Iron in PDB 1oj6: Human Brain Neuroglobin Three-Dimensional Structure

The structure of Human Brain Neuroglobin Three-Dimensional Structure, PDB code: 1oj6 was solved by A.Pesce, S.Dewilde, M.Nardini, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.598, 94.927, 67.563, 90.00, 94.38, 90.00
R / Rfree (%)	17.8 / 23.3

The binding sites of Iron atom in the Human Brain Neuroglobin Three-Dimensional Structure (pdb code 1oj6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Human Brain Neuroglobin Three-Dimensional Structure, PDB code: 1oj6:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Human Brain Neuroglobin Three-Dimensional Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Brain Neuroglobin Three-Dimensional Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1150 b:3.6 occ:1.00 FE A:HEM1150 0.0 3.6 1.0 NC A:HEM1150 2.0 13.6 1.0 NA A:HEM1150 2.0 26.8 1.0 NB A:HEM1150 2.1 18.8 1.0 NE2 A:HIS96 2.1 17.3 1.0 ND A:HEM1150 2.1 19.7 1.0 NE2 A:HIS64 2.1 12.5 1.0 CD2 A:HIS96 3.0 16.4 1.0 C1C A:HEM1150 3.0 16.4 1.0 C4C A:HEM1150 3.0 15.7 1.0 C1A A:HEM1150 3.0 25.6 1.0 C4A A:HEM1150 3.0 17.9 1.0 C4B A:HEM1150 3.1 13.3 1.0 C1B A:HEM1150 3.1 17.7 1.0 C4D A:HEM1150 3.1 14.9 1.0 C1D A:HEM1150 3.1 11.1 1.0 CE1 A:HIS64 3.1 18.3 1.0 CD2 A:HIS64 3.1 17.5 1.0 CE1 A:HIS96 3.1 19.9 1.0 CHC A:HEM1150 3.4 19.7 1.0 CHD A:HEM1150 3.4 17.6 1.0 CHA A:HEM1150 3.4 18.6 1.0 CHB A:HEM1150 3.4 14.6 1.0 CG A:HIS96 4.2 13.2 1.0 C3C A:HEM1150 4.2 20.1 1.0 C2C A:HEM1150 4.2 21.2 1.0 ND1 A:HIS96 4.2 18.3 1.0 ND1 A:HIS64 4.2 11.4 1.0 C2A A:HEM1150 4.3 26.2 1.0 C3A A:HEM1150 4.3 22.8 1.0 CG A:HIS64 4.3 18.5 1.0 C3B A:HEM1150 4.3 22.7 1.0 C2B A:HEM1150 4.3 26.5 1.0 C3D A:HEM1150 4.3 21.0 1.0 C2D A:HEM1150 4.3 16.9 1.0 CG2 A:VAL68 4.8 13.7 1.0

Iron binding site 2 out of 4 in the Human Brain Neuroglobin Three-Dimensional Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Brain Neuroglobin Three-Dimensional Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1152 b:2.0 occ:1.00 FE B:HEM1152 0.0 2.0 1.0 NC B:HEM1152 2.0 15.2 1.0 ND B:HEM1152 2.0 12.1 1.0 NE2 B:HIS96 2.0 14.6 1.0 NA B:HEM1152 2.1 23.5 1.0 NB B:HEM1152 2.1 26.8 1.0 NE2 B:HIS64 2.2 15.2 1.0 CD2 B:HIS96 2.9 19.3 1.0 C4C B:HEM1152 2.9 18.1 1.0 C1D B:HEM1152 3.0 18.7 1.0 C1C B:HEM1152 3.0 13.6 1.0 C4D B:HEM1152 3.0 15.9 1.0 C1A B:HEM1152 3.1 17.1 1.0 CE1 B:HIS96 3.1 22.9 1.0 C4B B:HEM1152 3.1 13.0 1.0 C4A B:HEM1152 3.1 19.1 1.0 CE1 B:HIS64 3.1 17.4 1.0 C1B B:HEM1152 3.1 15.9 1.0 CD2 B:HIS64 3.2 15.1 1.0 CHD B:HEM1152 3.3 13.6 1.0 CHA B:HEM1152 3.4 11.1 1.0 CHC B:HEM1152 3.4 12.3 1.0 CHB B:HEM1152 3.5 14.9 1.0 CG B:HIS96 4.1 18.4 1.0 ND1 B:HIS96 4.1 14.7 1.0 C3C B:HEM1152 4.2 15.9 1.0 C2C B:HEM1152 4.2 14.9 1.0 C2D B:HEM1152 4.2 15.3 1.0 C3D B:HEM1152 4.2 14.5 1.0 ND1 B:HIS64 4.3 17.4 1.0 CG B:HIS64 4.3 15.5 1.0 C2A B:HEM1152 4.3 20.1 1.0 C3B B:HEM1152 4.3 18.2 1.0 C3A B:HEM1152 4.3 17.9 1.0 C2B B:HEM1152 4.3 20.2 1.0 CG2 B:VAL68 4.9 11.6 1.0

Iron binding site 3 out of 4 in the Human Brain Neuroglobin Three-Dimensional Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Human Brain Neuroglobin Three-Dimensional Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1152 b:2.0 occ:1.00 FE C:HEM1152 0.0 2.0 1.0 ND C:HEM1152 2.0 16.0 1.0 NC C:HEM1152 2.0 15.1 1.0 NE2 C:HIS64 2.1 13.3 1.0 NA C:HEM1152 2.1 17.2 1.0 NB C:HEM1152 2.1 19.4 1.0 NE2 C:HIS96 2.1 16.4 1.0 C4C C:HEM1152 3.0 15.1 1.0 C1D C:HEM1152 3.0 22.4 1.0 CD2 C:HIS96 3.0 18.0 1.0 C4D C:HEM1152 3.0 16.1 1.0 CD2 C:HIS64 3.0 19.0 1.0 C1C C:HEM1152 3.0 13.9 1.0 C1A C:HEM1152 3.1 15.0 1.0 CE1 C:HIS64 3.1 16.8 1.0 C4B C:HEM1152 3.1 17.5 1.0 C1B C:HEM1152 3.1 5.5 1.0 C4A C:HEM1152 3.1 11.2 1.0 CE1 C:HIS96 3.2 19.4 1.0 CHD C:HEM1152 3.3 21.2 1.0 CHA C:HEM1152 3.4 15.3 1.0 CHC C:HEM1152 3.4 17.3 1.0 CHB C:HEM1152 3.5 11.2 1.0 CG C:HIS96 4.2 18.9 1.0 ND1 C:HIS64 4.2 12.7 1.0 CG C:HIS64 4.2 14.3 1.0 C3C C:HEM1152 4.2 11.4 1.0 C2D C:HEM1152 4.2 12.9 1.0 ND1 C:HIS96 4.2 19.0 1.0 C2C C:HEM1152 4.2 18.0 1.0 C3D C:HEM1152 4.2 15.1 1.0 C3B C:HEM1152 4.3 19.7 1.0 C2A C:HEM1152 4.3 16.9 1.0 C2B C:HEM1152 4.3 10.9 1.0 C3A C:HEM1152 4.3 21.0 1.0 CG2 C:VAL68 5.0 14.5 1.0

Iron binding site 4 out of 4 in the Human Brain Neuroglobin Three-Dimensional Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Human Brain Neuroglobin Three-Dimensional Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe1151 b:2.3 occ:1.00 FE D:HEM1151 0.0 2.3 1.0 NA D:HEM1151 1.9 20.0 1.0 NC D:HEM1151 2.0 20.6 1.0 NE2 D:HIS96 2.0 17.8 1.0 ND D:HEM1151 2.1 17.6 1.0 NE2 D:HIS64 2.1 19.4 1.0 NB D:HEM1151 2.1 26.4 1.0 C1A D:HEM1151 3.0 16.3 1.0 CD2 D:HIS96 3.0 19.9 1.0 C4A D:HEM1151 3.0 21.1 1.0 C4C D:HEM1151 3.0 22.7 1.0 CE1 D:HIS96 3.0 21.4 1.0 CE1 D:HIS64 3.0 17.6 1.0 C4D D:HEM1151 3.0 17.9 1.0 C1C D:HEM1151 3.1 17.2 1.0 C1D D:HEM1151 3.1 19.5 1.0 CD2 D:HIS64 3.1 23.1 1.0 C4B D:HEM1151 3.1 12.6 1.0 C1B D:HEM1151 3.1 19.3 1.0 CHA D:HEM1151 3.4 18.7 1.0 CHD D:HEM1151 3.4 17.7 1.0 CHB D:HEM1151 3.4 14.4 1.0 CHC D:HEM1151 3.5 11.9 1.0 ND1 D:HIS96 4.1 21.7 1.0 CG D:HIS96 4.1 19.9 1.0 ND1 D:HIS64 4.2 18.3 1.0 C2A D:HEM1151 4.2 23.2 1.0 C3A D:HEM1151 4.2 23.9 1.0 CG D:HIS64 4.2 20.3 1.0 C3C D:HEM1151 4.2 19.2 1.0 C2C D:HEM1151 4.3 18.3 1.0 C3D D:HEM1151 4.3 17.1 1.0 C2D D:HEM1151 4.3 24.6 1.0 C3B D:HEM1151 4.3 26.6 1.0 C2B D:HEM1151 4.3 21.3 1.0 CG2 D:VAL68 5.0 19.2 1.0

A.Pesce, S.Dewilde, M.Nardini, L.Moens, P.Ascenzi, T.Hankeln, T.Burmester, M.Bolognesi. Human Brain Neuroglobin Structure Reveals A Distinct Mode of Controlling Oxygen Affinity Structure V. 11 1087 2003.
ISSN: ISSN 0969-2126
PubMed: 12962627
DOI: 10.1016/S0969-2126(03)00166-7