Iron in PDB 4u9d: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3, PDB code: 4u9d was solved by F.A.Tezcan, W.J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.48 / 2.50
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	54.830, 54.830, 237.820, 90.00, 90.00, 120.00
R / Rfree (%)	23.8 / 29.6

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3 also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Iron atom in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3 (pdb code 4u9d). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3, PDB code: 4u9d:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:61.2 occ:1.00 FE A:HEM201 0.0 61.2 1.0 ND A:HEM201 1.9 65.1 1.0 NA A:HEM201 2.0 64.4 1.0 NC A:HEM201 2.1 62.0 1.0 NB A:HEM201 2.1 61.4 1.0 NE2 A:HIS102 2.1 52.9 1.0 SD A:MET7 2.3 57.7 1.0 C4D A:HEM201 2.9 65.5 1.0 C1D A:HEM201 2.9 64.5 1.0 C1A A:HEM201 3.0 65.3 1.0 C4A A:HEM201 3.0 64.2 1.0 CE1 A:HIS102 3.1 53.6 1.0 C4B A:HEM201 3.1 60.7 1.0 C1B A:HEM201 3.1 61.2 1.0 C4C A:HEM201 3.1 62.0 1.0 C1C A:HEM201 3.1 60.7 1.0 CD2 A:HIS102 3.1 53.9 1.0 CHA A:HEM201 3.4 65.5 1.0 CE A:MET7 3.4 58.7 1.0 CHD A:HEM201 3.4 63.6 1.0 CHB A:HEM201 3.5 62.8 1.0 CHC A:HEM201 3.5 60.1 1.0 CG A:MET7 3.5 59.2 1.0 C3D A:HEM201 4.2 66.3 1.0 ND1 A:HIS102 4.2 54.2 1.0 C2D A:HEM201 4.2 65.5 1.0 C2A A:HEM201 4.2 67.4 1.0 C3A A:HEM201 4.2 65.6 1.0 CB A:MET7 4.2 58.4 1.0 CG A:HIS102 4.3 54.9 1.0 C2C A:HEM201 4.3 61.1 1.0 C3C A:HEM201 4.3 60.9 1.0 C2B A:HEM201 4.3 60.2 1.0 C3B A:HEM201 4.3 60.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:72.0 occ:1.00 FE B:HEM201 0.0 72.0 1.0 ND B:HEM201 1.9 72.4 1.0 NA B:HEM201 2.0 76.0 1.0 NC B:HEM201 2.1 71.1 1.0 NB B:HEM201 2.1 71.7 1.0 NE2 B:HIS102 2.2 64.3 1.0 SD B:MET7 2.5 68.8 1.0 C4D B:HEM201 2.9 73.9 1.0 C1D B:HEM201 2.9 71.8 1.0 C1A B:HEM201 3.0 77.0 1.0 CD2 B:HIS102 3.0 64.5 1.0 C4A B:HEM201 3.0 76.4 1.0 C4B B:HEM201 3.1 70.9 1.0 C1B B:HEM201 3.1 72.8 1.0 C4C B:HEM201 3.1 70.2 1.0 C1C B:HEM201 3.1 70.1 1.0 CE1 B:HIS102 3.3 65.0 1.0 CHA B:HEM201 3.4 75.3 1.0 CHD B:HEM201 3.4 71.1 1.0 CE B:MET7 3.4 69.6 1.0 CHB B:HEM201 3.4 74.6 1.0 CHC B:HEM201 3.5 70.1 1.0 CG B:MET7 3.6 70.4 1.0 C3D B:HEM201 4.2 72.8 1.0 C2D B:HEM201 4.2 71.1 1.0 C2A B:HEM201 4.2 80.0 1.0 C3A B:HEM201 4.2 78.6 1.0 CG B:HIS102 4.2 65.0 1.0 C3C B:HEM201 4.3 69.5 1.0 C2C B:HEM201 4.3 69.6 1.0 C2B B:HEM201 4.3 71.8 1.0 CB B:MET7 4.3 70.3 1.0 C3B B:HEM201 4.3 70.8 1.0 ND1 B:HIS102 4.3 65.3 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:62.9 occ:1.00 FE C:HEM201 0.0 62.9 1.0 ND C:HEM201 1.9 64.7 1.0 NA C:HEM201 2.0 65.8 1.0 NC C:HEM201 2.1 62.0 1.0 NB C:HEM201 2.1 63.5 1.0 NE2 C:HIS102 2.3 58.8 1.0 SD C:MET7 2.4 66.1 1.0 C4D C:HEM201 2.9 66.0 1.0 C1D C:HEM201 2.9 64.3 1.0 C1A C:HEM201 3.0 67.6 1.0 C4A C:HEM201 3.0 67.0 1.0 C4B C:HEM201 3.1 62.3 1.0 C1B C:HEM201 3.1 64.2 1.0 C4C C:HEM201 3.1 61.7 1.0 C1C C:HEM201 3.1 61.6 1.0 CD2 C:HIS102 3.2 59.3 1.0 CE1 C:HIS102 3.3 59.3 1.0 CE C:MET7 3.4 66.1 1.0 CHA C:HEM201 3.4 66.7 1.0 CHD C:HEM201 3.4 62.8 1.0 CHB C:HEM201 3.4 65.6 1.0 CHC C:HEM201 3.5 62.0 1.0 CG C:MET7 3.6 66.2 1.0 C3D C:HEM201 4.2 67.2 1.0 C2D C:HEM201 4.2 65.5 1.0 C2A C:HEM201 4.2 70.0 1.0 C3A C:HEM201 4.2 68.9 1.0 C2B C:HEM201 4.3 63.1 1.0 C2C C:HEM201 4.3 61.4 1.0 CB C:MET7 4.3 66.2 1.0 C3C C:HEM201 4.3 61.0 1.0 C3B C:HEM201 4.3 62.3 1.0 CG C:HIS102 4.4 60.6 1.0 ND1 C:HIS102 4.4 60.0 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:0.0 occ:1.00 FE D:HEM201 0.0 0.0 1.0 ND D:HEM201 1.9 0.0 1.0 NA D:HEM201 2.0 0.0 1.0 NC D:HEM201 2.1 0.0 1.0 NB D:HEM201 2.1 0.0 1.0 NE2 D:HIS102 2.4 90.9 1.0 SD D:MET7 2.6 0.0 1.0 C4D D:HEM201 2.9 0.0 1.0 C1D D:HEM201 2.9 0.0 1.0 C1A D:HEM201 3.0 0.0 1.0 C4A D:HEM201 3.0 0.0 1.0 C4B D:HEM201 3.1 0.0 1.0 C1B D:HEM201 3.1 0.0 1.0 C4C D:HEM201 3.1 0.0 1.0 C1C D:HEM201 3.1 0.0 1.0 CD2 D:HIS102 3.3 92.3 1.0 CHA D:HEM201 3.4 0.0 1.0 CHD D:HEM201 3.4 0.0 1.0 CE1 D:HIS102 3.4 91.1 1.0 CHB D:HEM201 3.4 0.0 1.0 CHC D:HEM201 3.5 0.0 1.0 CE D:MET7 3.6 0.0 1.0 CG D:MET7 3.8 0.0 1.0 C3D D:HEM201 4.2 0.0 1.0 C2D D:HEM201 4.2 0.0 1.0 C2A D:HEM201 4.2 0.0 1.0 C3A D:HEM201 4.2 0.0 1.0 C3C D:HEM201 4.3 0.0 1.0 C2C D:HEM201 4.3 0.0 1.0 C2B D:HEM201 4.3 0.0 1.0 C3B D:HEM201 4.3 0.0 1.0 CB D:MET7 4.4 0.0 1.0 CG D:HIS102 4.5 93.6 1.0 ND1 D:HIS102 4.5 91.4 1.0

W.J.Song, F.A.Tezcan. A Designed Supramolecular Protein Assembly with in Vivo Enzymatic Activity. Science V. 346 1525 2014.
ISSN: ESSN 1095-9203
PubMed: 25525249
DOI: 10.1126/SCIENCE.1259680