Iron in PDB 6dy4: Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2E

The structure of Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2E, PDB code: 6dy4 was solved by J.Rittle, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.24 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	35.570, 48.370, 116.721, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 25.4

The binding sites of Iron atom in the Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2E (pdb code 6dy4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2E, PDB code: 6dy4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2E


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2E within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:20.4 occ:0.71 NE2 D:HIS63 2.0 20.6 1.0 O D:HOH381 2.2 26.2 1.0 OD2 A:ASP74 2.2 25.2 1.0 NE2 D:HIS67 2.2 24.8 1.0 O A:HOH314 2.2 27.5 1.0 O A:HOH315 2.3 23.6 1.0 CE1 D:HIS67 2.9 21.9 1.0 CD2 D:HIS63 3.0 16.2 1.0 CE1 D:HIS63 3.0 21.0 1.0 CG A:ASP74 3.1 20.1 1.0 OD1 A:ASP74 3.3 30.6 1.0 CD2 D:HIS67 3.4 25.1 1.0 O A:HOH317 4.1 23.3 1.0 ND1 D:HIS63 4.1 20.5 1.0 ND1 D:HIS67 4.1 25.0 1.0 CG D:HIS63 4.1 17.2 1.0 O A:GLY70 4.2 22.3 1.0 O D:HOH401 4.3 28.0 1.0 CG D:HIS67 4.4 22.9 1.0 O A:HOH408 4.5 33.5 1.0 CB A:ASP74 4.5 20.5 1.0 O D:HOH399 4.6 34.4 1.0

Iron binding site 2 out of 4 in the Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2E


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2E within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:20.2 occ:1.00 FE A:HEC202 0.0 20.2 1.0 NE2 A:HIS102 1.9 15.8 1.0 NC A:HEC202 2.0 18.5 1.0 ND A:HEC202 2.1 14.4 1.0 NB A:HEC202 2.1 19.8 1.0 NA A:HEC202 2.1 23.4 1.0 SD A:MET7 2.3 18.7 1.0 CD2 A:HIS102 2.9 15.6 1.0 CE1 A:HIS102 3.0 18.4 1.0 C1C A:HEC202 3.0 24.7 1.0 C4C A:HEC202 3.0 20.7 1.0 C1D A:HEC202 3.1 26.3 1.0 C4B A:HEC202 3.1 18.8 1.0 C4D A:HEC202 3.1 23.6 1.0 C1A A:HEC202 3.1 19.7 1.0 C1B A:HEC202 3.1 23.1 1.0 C4A A:HEC202 3.1 19.7 1.0 CE A:MET7 3.3 22.5 1.0 CHD A:HEC202 3.4 18.7 1.0 CHC A:HEC202 3.4 16.3 1.0 CHA A:HEC202 3.4 21.9 1.0 CHB A:HEC202 3.5 20.5 1.0 CG A:MET7 3.5 19.7 1.0 ND1 A:HIS102 4.0 15.7 1.0 CG A:HIS102 4.0 15.7 1.0 CB A:MET7 4.2 26.2 1.0 C2C A:HEC202 4.3 16.5 1.0 C3C A:HEC202 4.3 20.1 1.0 C2D A:HEC202 4.3 21.6 1.0 C2B A:HEC202 4.3 19.5 1.0 C2A A:HEC202 4.3 24.8 1.0 C3B A:HEC202 4.3 19.4 1.0 C3D A:HEC202 4.3 17.8 1.0 C3A A:HEC202 4.3 24.9 1.0

Iron binding site 3 out of 4 in the Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2E


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2E within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:19.1 occ:0.97 OE1 D:GLU97 2.1 19.6 1.0 NE2 A:HIS67 2.1 22.0 1.0 NE2 D:HIS71 2.2 20.9 1.0 NE2 A:HIS71 2.2 23.5 1.0 O A:HOH306 2.2 21.6 1.0 O D:HOH342 2.4 20.8 1.0 CE1 A:HIS67 2.9 25.8 1.0 CE1 A:HIS71 3.0 25.9 1.0 CD D:GLU97 3.1 24.8 1.0 CE1 D:HIS71 3.2 27.1 1.0 CD2 A:HIS67 3.2 21.4 1.0 CD2 D:HIS71 3.2 17.4 1.0 CD2 A:HIS71 3.3 21.2 1.0 CG D:GLU97 3.9 25.2 1.0 OE2 D:GLU97 4.0 25.4 1.0 ND1 A:HIS67 4.1 22.9 1.0 OE1 A:GLU97 4.1 30.0 1.0 O A:HOH369 4.2 22.6 1.0 ND1 A:HIS71 4.2 25.0 1.0 CG A:HIS67 4.2 24.3 1.0 ND1 D:HIS71 4.3 24.4 1.0 CG D:HIS71 4.3 22.3 1.0 O A:HOH360 4.3 31.9 1.0 O D:HOH352 4.4 15.7 1.0 CG A:HIS71 4.4 21.9 1.0 ND1 D:HIS67 4.5 25.0 1.0 CB D:HIS67 4.6 16.2 1.0 CG D:HIS67 5.0 22.9 1.0 O D:HIS67 5.0 19.7 1.0

Iron binding site 4 out of 4 in the Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2E


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH2E within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe202 b:14.7 occ:1.00 FE D:HEC202 0.0 14.7 1.0 NE2 D:HIS102 1.9 14.3 1.0 NC D:HEC202 2.0 15.2 1.0 NA D:HEC202 2.0 14.4 1.0 NB D:HEC202 2.0 13.1 1.0 ND D:HEC202 2.1 14.7 1.0 SD D:MET7 2.2 17.6 1.0 CE1 D:HIS102 2.8 14.6 1.0 CD2 D:HIS102 3.0 13.7 1.0 C1C D:HEC202 3.0 13.7 1.0 C4B D:HEC202 3.0 15.2 1.0 C1A D:HEC202 3.0 14.9 1.0 C4A D:HEC202 3.0 17.4 1.0 C1B D:HEC202 3.1 16.4 1.0 C4D D:HEC202 3.1 14.6 1.0 C4C D:HEC202 3.1 15.4 1.0 C1D D:HEC202 3.1 16.3 1.0 CE D:MET7 3.4 16.0 1.0 CHC D:HEC202 3.4 14.7 1.0 CHA D:HEC202 3.4 15.8 1.0 CG D:MET7 3.4 19.0 1.0 CHB D:HEC202 3.4 14.8 1.0 CHD D:HEC202 3.4 16.4 1.0 ND1 D:HIS102 3.9 15.4 1.0 CG D:HIS102 4.0 15.1 1.0 CB D:MET7 4.2 17.1 1.0 C2C D:HEC202 4.2 12.8 1.0 C3B D:HEC202 4.3 14.2 1.0 C2A D:HEC202 4.3 18.5 1.0 C3A D:HEC202 4.3 19.5 1.0 C3C D:HEC202 4.3 12.7 1.0 C2B D:HEC202 4.3 14.2 1.0 C3D D:HEC202 4.3 12.7 1.0 C2D D:HEC202 4.3 16.6 1.0 CA D:MET7 5.0 17.1 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