Iron in PDB 6dyg: Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y

The structure of Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y, PDB code: 6dyg 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)	38.50 / 1.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.739, 83.513, 39.088, 90.00, 99.99, 90.00
R / Rfree (%)	19.1 / 21.7

The structure of Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y (pdb code 6dyg). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y, PDB code: 6dyg:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y


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, CH3Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:27.9 occ:1.00 FE A:HEC201 0.0 27.9 1.0 NC A:HEC201 2.0 23.8 1.0 NA A:HEC201 2.0 31.4 1.0 NE2 A:HIS102 2.0 29.7 1.0 NB A:HEC201 2.0 26.6 1.0 ND A:HEC201 2.1 33.3 1.0 SD A:MET7 2.3 29.2 1.0 CE1 A:HIS102 3.0 27.8 1.0 C4C A:HEC201 3.0 28.1 1.0 C4A A:HEC201 3.0 32.0 1.0 CD2 A:HIS102 3.0 26.7 1.0 C1A A:HEC201 3.0 33.5 1.0 C1C A:HEC201 3.0 25.7 1.0 C1D A:HEC201 3.0 28.7 1.0 C4B A:HEC201 3.0 25.9 1.0 C1B A:HEC201 3.1 26.7 1.0 C4D A:HEC201 3.1 32.2 1.0 HE1 A:HIS102 3.1 33.4 1.0 HD2 A:HIS102 3.2 32.0 1.0 CE A:MET7 3.3 29.6 1.0 HG3 A:MET7 3.3 40.5 1.0 HE3 A:MET7 3.3 35.5 1.0 HE1 A:MET7 3.4 35.5 1.0 CHD A:HEC201 3.4 28.0 1.0 CHB A:HEC201 3.4 31.4 1.0 CG A:MET7 3.4 33.7 1.0 CHC A:HEC201 3.4 23.4 1.0 CHA A:HEC201 3.4 33.3 1.0 HB3 A:MET7 3.8 37.8 1.0 ND1 A:HIS102 4.1 30.6 1.0 HE2 A:MET7 4.1 35.5 1.0 CG A:HIS102 4.1 27.5 1.0 HG2 A:MET7 4.2 40.5 1.0 CB A:MET7 4.2 31.5 1.0 C3A A:HEC201 4.2 37.0 1.0 C2A A:HEC201 4.2 35.8 1.0 C3C A:HEC201 4.3 21.6 1.0 C2C A:HEC201 4.3 23.0 1.0 C3B A:HEC201 4.3 25.0 1.0 C2B A:HEC201 4.3 25.4 1.0 C2D A:HEC201 4.3 25.0 1.0 C3D A:HEC201 4.3 27.1 1.0 HHD A:HEC201 4.4 33.6 1.0 HHB A:HEC201 4.4 37.7 1.0 HHC A:HEC201 4.4 28.1 1.0 HHA A:HEC201 4.4 40.0 1.0 HD12 A:LEU10 4.5 34.8 1.0 HA A:MET7 4.6 33.3 1.0 HB3 A:CYS98 4.7 26.4 1.0 HD1 A:HIS102 4.9 36.7 1.0 HB2 A:MET7 5.0 37.8 1.0

Iron binding site 2 out of 3 in the Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y


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, CH3Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:28.4 occ:1.00 NE2 A:HIS97 2.1 24.2 1.0 NE2 B:HIS71 2.2 26.3 1.0 NE2 A:HIS71 2.2 28.5 1.0 NE2 A:HIS67 2.2 27.3 1.0 NE2 B:HIS67 2.2 31.0 1.0 O A:HOH363 2.4 30.3 1.0 CE1 A:HIS97 3.0 27.4 1.0 CD2 B:HIS67 3.0 26.5 1.0 CE1 B:HIS71 3.1 28.7 1.0 HD2 B:HIS67 3.1 31.8 1.0 CE1 A:HIS71 3.1 27.0 1.0 CD2 A:HIS97 3.1 28.3 1.0 HE1 A:HIS97 3.2 32.8 1.0 HE1 B:HIS71 3.2 34.5 1.0 CD2 A:HIS67 3.2 29.9 1.0 CD2 A:HIS71 3.2 27.3 1.0 CE1 A:HIS67 3.2 32.2 1.0 CD2 B:HIS71 3.3 24.4 1.0 HE1 A:HIS71 3.3 32.4 1.0 HD2 A:HIS67 3.3 35.9 1.0 CE1 B:HIS67 3.3 34.8 1.0 HD2 A:HIS71 3.4 32.8 1.0 HD2 A:HIS97 3.4 33.9 1.0 HE1 A:HIS67 3.4 38.6 1.0 HD2 B:HIS71 3.5 29.2 1.0 HE1 B:HIS67 3.6 41.8 1.0 ND1 A:HIS97 4.1 24.8 1.0 CG A:HIS97 4.2 23.6 1.0 ND1 B:HIS71 4.2 28.9 1.0 CG B:HIS67 4.3 28.2 1.0 ND1 A:HIS71 4.3 26.9 1.0 ND1 A:HIS67 4.3 32.6 1.0 CG A:HIS71 4.3 25.2 1.0 CG A:HIS67 4.3 23.9 1.0 HE1 B:HIS97 4.3 38.2 1.0 CG B:HIS71 4.3 25.5 1.0 HD1 B:TYR70 4.4 34.8 1.0 ND1 B:HIS67 4.4 27.7 1.0 O A:HOH378 4.5 50.3 1.0 CD1 B:TYR70 4.5 29.0 1.0 HE1 A:TYR70 4.6 65.5 1.0 HE1 B:TYR70 4.7 37.0 1.0 CE1 B:TYR70 4.7 30.8 1.0 HB3 B:TYR70 4.8 28.1 1.0 HD1 A:TYR70 4.8 53.5 1.0 HD1 A:HIS97 4.9 29.7 1.0 CE1 B:HIS97 4.9 31.8 1.0 HD1 B:HIS71 5.0 34.6 1.0

Iron binding site 3 out of 3 in the Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y


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, CH3Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:22.0 occ:1.00 FE B:HEC201 0.0 22.0 1.0 NE2 B:HIS102 2.0 20.4 1.0 NB B:HEC201 2.0 21.9 1.0 NA B:HEC201 2.0 21.8 1.0 ND B:HEC201 2.0 20.3 1.0 NC B:HEC201 2.0 21.7 1.0 SD B:MET7 2.3 23.1 1.0 CD2 B:HIS102 3.0 20.2 1.0 CE1 B:HIS102 3.0 27.2 1.0 C4A B:HEC201 3.0 22.1 1.0 C1D B:HEC201 3.0 20.2 1.0 C1B B:HEC201 3.0 19.9 1.0 C4B B:HEC201 3.1 22.2 1.0 C4C B:HEC201 3.1 21.5 1.0 C1C B:HEC201 3.1 23.1 1.0 C1A B:HEC201 3.1 23.6 1.0 C4D B:HEC201 3.1 22.9 1.0 HD2 B:HIS102 3.1 24.2 1.0 HG3 B:MET7 3.2 25.1 1.0 HE1 B:HIS102 3.2 32.7 1.0 CE B:MET7 3.3 26.5 1.0 HE3 B:MET7 3.3 31.8 1.0 CG B:MET7 3.3 20.9 1.0 CHB B:HEC201 3.4 23.1 1.0 HE1 B:MET7 3.4 31.8 1.0 CHD B:HEC201 3.4 24.9 1.0 CHC B:HEC201 3.4 20.1 1.0 CHA B:HEC201 3.5 23.4 1.0 HB3 B:MET7 3.8 28.0 1.0 ND1 B:HIS102 4.1 24.7 1.0 HG2 B:MET7 4.1 25.1 1.0 CG B:HIS102 4.1 23.4 1.0 HE2 B:MET7 4.1 31.8 1.0 CB B:MET7 4.2 23.3 1.0 HD2 B:ARG106 4.2 34.0 1.0 C3B B:HEC201 4.3 23.0 1.0 C3A B:HEC201 4.3 24.0 1.0 C2B B:HEC201 4.3 21.7 1.0 C2D B:HEC201 4.3 24.2 1.0 C2A B:HEC201 4.3 27.1 1.0 C2C B:HEC201 4.3 20.8 1.0 C3D B:HEC201 4.3 23.8 1.0 C3C B:HEC201 4.3 22.0 1.0 HHB B:HEC201 4.3 27.7 1.0 HHD B:HEC201 4.4 29.9 1.0 HHC B:HEC201 4.4 24.1 1.0 HHA B:HEC201 4.5 28.1 1.0 HA B:MET7 4.5 27.8 1.0 HB3 B:CYS98 4.7 27.6 1.0 HD12 B:LEU10 4.7 29.7 1.0 HD1 B:HIS102 4.9 29.6 1.0 HB2 B:MET7 4.9 28.0 1.0 HB2 B:ARG106 4.9 28.9 1.0 HD13 B:LEU10 4.9 29.7 1.0 HH21 B:ARG106 4.9 33.4 1.0 CA B:MET7 5.0 23.1 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