Iron in PDB 3m15: A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1)

The structure of A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1), PDB code: 3m15 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)	23.90 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.879, 74.819, 81.358, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 31.3

The structure of A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1) also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Iron atom in the A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1) (pdb code 3m15). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1), PDB code: 3m15:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1)


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 Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe150 b:6.5 occ:1.00 FE A:HEM150 0.0 6.5 1.0 NA A:HEM150 2.0 8.2 1.0 NC A:HEM150 2.0 5.4 1.0 NB A:HEM150 2.0 5.8 1.0 ND A:HEM150 2.1 7.2 1.0 NE2 A:HIS102 2.1 6.4 1.0 SD A:MET7 2.3 6.6 1.0 C1C A:HEM150 3.0 4.8 1.0 CD2 A:HIS102 3.0 5.6 1.0 C1A A:HEM150 3.0 8.8 1.0 C4D A:HEM150 3.0 8.9 1.0 C4A A:HEM150 3.0 7.0 1.0 C4B A:HEM150 3.0 5.5 1.0 C4C A:HEM150 3.1 6.1 1.0 C1B A:HEM150 3.1 5.3 1.0 C1D A:HEM150 3.1 6.5 1.0 CE1 A:HIS102 3.1 4.3 1.0 CHA A:HEM150 3.3 8.0 1.0 CHC A:HEM150 3.4 5.8 1.0 CHB A:HEM150 3.4 5.8 1.0 CG A:MET7 3.4 9.9 1.0 CHD A:HEM150 3.5 6.8 1.0 CE A:MET7 3.5 7.2 1.0 CB A:MET7 4.1 9.8 1.0 CG A:HIS102 4.2 6.8 1.0 ND1 A:HIS102 4.2 5.3 1.0 C2C A:HEM150 4.2 5.1 1.0 C2A A:HEM150 4.2 8.7 1.0 C3A A:HEM150 4.3 7.0 1.0 C3C A:HEM150 4.3 5.7 1.0 C3D A:HEM150 4.3 8.1 1.0 C3B A:HEM150 4.3 5.0 1.0 C2B A:HEM150 4.3 3.9 1.0 C2D A:HEM150 4.3 7.0 1.0 NH1 A:ARG106 5.0 10.8 1.0

Iron binding site 2 out of 3 in the A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1)


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 Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe150 b:15.1 occ:1.00 FE B:HEM150 0.0 15.1 1.0 NC B:HEM150 2.1 10.3 1.0 NB B:HEM150 2.1 10.8 1.0 ND B:HEM150 2.1 12.1 1.0 NA B:HEM150 2.2 13.2 1.0 NE2 B:HIS102 2.2 7.2 1.0 SD B:MET7 2.4 9.9 1.0 CD2 B:HIS102 3.0 10.8 1.0 C1C B:HEM150 3.0 8.2 1.0 C4B B:HEM150 3.1 10.4 1.0 C4D B:HEM150 3.1 13.1 1.0 C1D B:HEM150 3.1 12.8 1.0 C4C B:HEM150 3.1 10.5 1.0 C1B B:HEM150 3.1 11.9 1.0 C1A B:HEM150 3.2 14.2 1.0 C4A B:HEM150 3.2 14.2 1.0 CE1 B:HIS102 3.3 8.4 1.0 CHC B:HEM150 3.4 8.6 1.0 CHA B:HEM150 3.4 15.1 1.0 CHD B:HEM150 3.5 9.6 1.0 CHB B:HEM150 3.5 12.2 1.0 CG B:MET7 3.5 13.1 1.0 CE B:MET7 3.5 6.7 1.0 CB B:MET7 4.2 14.0 1.0 CG B:HIS102 4.2 13.2 1.0 C3B B:HEM150 4.3 10.6 1.0 C2C B:HEM150 4.3 7.9 1.0 C2B B:HEM150 4.3 11.8 1.0 C3C B:HEM150 4.3 9.5 1.0 C3D B:HEM150 4.3 13.0 1.0 C2D B:HEM150 4.3 14.1 1.0 ND1 B:HIS102 4.4 11.8 1.0 C3A B:HEM150 4.4 15.5 1.0 C2A B:HEM150 4.4 17.2 1.0

Iron binding site 3 out of 3 in the A Zn-Mediated Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1)


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 Asymmetric Trimer of A Cytochrome CB562 Variant (D74A- RIDC1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe150 b:11.4 occ:1.00 FE C:HEM150 0.0 11.4 1.0 NB C:HEM150 2.0 6.4 1.0 NA C:HEM150 2.0 9.8 1.0 NE2 C:HIS102 2.0 5.4 1.0 NC C:HEM150 2.1 7.0 1.0 ND C:HEM150 2.1 8.6 1.0 SD C:MET7 2.4 9.2 1.0 CE1 C:HIS102 3.0 4.5 1.0 C4B C:HEM150 3.0 6.5 1.0 C1A C:HEM150 3.0 9.8 1.0 C4D C:HEM150 3.1 8.4 1.0 C1B C:HEM150 3.1 7.2 1.0 C1C C:HEM150 3.1 5.3 1.0 CD2 C:HIS102 3.1 5.3 1.0 C4A C:HEM150 3.1 9.5 1.0 C1D C:HEM150 3.2 7.5 1.0 C4C C:HEM150 3.2 6.5 1.0 CHA C:HEM150 3.3 7.9 1.0 CHC C:HEM150 3.3 5.9 1.0 CE C:MET7 3.4 10.3 1.0 CHB C:HEM150 3.5 8.6 1.0 CG C:MET7 3.5 10.9 1.0 CHD C:HEM150 3.6 7.4 1.0 ND1 C:HIS102 4.1 5.4 1.0 CB C:MET7 4.2 12.3 1.0 CG C:HIS102 4.2 7.4 1.0 C3B C:HEM150 4.2 6.5 1.0 C2A C:HEM150 4.2 10.4 1.0 C2B C:HEM150 4.3 6.7 1.0 C3A C:HEM150 4.3 9.2 1.0 C3D C:HEM150 4.3 7.9 1.0 C2C C:HEM150 4.3 5.4 1.0 C3C C:HEM150 4.4 5.6 1.0 C2D C:HEM150 4.4 6.5 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