Iron in PDB 3nmj: Crystal Structure of A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2

The structure of Crystal Structure of A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2, PDB code: 3nmj was solved by R.J.Radford, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.99 / 3.10
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	99.291, 99.291, 109.317, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 23.8

The structure of Crystal Structure of A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2 also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Iron atom in the Crystal Structure of A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2 (pdb code 3nmj). 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 A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2, PDB code: 3nmj:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2


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 A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe150 b:44.6 occ:1.00 FE A:HEM150 0.0 44.6 1.0 NE2 A:HIS102 1.9 51.3 1.0 NC A:HEM150 2.0 42.1 1.0 NA A:HEM150 2.1 45.3 1.0 NB A:HEM150 2.1 44.1 1.0 ND A:HEM150 2.1 44.8 1.0 SD A:MET7 2.3 42.6 1.0 CE1 A:HIS102 2.7 51.8 1.0 CD2 A:HIS102 2.9 52.0 1.0 C1C A:HEM150 3.0 42.5 1.0 C4C A:HEM150 3.0 43.7 1.0 C4A A:HEM150 3.1 46.6 1.0 C1A A:HEM150 3.1 47.2 1.0 C1B A:HEM150 3.1 43.8 1.0 C4B A:HEM150 3.1 42.3 1.0 C4D A:HEM150 3.1 44.8 1.0 C1D A:HEM150 3.1 43.9 1.0 CE A:MET7 3.4 44.0 1.0 CHC A:HEM150 3.4 42.1 1.0 CHD A:HEM150 3.4 41.1 1.0 CG A:MET7 3.4 50.2 1.0 CHA A:HEM150 3.4 44.1 1.0 CHB A:HEM150 3.4 43.0 1.0 ND1 A:HIS102 3.9 51.6 1.0 CG A:HIS102 4.0 49.7 1.0 CB A:MET7 4.1 52.5 1.0 C2C A:HEM150 4.3 43.6 1.0 C3C A:HEM150 4.3 45.2 1.0 C3A A:HEM150 4.3 50.7 1.0 C2A A:HEM150 4.3 52.8 1.0 C2B A:HEM150 4.3 42.6 1.0 C3B A:HEM150 4.3 41.5 1.0 C3D A:HEM150 4.3 45.3 1.0 C2D A:HEM150 4.3 43.5 1.0 CA A:MET7 5.0 53.3 1.0

Iron binding site 2 out of 4 in the Crystal Structure of A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2


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 A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe150 b:45.6 occ:1.00 FE B:HEM150 0.0 45.6 1.0 NE2 B:HIS102 1.9 51.8 1.0 NA B:HEM150 2.0 51.7 1.0 NB B:HEM150 2.0 46.0 1.0 NC B:HEM150 2.0 44.4 1.0 ND B:HEM150 2.1 49.3 1.0 SD B:MET7 2.3 43.0 1.0 CE1 B:HIS102 2.8 52.0 1.0 CD2 B:HIS102 3.0 52.8 1.0 C1A B:HEM150 3.0 59.0 1.0 C4A B:HEM150 3.0 53.9 1.0 C1B B:HEM150 3.1 48.8 1.0 C4B B:HEM150 3.1 44.2 1.0 C4C B:HEM150 3.1 43.9 1.0 C1C B:HEM150 3.1 43.4 1.0 C4D B:HEM150 3.1 53.9 1.0 C1D B:HEM150 3.1 50.9 1.0 CE B:MET7 3.4 43.8 1.0 CG B:MET7 3.4 50.5 1.0 CHA B:HEM150 3.4 59.7 1.0 CHB B:HEM150 3.4 51.9 1.0 CHC B:HEM150 3.4 44.1 1.0 CHD B:HEM150 3.5 46.7 1.0 ND1 B:HIS102 3.9 51.1 1.0 CG B:HIS102 4.0 50.0 1.0 CB B:MET7 4.2 53.1 1.0 C2A B:HEM150 4.3 61.1 1.0 C3A B:HEM150 4.3 57.2 1.0 C3B B:HEM150 4.3 45.5 1.0 C2B B:HEM150 4.3 46.9 1.0 C3C B:HEM150 4.3 44.6 1.0 C2C B:HEM150 4.3 41.8 1.0 C3D B:HEM150 4.3 53.7 1.0 C2D B:HEM150 4.3 51.8 1.0 CA B:MET7 5.0 53.6 1.0

Iron binding site 3 out of 4 in the Crystal Structure of A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2


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 A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe150 b:44.8 occ:1.00 FE C:HEM150 0.0 44.8 1.0 NE2 C:HIS102 1.9 51.8 1.0 NA C:HEM150 2.0 51.1 1.0 NC C:HEM150 2.0 43.5 1.0 NB C:HEM150 2.1 44.0 1.0 ND C:HEM150 2.1 46.6 1.0 SD C:MET7 2.3 43.5 1.0 CE1 C:HIS102 2.8 52.1 1.0 CD2 C:HIS102 3.0 52.7 1.0 C1A C:HEM150 3.0 56.5 1.0 C4A C:HEM150 3.1 53.0 1.0 C4C C:HEM150 3.1 44.5 1.0 C1C C:HEM150 3.1 41.6 1.0 C4B C:HEM150 3.1 42.9 1.0 C1B C:HEM150 3.1 47.4 1.0 C4D C:HEM150 3.1 51.1 1.0 C1D C:HEM150 3.1 48.9 1.0 CE C:MET7 3.3 44.0 1.0 CG C:MET7 3.4 50.8 1.0 CHA C:HEM150 3.4 55.8 1.0 CHC C:HEM150 3.4 44.5 1.0 CHB C:HEM150 3.4 50.0 1.0 CHD C:HEM150 3.4 47.1 1.0 ND1 C:HIS102 3.9 51.1 1.0 CG C:HIS102 4.0 49.9 1.0 CB C:MET7 4.2 53.1 1.0 C2A C:HEM150 4.3 60.0 1.0 C3A C:HEM150 4.3 57.2 1.0 C3C C:HEM150 4.3 43.9 1.0 C2C C:HEM150 4.3 39.6 1.0 C3B C:HEM150 4.3 43.0 1.0 C2B C:HEM150 4.3 45.4 1.0 C3D C:HEM150 4.3 50.8 1.0 C2D C:HEM150 4.3 49.2 1.0 CA C:MET7 5.0 53.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2


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 A Nickel Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe150 b:43.5 occ:1.00 FE D:HEM150 0.0 43.5 1.0 NE2 D:HIS102 1.9 51.3 1.0 NC D:HEM150 2.0 43.0 1.0 NA D:HEM150 2.1 45.0 1.0 NB D:HEM150 2.1 42.8 1.0 ND D:HEM150 2.1 44.2 1.0 SD D:MET7 2.3 43.1 1.0 CE1 D:HIS102 2.8 51.9 1.0 CD2 D:HIS102 2.9 51.9 1.0 C1C D:HEM150 3.0 43.0 1.0 C4C D:HEM150 3.0 44.0 1.0 C4B D:HEM150 3.1 43.7 1.0 C1A D:HEM150 3.1 45.9 1.0 C4A D:HEM150 3.1 45.8 1.0 C1D D:HEM150 3.1 43.8 1.0 C1B D:HEM150 3.1 43.0 1.0 C4D D:HEM150 3.1 44.4 1.0 CE D:MET7 3.4 44.0 1.0 CHC D:HEM150 3.4 44.6 1.0 CHD D:HEM150 3.4 42.0 1.0 CHA D:HEM150 3.5 41.9 1.0 CHB D:HEM150 3.5 43.5 1.0 CG D:MET7 3.5 50.4 1.0 ND1 D:HIS102 3.9 51.7 1.0 CG D:HIS102 4.0 49.9 1.0 CB D:MET7 4.2 52.5 1.0 C2C D:HEM150 4.2 42.2 1.0 C3C D:HEM150 4.2 44.0 1.0 C3B D:HEM150 4.3 43.1 1.0 C2B D:HEM150 4.3 43.1 1.0 C3A D:HEM150 4.3 48.6 1.0 C2A D:HEM150 4.3 51.3 1.0 C2D D:HEM150 4.3 44.2 1.0 C3D D:HEM150 4.3 45.1 1.0

R.J.Radford, M.Lawrenz, P.C.Nguyen, J.A.Mccammon, F.A.Tezcan. Porous Protein Frameworks with Unsaturated Metal Centers in Sterically Encumbered Coordination Sites. Chem.Commun.(Camb.) V. 47 313 2011.
ISSN: ISSN 1359-7345
PubMed: 20740227
DOI: 10.1039/C0CC02168G