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

The structure of Crystal Structure of A Zinc Mediated Dimer For the Phenanthroline- Modified Cytochrome CB562 Variant, Mbp-PHEN2, PDB code: 3nmk 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)	86.14 / 2.80
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	99.467, 99.467, 109.544, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 23.3

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

Zinc

(Zn)

2 atoms

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

Iron binding site 1 out of 4 in the Crystal Structure of A Zinc 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 Zinc 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:30.2 occ:1.00 FE A:HEM150 0.0 30.2 1.0 NE2 A:HIS102 1.9 34.0 1.0 NC A:HEM150 2.0 31.2 1.0 NB A:HEM150 2.0 29.4 1.0 NA A:HEM150 2.1 34.1 1.0 ND A:HEM150 2.1 29.8 1.0 SD A:MET7 2.3 29.5 1.0 CE1 A:HIS102 2.8 34.5 1.0 C1C A:HEM150 3.0 32.7 1.0 C4C A:HEM150 3.0 27.6 1.0 CD2 A:HIS102 3.0 34.6 1.0 C4B A:HEM150 3.0 32.5 1.0 C1B A:HEM150 3.0 28.0 1.0 C4A A:HEM150 3.1 35.1 1.0 C1D A:HEM150 3.1 30.9 1.0 C1A A:HEM150 3.1 37.5 1.0 C4D A:HEM150 3.1 34.8 1.0 CE A:MET7 3.3 28.1 1.0 CHC A:HEM150 3.4 33.2 1.0 CHD A:HEM150 3.4 28.9 1.0 CHB A:HEM150 3.4 30.8 1.0 CG A:MET7 3.5 36.2 1.0 CHA A:HEM150 3.5 36.1 1.0 ND1 A:HIS102 4.0 32.5 1.0 CG A:HIS102 4.1 33.5 1.0 CB A:MET7 4.2 38.0 1.0 C2C A:HEM150 4.2 31.5 1.0 C3C A:HEM150 4.2 29.3 1.0 C3B A:HEM150 4.3 29.5 1.0 C2B A:HEM150 4.3 31.5 1.0 C3A A:HEM150 4.3 37.3 1.0 C2A A:HEM150 4.3 41.5 1.0 C2D A:HEM150 4.4 32.4 1.0 C3D A:HEM150 4.4 34.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of A Zinc 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 Zinc 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:28.4 occ:1.00 FE B:HEM150 0.0 28.4 1.0 NE2 B:HIS102 1.9 33.9 1.0 NC B:HEM150 2.0 25.0 1.0 NA B:HEM150 2.0 33.6 1.0 NB B:HEM150 2.1 30.5 1.0 ND B:HEM150 2.1 25.6 1.0 SD B:MET7 2.3 31.9 1.0 CE1 B:HIS102 2.8 34.1 1.0 CD2 B:HIS102 3.0 34.7 1.0 C4C B:HEM150 3.0 27.2 1.0 C4A B:HEM150 3.1 33.5 1.0 C1C B:HEM150 3.1 24.6 1.0 C1A B:HEM150 3.1 39.6 1.0 C1D B:HEM150 3.1 23.7 1.0 C1B B:HEM150 3.1 31.4 1.0 C4D B:HEM150 3.1 31.1 1.0 C4B B:HEM150 3.1 28.6 1.0 CE B:MET7 3.3 28.7 1.0 CHD B:HEM150 3.4 28.7 1.0 CHB B:HEM150 3.4 33.3 1.0 CHA B:HEM150 3.4 35.4 1.0 CHC B:HEM150 3.5 27.3 1.0 CG B:MET7 3.5 36.0 1.0 ND1 B:HIS102 4.0 31.9 1.0 CG B:HIS102 4.1 33.3 1.0 CB B:MET7 4.2 38.2 1.0 C3C B:HEM150 4.3 25.3 1.0 C2C B:HEM150 4.3 23.4 1.0 C3A B:HEM150 4.3 36.7 1.0 C2A B:HEM150 4.3 40.7 1.0 C2B B:HEM150 4.3 30.6 1.0 C3B B:HEM150 4.3 26.3 1.0 C2D B:HEM150 4.3 25.8 1.0 C3D B:HEM150 4.3 30.9 1.0

Iron binding site 3 out of 4 in the Crystal Structure of A Zinc 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 Zinc 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:27.2 occ:1.00 FE C:HEM150 0.0 27.2 1.0 NE2 C:HIS102 1.9 33.6 1.0 NC C:HEM150 2.0 24.3 1.0 NA C:HEM150 2.1 34.6 1.0 NB C:HEM150 2.1 31.5 1.0 ND C:HEM150 2.1 26.2 1.0 SD C:MET7 2.3 30.9 1.0 CE1 C:HIS102 2.8 34.0 1.0 CD2 C:HIS102 3.0 34.5 1.0 C1C C:HEM150 3.0 26.3 1.0 C4C C:HEM150 3.0 27.3 1.0 C4B C:HEM150 3.1 31.7 1.0 C1A C:HEM150 3.1 39.0 1.0 C4D C:HEM150 3.1 29.5 1.0 C1D C:HEM150 3.1 24.8 1.0 C1B C:HEM150 3.1 31.6 1.0 C4A C:HEM150 3.1 31.8 1.0 CE C:MET7 3.3 28.7 1.0 CHC C:HEM150 3.4 30.3 1.0 CHA C:HEM150 3.4 34.2 1.0 CHD C:HEM150 3.4 27.9 1.0 CHB C:HEM150 3.5 32.2 1.0 CG C:MET7 3.5 36.0 1.0 ND1 C:HIS102 3.9 31.9 1.0 CG C:HIS102 4.1 33.1 1.0 CB C:MET7 4.2 38.1 1.0 C2C C:HEM150 4.3 26.9 1.0 C3C C:HEM150 4.3 26.9 1.0 C3B C:HEM150 4.3 29.4 1.0 C2B C:HEM150 4.3 29.8 1.0 C2A C:HEM150 4.3 40.4 1.0 C3A C:HEM150 4.3 34.4 1.0 C3D C:HEM150 4.3 30.7 1.0 C2D C:HEM150 4.3 27.5 1.0

Iron binding site 4 out of 4 in the Crystal Structure of A Zinc 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 Zinc 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:30.3 occ:1.00 FE D:HEM150 0.0 30.3 1.0 NE2 D:HIS102 1.9 34.0 1.0 NC D:HEM150 2.0 30.2 1.0 NB D:HEM150 2.0 33.1 1.0 NA D:HEM150 2.1 36.3 1.0 ND D:HEM150 2.1 33.3 1.0 SD D:MET7 2.3 30.4 1.0 CE1 D:HIS102 2.8 34.2 1.0 CD2 D:HIS102 3.0 35.0 1.0 C1C D:HEM150 3.0 29.4 1.0 C4B D:HEM150 3.0 33.7 1.0 C4C D:HEM150 3.0 26.5 1.0 C1B D:HEM150 3.1 31.7 1.0 C1A D:HEM150 3.1 40.6 1.0 C4A D:HEM150 3.1 36.6 1.0 C4D D:HEM150 3.1 38.4 1.0 C1D D:HEM150 3.1 32.1 1.0 CE D:MET7 3.4 27.6 1.0 CHC D:HEM150 3.4 29.9 1.0 CHD D:HEM150 3.4 28.6 1.0 CHA D:HEM150 3.4 37.7 1.0 CHB D:HEM150 3.5 34.8 1.0 CG D:MET7 3.5 36.3 1.0 ND1 D:HIS102 4.0 32.8 1.0 CG D:HIS102 4.1 33.5 1.0 CB D:MET7 4.2 38.0 1.0 C2C D:HEM150 4.2 28.8 1.0 C3C D:HEM150 4.3 28.8 1.0 C3B D:HEM150 4.3 32.8 1.0 C2B D:HEM150 4.3 33.4 1.0 C2A D:HEM150 4.3 42.9 1.0 C3A D:HEM150 4.3 36.9 1.0 C3D D:HEM150 4.4 39.1 1.0 C2D D:HEM150 4.4 32.1 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