Iron in PDB 6dy8: Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY

The structure of Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY, PDB code: 6dy8 was solved by F.A.Tezcan, J.Rittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.59 / 1.90
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.661, 37.591, 77.323, 90.00, 104.39, 90.00
R / Rfree (%)	22.6 / 27.8

The structure of Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Iron atom in the Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY (pdb code 6dy8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY, PDB code: 6dy8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:23.7 occ:1.00 FE A:HEC201 0.0 23.7 1.0 NE2 A:HIS102 1.9 18.8 1.0 NC A:HEC201 2.1 27.1 1.0 NA A:HEC201 2.1 24.5 1.0 NB A:HEC201 2.1 19.6 1.0 ND A:HEC201 2.1 21.6 1.0 SD A:MET7 2.4 23.1 1.0 CD2 A:HIS102 2.9 20.8 1.0 CE1 A:HIS102 2.9 19.4 1.0 C4C A:HEC201 3.1 24.8 1.0 C1A A:HEC201 3.1 21.8 1.0 C1C A:HEC201 3.1 24.8 1.0 C4A A:HEC201 3.1 26.1 1.0 C4B A:HEC201 3.1 23.8 1.0 C1B A:HEC201 3.1 26.8 1.0 C1D A:HEC201 3.1 25.1 1.0 C4D A:HEC201 3.1 25.7 1.0 CE A:MET7 3.4 16.1 1.0 CG A:MET7 3.4 28.3 1.0 CHD A:HEC201 3.4 21.2 1.0 CHA A:HEC201 3.4 27.3 1.0 CHC A:HEC201 3.4 28.2 1.0 CHB A:HEC201 3.5 22.4 1.0 ND1 A:HIS102 4.0 13.6 1.0 CG A:HIS102 4.0 23.5 1.0 CB A:MET7 4.1 24.0 1.0 C3C A:HEC201 4.3 21.1 1.0 C2A A:HEC201 4.3 21.8 1.0 C2C A:HEC201 4.3 25.5 1.0 C3A A:HEC201 4.3 21.0 1.0 C3B A:HEC201 4.3 21.9 1.0 C2B A:HEC201 4.3 28.9 1.0 C2D A:HEC201 4.3 23.5 1.0 C3D A:HEC201 4.3 26.9 1.0

Iron binding site 2 out of 4 in the Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:48.1 occ:1.00 FE B:HEC202 0.0 48.1 1.0 NA B:HEC202 2.1 62.1 1.0 NC B:HEC202 2.1 56.9 1.0 NB B:HEC202 2.1 52.5 1.0 NE2 B:HIS102 2.1 52.2 1.0 ND B:HEC202 2.1 53.4 1.0 SD B:MET7 2.2 63.5 1.0 CE B:MET7 2.6 51.5 1.0 CD2 B:HIS102 3.0 52.8 1.0 C1C B:HEC202 3.1 57.2 1.0 C1A B:HEC202 3.1 57.4 1.0 C4B B:HEC202 3.1 62.6 1.0 C4A B:HEC202 3.1 60.3 1.0 C1B B:HEC202 3.1 58.3 1.0 C4D B:HEC202 3.1 59.6 1.0 C4C B:HEC202 3.1 56.0 1.0 CE1 B:HIS102 3.1 53.0 1.0 C1D B:HEC202 3.1 54.6 1.0 CHC B:HEC202 3.4 60.3 1.0 CHA B:HEC202 3.4 60.2 1.0 CHB B:HEC202 3.5 62.5 1.0 CHD B:HEC202 3.5 50.4 1.0 CG B:MET7 3.6 55.1 1.0 CB B:MET7 4.1 56.6 1.0 CG B:HIS102 4.2 54.9 1.0 ND1 B:HIS102 4.2 59.9 1.0 C2A B:HEC202 4.3 61.7 1.0 C3B B:HEC202 4.3 58.9 1.0 C2C B:HEC202 4.3 51.9 1.0 C3A B:HEC202 4.3 64.1 1.0 C2B B:HEC202 4.3 59.5 1.0 C3C B:HEC202 4.3 45.5 1.0 C3D B:HEC202 4.3 57.4 1.0 C2D B:HEC202 4.3 50.7 1.0

Iron binding site 3 out of 4 in the Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:29.1 occ:1.00 FE C:HEC202 0.0 29.1 1.0 NE2 C:HIS102 1.9 25.4 1.0 NA C:HEC202 2.1 26.4 1.0 NC C:HEC202 2.1 20.7 1.0 NB C:HEC202 2.1 27.3 1.0 ND C:HEC202 2.1 29.6 1.0 SD C:MET7 2.3 27.5 1.0 CE1 C:HIS102 2.8 28.3 1.0 CD2 C:HIS102 3.0 28.3 1.0 C1A C:HEC202 3.1 29.1 1.0 C1C C:HEC202 3.1 23.9 1.0 C4D C:HEC202 3.1 27.0 1.0 C4B C:HEC202 3.1 31.0 1.0 C1D C:HEC202 3.1 27.3 1.0 C4C C:HEC202 3.1 26.6 1.0 C4A C:HEC202 3.1 31.9 1.0 C1B C:HEC202 3.1 30.7 1.0 CE C:MET7 3.3 26.7 1.0 CHA C:HEC202 3.4 31.8 1.0 CHC C:HEC202 3.4 26.8 1.0 CG C:MET7 3.4 28.4 1.0 CHD C:HEC202 3.4 31.1 1.0 CHB C:HEC202 3.5 34.8 1.0 ND1 C:HIS102 4.0 32.1 1.0 CG C:HIS102 4.1 29.9 1.0 CB C:MET7 4.2 35.8 1.0 C2A C:HEC202 4.3 34.9 1.0 C2C C:HEC202 4.3 21.7 1.0 C3A C:HEC202 4.3 37.1 1.0 C3C C:HEC202 4.3 23.4 1.0 C3B C:HEC202 4.3 28.2 1.0 C3D C:HEC202 4.3 26.6 1.0 C2D C:HEC202 4.3 27.6 1.0 C2B C:HEC202 4.3 25.0 1.0 CA C:MET7 5.0 36.0 1.0

Iron binding site 4 out of 4 in the Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Mn(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2EY within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:37.2 occ:1.00 FE D:HEC201 0.0 37.2 1.0 NE2 D:HIS102 1.9 33.3 1.0 NC D:HEC201 2.1 34.4 1.0 NA D:HEC201 2.1 42.6 1.0 ND D:HEC201 2.1 37.8 1.0 NB D:HEC201 2.1 41.0 1.0 SD D:MET7 2.4 33.0 1.0 CD2 D:HIS102 2.9 32.2 1.0 CE1 D:HIS102 2.9 40.4 1.0 C1A D:HEC201 3.1 42.6 1.0 C4D D:HEC201 3.1 36.4 1.0 C1C D:HEC201 3.1 35.5 1.0 C4B D:HEC201 3.1 38.5 1.0 C1D D:HEC201 3.1 36.5 1.0 C4C D:HEC201 3.1 33.0 1.0 C4A D:HEC201 3.1 40.5 1.0 C1B D:HEC201 3.1 41.3 1.0 CE D:MET7 3.2 41.6 1.0 CHA D:HEC201 3.4 37.8 1.0 CHC D:HEC201 3.4 34.6 1.0 CHD D:HEC201 3.4 36.0 1.0 CG D:MET7 3.5 39.1 1.0 CHB D:HEC201 3.5 36.7 1.0 ND1 D:HIS102 4.0 34.6 1.0 CG D:HIS102 4.0 39.8 1.0 C2A D:HEC201 4.3 45.9 1.0 C2C D:HEC201 4.3 33.5 1.0 C3D D:HEC201 4.3 41.7 1.0 C3B D:HEC201 4.3 39.5 1.0 C3A D:HEC201 4.3 44.8 1.0 C2D D:HEC201 4.3 37.3 1.0 C3C D:HEC201 4.3 31.5 1.0 C2B D:HEC201 4.3 41.8 1.0 CB D:MET7 4.3 32.2 1.0

J.Rittle, M.J.Field, M.T.Green, F.A.Tezcan. An Efficient, Step-Economical Strategy For the Design of Functional Metalloproteins. Nat.Chem. V. 11 434 2019.
ISSN: ESSN 1755-4349
PubMed: 30778140
DOI: 10.1038/S41557-019-0218-9