Iron in PDB 3m4b: A Zn-Mediated Tetrahedral Protein Lattice Cage

The structure of A Zn-Mediated Tetrahedral Protein Lattice Cage, PDB code: 3m4b 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)	41.27 / 2.50
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	125.363, 125.363, 164.509, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 25.6

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

Zinc

(Zn)

12 atoms

The binding sites of Iron atom in the A Zn-Mediated Tetrahedral Protein Lattice Cage (pdb code 3m4b). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the A Zn-Mediated Tetrahedral Protein Lattice Cage, PDB code: 3m4b:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the A Zn-Mediated Tetrahedral Protein Lattice Cage


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe150 b:27.9 occ:1.00 FE A:HEM150 0.0 27.9 1.0 NA A:HEM150 2.0 28.3 1.0 ND A:HEM150 2.0 28.5 1.0 NB A:HEM150 2.0 27.6 1.0 NC A:HEM150 2.0 27.9 1.0 NE2 A:HIS102 2.0 26.4 1.0 SD A:MET7 2.3 31.7 1.0 C1A A:HEM150 3.0 29.7 1.0 C4D A:HEM150 3.0 29.0 1.0 C4B A:HEM150 3.0 27.6 1.0 CD2 A:HIS102 3.0 26.1 1.0 CE1 A:HIS102 3.0 25.5 1.0 C1C A:HEM150 3.0 28.2 1.0 C1D A:HEM150 3.1 29.7 1.0 C4A A:HEM150 3.1 28.1 1.0 C4C A:HEM150 3.1 27.6 1.0 C1B A:HEM150 3.1 26.9 1.0 CE A:MET7 3.2 27.4 1.0 CHA A:HEM150 3.3 29.6 1.0 CHC A:HEM150 3.4 27.5 1.0 CG A:MET7 3.4 27.8 1.0 CHD A:HEM150 3.5 28.5 1.0 CHB A:HEM150 3.5 27.7 1.0 ND1 A:HIS102 4.1 26.0 1.0 CG A:HIS102 4.2 28.2 1.0 CB A:MET7 4.2 28.2 1.0 C2A A:HEM150 4.2 29.9 1.0 C3A A:HEM150 4.3 28.7 1.0 C3D A:HEM150 4.3 29.9 1.0 C2D A:HEM150 4.3 30.3 1.0 C3B A:HEM150 4.3 26.6 1.0 C2C A:HEM150 4.3 28.1 1.0 C3C A:HEM150 4.3 27.6 1.0 C2B A:HEM150 4.3 25.7 1.0

Iron binding site 2 out of 4 in the A Zn-Mediated Tetrahedral Protein Lattice Cage


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe150 b:25.4 occ:1.00 FE B:HEM150 0.0 25.4 1.0 NC B:HEM150 2.0 24.8 1.0 NE2 B:HIS102 2.0 29.2 1.0 NB B:HEM150 2.0 23.0 1.0 NA B:HEM150 2.0 24.0 1.0 ND B:HEM150 2.1 24.9 1.0 SD B:MET7 2.3 30.1 1.0 CE1 B:HIS102 2.9 30.3 1.0 C1C B:HEM150 3.0 24.5 1.0 C4C B:HEM150 3.0 25.1 1.0 C4B B:HEM150 3.0 23.4 1.0 C1D B:HEM150 3.0 25.9 1.0 C4A B:HEM150 3.1 25.0 1.0 C1B B:HEM150 3.1 22.5 1.0 C4D B:HEM150 3.1 25.6 1.0 CD2 B:HIS102 3.1 30.4 1.0 C1A B:HEM150 3.1 25.5 1.0 CE B:MET7 3.3 30.1 1.0 CG B:MET7 3.3 30.4 1.0 CHC B:HEM150 3.4 24.0 1.0 CHD B:HEM150 3.4 24.9 1.0 CHB B:HEM150 3.4 24.0 1.0 CHA B:HEM150 3.5 25.2 1.0 ND1 B:HIS102 4.1 29.8 1.0 CB B:MET7 4.2 29.8 1.0 CG B:HIS102 4.2 30.4 1.0 C2C B:HEM150 4.2 25.6 1.0 C3C B:HEM150 4.2 26.1 1.0 C3B B:HEM150 4.3 21.9 1.0 C3A B:HEM150 4.3 26.4 1.0 C2B B:HEM150 4.3 22.5 1.0 C2D B:HEM150 4.3 25.8 1.0 C2A B:HEM150 4.3 27.9 1.0 C3D B:HEM150 4.3 25.9 1.0 NH1 B:ARG106 4.8 41.7 1.0 CA B:MET7 4.9 30.2 1.0

Iron binding site 3 out of 4 in the A Zn-Mediated Tetrahedral Protein Lattice Cage


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe150 b:21.9 occ:1.00 FE C:HEM150 0.0 21.9 1.0 NE2 C:HIS102 2.0 23.9 1.0 ND C:HEM150 2.0 19.2 1.0 NC C:HEM150 2.0 19.2 1.0 NB C:HEM150 2.1 18.4 1.0 NA C:HEM150 2.1 19.2 1.0 SD C:MET7 2.3 24.7 1.0 CD2 C:HIS102 3.0 23.6 1.0 C1D C:HEM150 3.0 20.2 1.0 CE1 C:HIS102 3.0 23.2 1.0 C4C C:HEM150 3.0 19.7 1.0 C4D C:HEM150 3.0 21.6 1.0 C1B C:HEM150 3.1 17.9 1.0 C1C C:HEM150 3.1 19.6 1.0 C4B C:HEM150 3.1 18.8 1.0 C4A C:HEM150 3.1 20.4 1.0 C1A C:HEM150 3.1 20.4 1.0 CE C:MET7 3.2 23.4 1.0 CHD C:HEM150 3.4 20.8 1.0 CG C:MET7 3.4 23.9 1.0 CHA C:HEM150 3.4 19.8 1.0 CHB C:HEM150 3.5 19.9 1.0 CHC C:HEM150 3.5 19.2 1.0 ND1 C:HIS102 4.1 22.6 1.0 CG C:HIS102 4.1 23.6 1.0 CB C:MET7 4.2 25.9 1.0 C2D C:HEM150 4.2 20.9 1.0 C3D C:HEM150 4.3 21.9 1.0 C3C C:HEM150 4.3 20.2 1.0 C2C C:HEM150 4.3 20.3 1.0 C2B C:HEM150 4.3 16.4 1.0 C3B C:HEM150 4.3 17.0 1.0 C3A C:HEM150 4.4 21.5 1.0 C2A C:HEM150 4.4 21.6 1.0 CA C:MET7 5.0 25.5 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe150 b:28.4 occ:1.00 FE D:HEM150 0.0 28.4 1.0 NE2 D:HIS102 2.0 26.4 1.0 NC D:HEM150 2.0 28.4 1.0 NB D:HEM150 2.1 27.8 1.0 ND D:HEM150 2.1 29.1 1.0 NA D:HEM150 2.1 29.7 1.0 SD D:MET7 2.3 30.0 1.0 CE1 D:HIS102 2.9 25.9 1.0 CD2 D:HIS102 3.0 26.7 1.0 C1D D:HEM150 3.0 29.6 1.0 C4C D:HEM150 3.0 28.3 1.0 C1C D:HEM150 3.1 28.5 1.0 C1B D:HEM150 3.1 27.2 1.0 C4A D:HEM150 3.1 29.7 1.0 C4B D:HEM150 3.1 28.1 1.0 C4D D:HEM150 3.1 29.8 1.0 C1A D:HEM150 3.1 30.3 1.0 CHD D:HEM150 3.4 29.1 1.0 CE D:MET7 3.4 28.5 1.0 CHB D:HEM150 3.4 29.2 1.0 CHC D:HEM150 3.5 28.3 1.0 CG D:MET7 3.5 29.1 1.0 CHA D:HEM150 3.5 30.0 1.0 ND1 D:HIS102 4.0 26.7 1.0 CG D:HIS102 4.1 28.8 1.0 C2D D:HEM150 4.3 30.2 1.0 C3C D:HEM150 4.3 27.7 1.0 C2C D:HEM150 4.3 28.2 1.0 CB D:MET7 4.3 28.9 1.0 C2B D:HEM150 4.3 27.0 1.0 C3B D:HEM150 4.3 27.6 1.0 C3A D:HEM150 4.3 31.1 1.0 C3D D:HEM150 4.3 29.8 1.0 C2A D:HEM150 4.3 31.3 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