 3.4 35.7 0.7 CHC A:HEM201 3.4 34.9 0.7 CHB A:HEM201 3.4 34.8 0.7 CHD A:HEM201 3.4 34.4 0.7 C2B A:HEM201 3.6 31.8 0.3 C3B A:HEM201 3.6 32.3 0.3 C1D A:HEM201 3.6 32.4 0.3 C4D A:HEM201 3.6 33.5 0.3 CHD A:HEM201 3.9 32.0 0.3 ND1 A:HIS83 3.9 39.7 0.3 CHA A:HEM201 3.9 33.8 0.3 CG A:HIS83 4.0 37.8 0.3 ND1 A:HIS51 4.1 25.5 0.7 ND1 A:HIS83 4.1 38.7 0.7 CG A:HIS83 4.1 37.0 0.7 CG A:HIS51 4.2 28.6 0.7 C2C A:HEM201 4.2 30.3 0.3 C3A A:HEM201 4.2 32.4 0.3 C3D A:HEM201 4.2 29.2 0.7 C2A A:HEM201 4.2 36.3 0.7 C2D A:HEM201 4.2 30.9 0.7 C3A A:HEM201 4.2 38.3 0.7 C2C A:HEM201 4.2 36.5 0.7 C3C A:HEM201 4.2 35.3 0.7 C2B A:HEM201 4.3 32.2 0.7 CG A:HIS51 4.3 39.1 0.3 C3B A:HEM201 4.3 37.0 0.7 ND1 A:HIS51 4.3 41.3 0.3 C3C A:HEM201 4.4 29.8 0.3 C2A A:HEM201 4.4 35.1 0.3 CG2 A:VAL55 4.9 35.4 1.0 C2D A:HEM201 4.9 33.6 0.3 C3D A:HEM201 4.9 32.7 0.3 CAB A:HEM201 5.0 33.2 0.3 CMB A:HEM201 5.0 34.3 0.3

Iron binding site 2 out of 4 in the Crystal Structure of Ferric Murine Neuroglobin Cdless Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Ferric Murine Neuroglobin Cdless Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:31.4 occ:0.29 FE A:HEM201 0.0 31.4 0.3 FE A:HEM201 0.8 34.4 0.7 NA A:HEM201 1.2 36.6 0.7 ND A:HEM201 1.9 33.7 0.3 NE2 A:HIS51 1.9 26.6 0.7 NA A:HEM201 2.0 31.3 0.3 NC A:HEM201 2.1 30.0 0.3 NE2 A:HIS83 2.1 39.0 0.3 ND A:HEM201 2.1 33.2 0.7 NB A:HEM201 2.1 29.2 0.3 NE2 A:HIS51 2.1 42.6 0.3 NE2 A:HIS83 2.2 37.9 0.7 NB A:HEM201 2.2 34.7 0.7 C1A A:HEM201 2.3 35.2 0.7 C4A A:HEM201 2.3 35.4 0.7 C4D A:HEM201 2.7 31.8 0.7 CD2 A:HIS51 2.7 40.4 0.3 CD2 A:HIS51 2.7 26.4 0.7 NC A:HEM201 2.8 34.9 0.7 C1B A:HEM201 2.8 34.4 0.7 C1D A:HEM201 2.9 32.4 0.3 C4D A:HEM201 2.9 33.5 0.3 CHA A:HEM201 2.9 35.7 0.7 CHB A:HEM201 2.9 34.8 0.7 C1A A:HEM201 3.0 34.1 0.3 CE1 A:HIS51 3.0 27.4 0.7 CE1 A:HIS83 3.0 41.0 0.3 C4C A:HEM201 3.0 29.8 0.3 CD2 A:HIS83 3.0 40.0 0.3 C4A A:HEM201 3.1 32.9 0.3 CD2 A:HIS83 3.1 39.1 0.7 C1B A:HEM201 3.1 31.7 0.3 C4B A:HEM201 3.1 30.2 0.3 C1C A:HEM201 3.1 31.2 0.3 CE1 A:HIS83 3.3 39.9 0.7 C1D A:HEM201 3.3 31.6 0.7 CHD A:HEM201 3.3 32.0 0.3 CHA A:HEM201 3.3 33.8 0.3 C4B A:HEM201 3.4 34.0 0.7 CE1 A:HIS51 3.4 40.4 0.3 C2A A:HEM201 3.5 36.3 0.7 CHB A:HEM201 3.5 30.9 0.3 C3A A:HEM201 3.5 38.3 0.7 CHC A:HEM201 3.6 28.0 0.3 C4C A:HEM201 3.8 34.2 0.7 C1C A:HEM201 3.8 35.1 0.7 CG A:HIS51 3.9 28.6 0.7 CHC A:HEM201 4.0 34.9 0.7 CHD A:HEM201 4.0 34.4 0.7 CG A:HIS51 4.0 39.1 0.3 ND1 A:HIS51 4.0 25.5 0.7 ND1 A:HIS83 4.1 39.7 0.3 C3D A:HEM201 4.1 32.7 0.3 C2D A:HEM201 4.1 33.6 0.3 CG A:HIS83 4.1 37.8 0.3 C3D A:HEM201 4.2 29.2 0.7 C2B A:HEM201 4.2 32.2 0.7 C2A A:HEM201 4.2 35.1 0.3 C3C A:HEM201 4.2 29.8 0.3 C3A A:HEM201 4.2 32.4 0.3 CG A:HIS83 4.2 37.0 0.7 ND1 A:HIS51 4.3 41.3 0.3 C2C A:HEM201 4.3 30.3 0.3 ND1 A:HIS83 4.3 38.7 0.7 C2B A:HEM201 4.3 31.8 0.3 C3B A:HEM201 4.3 32.3 0.3 C2D A:HEM201 4.4 30.9 0.7 C3B A:HEM201 4.5 37.0 0.7 CAA A:HEM201 4.9 41.3 0.7 CMA A:HEM201 4.9 38.9 0.7

Iron binding site 3 out of 4 in the Crystal Structure of Ferric Murine Neuroglobin Cdless Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Ferric Murine Neuroglobin Cdless Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:43.9 occ:0.67 FE B:HEM201 0.0 43.9 0.7 FE B:HEM201 0.2 36.0 0.3 ND B:HEM201 1.8 36.1 0.3 NE2 B:HIS51 1.9 37.3 0.3 ND B:HEM201 2.0 38.6 0.7 NA B:HEM201 2.0 46.6 0.7 NC B:HEM201 2.0 39.5 0.7 NA B:HEM201 2.0 33.3 0.3 NE2 B:HIS83 2.0 41.9 0.3 NE2 B:HIS51 2.1 43.0 0.7 NC B:HEM201 2.1 34.2 0.3 NB B:HEM201 2.1 44.0 0.7 NB B:HEM201 2.1 33.9 0.3 NE2 B:HIS83 2.3 37.2 0.7 C4D B:HEM201 2.9 34.5 0.3 C1D B:HEM201 2.9 36.5 0.3 CE1 B:HIS51 2.9 39.6 0.3 C1D B:HEM201 2.9 40.0 0.7 C4C B:HEM201 3.0 35.4 0.3 C4D B:HEM201 3.0 40.4 0.7 CD2 B:HIS51 3.0 39.2 0.3 C1A B:HEM201 3.0 42.5 0.7 C4C B:HEM201 3.0 43.4 0.7 C1A B:HEM201 3.0 35.0 0.3 CE1 B:HIS83 3.0 46.6 0.3 CD2 B:HIS83 3.1 40.8 0.3 CD2 B:HIS51 3.1 44.0 0.7 CE1 B:HIS51 3.1 45.9 0.7 C1B B:HEM201 3.1 43.1 0.7 C4A B:HEM201 3.1 45.3 0.7 C4B B:HEM201 3.1 43.4 0.7 C1C B:HEM201 3.1 41.6 0.7 C4A B:HEM201 3.1 35.0 0.3 C4B B:HEM201 3.1 33.9 0.3 C1B B:HEM201 3.1 35.1 0.3 C1C B:HEM201 3.1 34.9 0.3 CE1 B:HIS83 3.2 41.8 0.7 CD2 B:HIS83 3.3 37.7 0.7 CHD B:HEM201 3.3 34.3 0.3 CHA B:HEM201 3.4 35.0 0.3 CHD B:HEM201 3.4 39.7 0.7 CHA B:HEM201 3.4 42.5 0.7 CHC B:HEM201 3.4 43.5 0.7 CHB B:HEM201 3.5 43.5 0.7 CHB B:HEM201 3.5 34.6 0.3 CHC B:HEM201 3.6 34.3 0.3 ND1 B:HIS51 4.0 38.9 0.3 CG B:HIS51 4.1 39.0 0.3 C3D B:HEM201 4.1 36.5 0.3 C2D B:HEM201 4.1 35.5 0.3 ND1 B:HIS83 4.2 45.3 0.3 ND1 B:HIS51 4.2 44.7 0.7 CG B:HIS83 4.2 42.0 0.3 CG B:HIS51 4.2 42.6 0.7 C3C B:HEM201 4.2 34.7 0.3 C2A B:HEM201 4.2 48.4 0.7 C2D B:HEM201 4.2 40.9 0.7 C3C B:HEM201 4.2 39.6 0.7 C3A B:HEM201 4.2 46.8 0.7 C2A B:HEM201 4.2 35.6 0.3 C2C B:HEM201 4.3 41.2 0.7 C3D B:HEM201 4.3 41.6 0.7 C3A B:HEM201 4.3 35.5 0.3 C2C B:HEM201 4.3 34.6 0.3 C2B B:HEM201 4.3 40.0 0.7 ND1 B:HIS83 4.3 42.4 0.7 C3B B:HEM201 4.3 41.7 0.7 C2B B:HEM201 4.3 33.4 0.3 C3B B:HEM201 4.4 35.8 0.3 CG B:HIS83 4.4 38.9 0.7

Iron binding site 4 out of 4 in the Crystal Structure of Ferric Murine Neuroglobin Cdless Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Ferric Murine Neuroglobin Cdless Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:36.0 occ:0.33 FE B:HEM201 0.0 36.0 0.3 FE B:HEM201 0.2 43.9 0.7 NE2 B:HIS83 1.9 41.9 0.3 ND B:HEM201 1.9 36.1 0.3 ND B:HEM201 1.9 38.6 0.7 NC B:HEM201 2.0 39.5 0.7 NA B:HEM201 2.0 33.3 0.3 NA B:HEM201 2.1 46.6 0.7 NC B:HEM201 2.1 34.2 0.3 NB B:HEM201 2.1 33.9 0.3 NE2 B:HIS51 2.1 37.3 0.3 NE2 B:HIS83 2.1 37.2 0.7 NB B:HEM201 2.1 44.0 0.7 NE2 B:HIS51 2.2 43.0 0.7 CE1 B:HIS83 2.9 46.6 0.3 C4D B:HEM201 2.9 34.5 0.3 CD2 B:HIS83 2.9 40.8 0.3 C1D B:HEM201 2.9 36.5 0.3 C1D B:HEM201 2.9 40.0 0.7 C4C B:HEM201 3.0 43.4 0.7 C4D B:HEM201 3.0 40.4 0.7 C4C B:HEM201 3.0 35.4 0.3 C1A B:HEM201 3.0 35.0 0.3 CE1 B:HIS83 3.0 41.8 0.7 CE1 B:HIS51 3.0 39.6 0.3 C1A B:HEM201 3.0 42.5 0.7 C1C B:HEM201 3.0 41.6 0.7 C4B B:HEM201 3.1 33.9 0.3 C4A B:HEM201 3.1 35.0 0.3 C1B B:HEM201 3.1 35.1 0.3 C4B B:HEM201 3.1 43.4 0.7 C1C B:HEM201 3.1 34.9 0.3 C1B B:HEM201 3.1 43.1 0.7 C4A B:HEM201 3.1 45.3 0.7 CD2 B:HIS83 3.1 37.7 0.7 CD2 B:HIS51 3.2 39.2 0.3 CE1 B:HIS51 3.2 45.9 0.7 CD2 B:HIS51 3.2 44.0 0.7 CHD B:HEM201 3.3 39.7 0.7 CHD B:HEM201 3.4 34.3 0.3 CHA B:HEM201 3.4 35.0 0.3 CHA B:HEM201 3.4 42.5 0.7 CHC B:HEM201 3.4 43.5 0.7 CHB B:HEM201 3.5 34.6 0.3 CHC B:HEM201 3.5 34.3 0.3 CHB B:HEM201 3.5 43.5 0.7 ND1 B:HIS83 4.0 45.3 0.3 CG B:HIS83 4.0 42.0 0.3 ND1 B:HIS83 4.1 42.4 0.7 C3D B:HEM201 4.2 36.5 0.3 ND1 B:HIS51 4.2 38.9 0.3 C2D B:HEM201 4.2 35.5 0.3 C3C B:HEM201 4.2 39.6 0.7 C2C B:HEM201 4.2 41.2 0.7 C2D B:HEM201 4.2 40.9 0.7 C3C B:HEM201 4.2 34.7 0.3 CG B:HIS83 4.2 38.9 0.7 C2A B:HEM201 4.2 35.6 0.3 C3A B:HEM201 4.2 35.5 0.3 C3D B:HEM201 4.3 41.6 0.7 CG B:HIS51 4.3 39.0 0.3 C2A B:HEM201 4.3 48.4 0.7 C2C B:HEM201 4.3 34.6 0.3 C2B B:HEM201 4.3 33.4 0.3 C3A B:HEM201 4.3 46.8 0.7 C3B B:HEM201 4.3 35.8 0.3 ND1 B:HIS51 4.3 44.7 0.7 C2B B:HEM201 4.4 40.0 0.7 C3B B:HEM201 4.4 41.7 0.7 CG B:HIS51 4.4 42.6 0.7

C.Exertier, F.Sebastiani, I.Freda, E.Gugole, G.Cerutti, G.Parisi, L.C.Montemiglio, M.Becucci, C.Viappiani, S.Bruno, C.Savino, C.Zamparelli, M.Anselmi, S.Abbruzzetti, G.Smulevich, B.Vallone. Probing the Role of Murine Neuroglobin Cdloop-D-Helix Unit in Co Ligand Binding and Structural Dynamics. Acs Chem.Biol. V. 17 2099 2022.
ISSN: ESSN 1554-8937
PubMed: 35797699
DOI: 10.1021/ACSCHEMBIO.2C00172