Iron in PDB 3gkt: Crystal Structure of Murine Neuroglobin Under Kr Pressure

The structure of Crystal Structure of Murine Neuroglobin Under Kr Pressure, PDB code: 3gkt was solved by T.Moschetti, U.Mueller, J.Schultze, M.Brunori, B.Vallone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.55 / 1.86
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	88.800, 88.800, 113.500, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 20.8

The structure of Crystal Structure of Murine Neuroglobin Under Kr Pressure also contains other interesting chemical elements:

Krypton

(Kr)

2 atoms

The binding sites of Iron atom in the Crystal Structure of Murine Neuroglobin Under Kr Pressure (pdb code 3gkt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Murine Neuroglobin Under Kr Pressure, PDB code: 3gkt:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Murine Neuroglobin Under Kr Pressure


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 Murine Neuroglobin Under Kr Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe155 b:26.5 occ:0.75 FE A:HEM155 0.0 26.5 0.8 FE A:HEM155 0.9 11.5 0.2 NB A:HEM155 1.4 10.3 0.2 NE2 A:HIS64 1.9 23.1 0.7 NC A:HEM155 2.0 26.4 0.8 NA A:HEM155 2.0 10.9 0.2 NA A:HEM155 2.1 26.1 0.8 ND A:HEM155 2.1 25.9 0.8 NB A:HEM155 2.1 26.6 0.8 NE2 A:HIS96 2.2 21.9 0.7 NE2 A:HIS64 2.3 28.8 0.3 NE2 A:HIS96 2.3 23.9 0.3 C1B A:HEM155 2.4 11.1 0.2 NC A:HEM155 2.5 9.9 0.2 C4B A:HEM155 2.6 12.3 0.2 C4A A:HEM155 2.6 10.7 0.2 CE1 A:HIS64 2.7 24.2 0.7 CHB A:HEM155 2.8 11.8 0.2 CE1 A:HIS96 2.8 20.0 0.7 ND A:HEM155 2.9 12.6 0.2 C1C A:HEM155 2.9 29.4 0.8 CD2 A:HIS64 3.0 24.0 0.7 C4C A:HEM155 3.0 27.8 0.8 C4B A:HEM155 3.1 27.9 0.8 C1A A:HEM155 3.1 29.6 0.8 C4D A:HEM155 3.1 29.4 0.8 CD2 A:HIS64 3.1 26.6 0.3 C1D A:HEM155 3.1 29.2 0.8 C4A A:HEM155 3.1 27.7 0.8 CE1 A:HIS96 3.2 22.4 0.3 C1A A:HEM155 3.2 12.4 0.2 C1B A:HEM155 3.2 27.1 0.8 C1C A:HEM155 3.2 11.9 0.2 CHC A:HEM155 3.2 11.8 0.2 CE1 A:HIS64 3.3 26.4 0.3 CHC A:HEM155 3.3 29.2 0.8 CD2 A:HIS96 3.4 22.0 0.7 CD2 A:HIS96 3.4 22.7 0.3 CHA A:HEM155 3.5 28.1 0.8 CHD A:HEM155 3.5 29.0 0.8 CHB A:HEM155 3.6 27.8 0.8 C2B A:HEM155 3.6 13.2 0.2 C3B A:HEM155 3.7 13.0 0.2 C4C A:HEM155 3.7 11.5 0.2 C4D A:HEM155 3.7 13.3 0.2 CHA A:HEM155 3.8 12.6 0.2 C1D A:HEM155 3.9 13.1 0.2 ND1 A:HIS64 3.9 26.0 0.7 C3A A:HEM155 3.9 11.8 0.2 ND1 A:HIS96 4.1 20.7 0.7 CG A:HIS64 4.1 25.7 0.7 C2C A:HEM155 4.1 30.9 0.8 C2A A:HEM155 4.2 12.9 0.2 C3C A:HEM155 4.2 30.0 0.8 CHD A:HEM155 4.2 12.3 0.2 CG A:HIS64 4.3 27.1 0.3 ND1 A:HIS96 4.3 21.0 0.3 C2A A:HEM155 4.3 28.6 0.8 ND1 A:HIS64 4.3 27.7 0.3 C3B A:HEM155 4.3 29.9 0.8 C3A A:HEM155 4.3 26.3 0.8 CG A:HIS96 4.4 20.5 0.7 C3D A:HEM155 4.4 28.8 0.8 C2D A:HEM155 4.4 29.3 0.8 C2B A:HEM155 4.4 28.1 0.8 CG A:HIS96 4.5 21.6 0.3 CG2 A:VAL68 4.5 27.5 1.0 C2C A:HEM155 4.6 11.1 0.2 C3C A:HEM155 4.8 10.7 0.2 CMB A:HEM155 5.0 12.2 0.2 C3D A:HEM155 5.0 14.4 0.2

Iron binding site 2 out of 2 in the Crystal Structure of Murine Neuroglobin Under Kr Pressure


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 Murine Neuroglobin Under Kr Pressure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe155 b:11.5 occ:0.25 FE A:HEM155 0.0 11.5 0.2 FE A:HEM155 0.9 26.5 0.8 NA A:HEM155 1.4 26.1 0.8 NE2 A:HIS96 1.8 21.9 0.7 NB A:HEM155 1.9 26.6 0.8 NE2 A:HIS96 2.0 23.9 0.3 NC A:HEM155 2.0 9.9 0.2 NB A:HEM155 2.1 10.3 0.2 ND A:HEM155 2.1 12.6 0.2 NA A:HEM155 2.1 10.9 0.2 NE2 A:HIS64 2.2 23.1 0.7 C4A A:HEM155 2.4 27.7 0.8 NE2 A:HIS64 2.5 28.8 0.3 C1A A:HEM155 2.6 29.6 0.8 ND A:HEM155 2.6 25.9 0.8 C1B A:HEM155 2.7 27.1 0.8 CE1 A:HIS96 2.7 20.0 0.7 NC A:HEM155 2.8 26.4 0.8 CHB A:HEM155 2.8 27.8 0.8 CD2 A:HIS96 2.9 22.7 0.3 CD2 A:HIS96 2.9 22.0 0.7 C1C A:HEM155 3.0 11.9 0.2 C4B A:HEM155 3.1 12.3 0.2 C4C A:HEM155 3.1 11.5 0.2 CE1 A:HIS64 3.1 24.2 0.7 C4D A:HEM155 3.1 13.3 0.2 C1D A:HEM155 3.1 13.1 0.2 C4A A:HEM155 3.1 10.7 0.2 C4B A:HEM155 3.1 27.9 0.8 C1B A:HEM155 3.1 11.1 0.2 C1A A:HEM155 3.1 12.4 0.2 CE1 A:HIS96 3.2 22.4 0.3 CHA A:HEM155 3.2 28.1 0.8 CD2 A:HIS64 3.2 24.0 0.7 C4D A:HEM155 3.3 29.4 0.8 CD2 A:HIS64 3.3 26.6 0.3 CHC A:HEM155 3.4 11.8 0.2 CHD A:HEM155 3.4 12.3 0.2 CHA A:HEM155 3.5 12.6 0.2 CHB A:HEM155 3.5 11.8 0.2 C1C A:HEM155 3.5 29.4 0.8 C3A A:HEM155 3.6 26.3 0.8 CE1 A:HIS64 3.6 26.4 0.3 CHC A:HEM155 3.7 29.2 0.8 C2A A:HEM155 3.7 28.6 0.8 C1D A:HEM155 3.8 29.2 0.8 ND1 A:HIS96 3.8 20.7 0.7 C4C A:HEM155 3.9 27.8 0.8 CG A:HIS96 3.9 20.5 0.7 C2B A:HEM155 4.0 28.1 0.8 CG A:HIS96 4.1 21.6 0.3 ND1 A:HIS96 4.2 21.0 0.3 ND1 A:HIS64 4.2 26.0 0.7 C3B A:HEM155 4.2 29.9 0.8 C2C A:HEM155 4.3 11.1 0.2 CHD A:HEM155 4.3 29.0 0.8 C3C A:HEM155 4.3 10.7 0.2 C3B A:HEM155 4.3 13.0 0.2 CG A:HIS64 4.3 25.7 0.7 C3D A:HEM155 4.3 14.4 0.2 C2D A:HEM155 4.3 13.1 0.2 C3A A:HEM155 4.3 11.8 0.2 C2B A:HEM155 4.3 13.2 0.2 C2A A:HEM155 4.3 12.9 0.2 CG A:HIS64 4.5 27.1 0.3 C3D A:HEM155 4.6 28.8 0.8 ND1 A:HIS64 4.7 27.7 0.3 C2C A:HEM155 4.8 30.9 0.8 C2D A:HEM155 4.9 29.3 0.8 C3C A:HEM155 5.0 30.0 0.8 CMA A:HEM155 5.0 28.1 0.8

T.Moschetti, U.Mueller, J.Schulze, M.Brunori, B.Vallone. The Structure of Neuroglobin at High Xe and Kr Pressure Reveals Partial Conservation of Globin Internal Cavities. Biophys. J. V. 97 1700 2009.
ISSN: ESSN 1542-0086
PubMed: 19751675
DOI: 10.1016/J.BPJ.2009.05.059