Iron in PDB 3m4c: A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase

The structure of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase, PDB code: 3m4c was solved by F.A.Tezcan, T.W.Ni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.66 / 1.90
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	126.892, 126.892, 167.944, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 22.3

The structure of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase also contains other interesting chemical elements:

Zinc

(Zn)

10 atoms

The binding sites of Iron atom in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase (pdb code 3m4c). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase, PDB code: 3m4c:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe150 b:15.0 occ:1.00 FE A:HEM150 0.0 15.0 1.0 ND A:HEM150 2.0 14.5 1.0 NC A:HEM150 2.1 13.4 1.0 NB A:HEM150 2.1 13.6 1.0 NA A:HEM150 2.1 14.2 1.0 NE2 A:HIS102 2.1 14.1 1.0 SD A:MET7 2.4 14.3 1.0 CD2 A:HIS102 3.0 14.8 1.0 C1D A:HEM150 3.0 14.0 1.0 C4D A:HEM150 3.1 14.8 1.0 C1C A:HEM150 3.1 14.2 1.0 C4B A:HEM150 3.1 13.3 1.0 C4C A:HEM150 3.1 13.7 1.0 C1A A:HEM150 3.1 14.6 1.0 C1B A:HEM150 3.1 14.1 1.0 CE1 A:HIS102 3.1 14.3 1.0 C4A A:HEM150 3.1 14.4 1.0 CE A:MET7 3.4 14.0 1.0 CHD A:HEM150 3.4 14.1 1.0 CHA A:HEM150 3.4 14.9 1.0 CHC A:HEM150 3.4 13.7 1.0 CG A:MET7 3.5 14.1 1.0 CHB A:HEM150 3.5 14.3 1.0 CG A:HIS102 4.2 15.9 1.0 ND1 A:HIS102 4.2 15.0 1.0 CB A:MET7 4.2 14.2 1.0 C2C A:HEM150 4.3 13.5 1.0 C2D A:HEM150 4.3 14.1 1.0 C3D A:HEM150 4.3 15.1 1.0 C3C A:HEM150 4.3 14.1 1.0 C3B A:HEM150 4.3 13.4 1.0 C2B A:HEM150 4.3 13.9 1.0 C2A A:HEM150 4.3 15.1 1.0 C3A A:HEM150 4.3 14.8 1.0

Iron binding site 2 out of 5 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe150 b:16.2 occ:1.00 FE B:HEM150 0.0 16.2 1.0 NE2 B:HIS102 2.0 15.6 1.0 NA B:HEM150 2.1 16.9 1.0 NB B:HEM150 2.1 15.8 1.0 NC B:HEM150 2.1 15.0 1.0 ND B:HEM150 2.1 16.8 1.0 SD B:MET7 2.4 15.3 1.0 CD2 B:HIS102 3.0 16.8 1.0 CE1 B:HIS102 3.1 16.0 1.0 C4A B:HEM150 3.1 17.2 1.0 C1B B:HEM150 3.1 16.0 1.0 C4B B:HEM150 3.1 15.6 1.0 C1A B:HEM150 3.1 17.6 1.0 C1C B:HEM150 3.1 15.5 1.0 C1D B:HEM150 3.1 16.8 1.0 C4C B:HEM150 3.1 15.3 1.0 C4D B:HEM150 3.1 17.6 1.0 CE B:MET7 3.3 16.5 1.0 CHB B:HEM150 3.4 17.1 1.0 CHD B:HEM150 3.4 17.0 1.0 CHC B:HEM150 3.4 15.9 1.0 CHA B:HEM150 3.4 17.8 1.0 CG B:MET7 3.5 16.1 1.0 ND1 B:HIS102 4.1 15.9 1.0 CG B:HIS102 4.2 18.0 1.0 CB B:MET7 4.3 16.2 1.0 C2B B:HEM150 4.3 15.8 1.0 C3A B:HEM150 4.3 18.5 1.0 C3B B:HEM150 4.3 15.8 1.0 C2A B:HEM150 4.3 18.8 1.0 C2C B:HEM150 4.3 15.2 1.0 C3C B:HEM150 4.3 15.5 1.0 C2D B:HEM150 4.3 17.8 1.0 C3D B:HEM150 4.3 18.5 1.0

Iron binding site 3 out of 5 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe150 b:12.4 occ:1.00 FE C:HEM150 0.0 12.4 1.0 NA C:HEM150 2.0 12.8 1.0 NE2 C:HIS102 2.0 11.1 1.0 NB C:HEM150 2.1 12.8 1.0 NC C:HEM150 2.1 12.7 1.0 ND C:HEM150 2.1 13.0 1.0 SD C:MET7 2.4 13.1 1.0 CD2 C:HIS102 3.0 11.6 1.0 C4A C:HEM150 3.0 13.3 1.0 CE1 C:HIS102 3.1 11.6 1.0 C1B C:HEM150 3.1 12.7 1.0 C1A C:HEM150 3.1 13.6 1.0 C1C C:HEM150 3.1 12.3 1.0 C4B C:HEM150 3.1 12.3 1.0 C1D C:HEM150 3.1 12.2 1.0 C4C C:HEM150 3.1 12.8 1.0 C4D C:HEM150 3.1 13.7 1.0 CE C:MET7 3.3 12.2 1.0 CHB C:HEM150 3.4 13.9 1.0 CHC C:HEM150 3.4 12.3 1.0 CHD C:HEM150 3.5 12.3 1.0 CHA C:HEM150 3.5 13.2 1.0 CG C:MET7 3.5 12.1 1.0 ND1 C:HIS102 4.2 11.7 1.0 CG C:HIS102 4.2 11.7 1.0 CB C:MET7 4.2 12.4 1.0 C3A C:HEM150 4.3 14.0 1.0 C2A C:HEM150 4.3 14.9 1.0 C2B C:HEM150 4.3 13.7 1.0 C3B C:HEM150 4.3 13.1 1.0 C2C C:HEM150 4.3 12.6 1.0 C3C C:HEM150 4.3 12.8 1.0 C2D C:HEM150 4.3 13.2 1.0 C3D C:HEM150 4.3 13.7 1.0

Iron binding site 4 out of 5 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe150 b:19.4 occ:1.00 FE D:HEM150 0.0 19.4 1.0 NE2 D:HIS102 2.0 19.9 1.0 NA D:HEM150 2.1 19.0 1.0 ND D:HEM150 2.1 19.5 1.0 NC D:HEM150 2.1 18.7 1.0 NB D:HEM150 2.1 18.4 1.0 SD D:MET7 2.4 18.1 1.0 CE1 D:HIS102 3.0 20.2 1.0 CD2 D:HIS102 3.0 20.5 1.0 C1D D:HEM150 3.1 19.1 1.0 C4A D:HEM150 3.1 19.3 1.0 C4D D:HEM150 3.1 19.8 1.0 C1A D:HEM150 3.1 19.9 1.0 C4C D:HEM150 3.1 18.6 1.0 C1C D:HEM150 3.1 18.2 1.0 C4B D:HEM150 3.1 17.5 1.0 C1B D:HEM150 3.1 18.1 1.0 CE D:MET7 3.4 18.7 1.0 CHD D:HEM150 3.4 19.1 1.0 CG D:MET7 3.4 17.6 1.0 CHA D:HEM150 3.4 19.3 1.0 CHB D:HEM150 3.5 19.0 1.0 CHC D:HEM150 3.5 18.5 1.0 ND1 D:HIS102 4.1 20.7 1.0 CG D:HIS102 4.2 21.7 1.0 CB D:MET7 4.2 18.3 1.0 C2D D:HEM150 4.3 19.8 1.0 C3A D:HEM150 4.3 19.8 1.0 C2A D:HEM150 4.3 20.5 1.0 C3D D:HEM150 4.3 20.2 1.0 C2C D:HEM150 4.3 18.2 1.0 C3C D:HEM150 4.3 18.5 1.0 C3B D:HEM150 4.3 17.9 1.0 C2B D:HEM150 4.3 18.5 1.0

Iron binding site 5 out of 5 in the A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of A Zn-Mediated Tetrahedral Protein Lattice Cage Encapsulating A Microperoxidase within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe150 b:24.0 occ:1.00 FE E:HEM150 0.0 24.0 1.0 NE2 B:HIS73 2.0 19.3 1.0 NC E:HEM150 2.0 24.5 1.0 NA E:HEM150 2.0 24.6 1.0 ND E:HEM150 2.1 24.4 1.0 NB E:HEM150 2.1 24.3 1.0 NE2 E:HIS102 2.2 26.3 1.0 CD2 B:HIS73 3.0 18.9 1.0 CE1 E:HIS102 3.0 28.5 1.0 C4C E:HEM150 3.0 25.0 1.0 CE1 B:HIS73 3.1 17.2 1.0 C4A E:HEM150 3.1 25.5 1.0 C1D E:HEM150 3.1 24.5 1.0 C1A E:HEM150 3.1 25.6 1.0 C1B E:HEM150 3.1 24.8 1.0 C1C E:HEM150 3.1 25.0 1.0 C4D E:HEM150 3.1 25.2 1.0 C4B E:HEM150 3.1 24.9 1.0 CD2 E:HIS102 3.3 30.0 1.0 CHD E:HEM150 3.4 24.9 1.0 CHB E:HEM150 3.4 25.8 1.0 CHA E:HEM150 3.5 25.5 1.0 CHC E:HEM150 3.5 25.2 1.0 CG B:HIS73 4.1 17.6 1.0 ND1 B:HIS73 4.1 17.6 1.0 ND1 E:HIS102 4.2 30.8 1.0 C3C E:HEM150 4.3 25.6 1.0 C3A E:HEM150 4.3 25.8 1.0 C2A E:HEM150 4.3 26.0 1.0 C2C E:HEM150 4.3 25.6 1.0 C2D E:HEM150 4.3 24.6 1.0 C2B E:HEM150 4.3 25.3 1.0 C3B E:HEM150 4.3 25.2 1.0 C3D E:HEM150 4.3 25.2 1.0 CG E:HIS102 4.4 31.7 1.0

T.W.Ni, F.A.Tezcan. Structural Characterization of A Microperoxidase Inside A Metal-Directed Protein Cage. Angew.Chem.Int.Ed.Engl. V. 49 7014 2010.
ISSN: ISSN 1433-7851
PubMed: 20721993
DOI: 10.1002/ANIE.201001487