Iron in PDB 5l32: Crystal Structure of the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds

The structure of Crystal Structure of the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds, PDB code: 5l32 was solved by L.A.Churchfield, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.81 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.060, 62.533, 72.437, 90.00, 99.01, 90.00
R / Rfree (%)	21.4 / 25

The structure of Crystal Structure of the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Iron atom in the Crystal Structure of the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds (pdb code 5l32). 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-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds, PDB code: 5l32:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds


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-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:33.3 occ:1.00 FE A:HEM201 0.0 33.3 1.0 ND A:HEM201 1.9 36.0 1.0 NA A:HEM201 2.0 33.3 1.0 NB A:HEM201 2.1 32.0 1.0 NC A:HEM201 2.1 29.3 1.0 NE2 A:HIS102 2.1 31.8 1.0 SD A:MET7 2.4 32.0 1.0 C4D A:HEM201 2.9 33.8 1.0 C1D A:HEM201 2.9 35.6 1.0 C1A A:HEM201 3.0 32.0 1.0 C4A A:HEM201 3.0 34.2 1.0 C1B A:HEM201 3.0 35.6 1.0 CE1 A:HIS102 3.0 35.0 1.0 C4B A:HEM201 3.1 35.5 1.0 C4C A:HEM201 3.1 34.2 1.0 C1C A:HEM201 3.1 31.7 1.0 CD2 A:HIS102 3.2 32.8 1.0 CHA A:HEM201 3.4 32.8 1.0 CHB A:HEM201 3.4 31.8 1.0 CG A:MET7 3.4 35.1 1.0 CHD A:HEM201 3.5 35.2 1.0 CHC A:HEM201 3.5 35.0 1.0 CE A:MET7 3.5 33.5 1.0 C2A A:HEM201 4.2 37.3 1.0 C3D A:HEM201 4.2 36.1 1.0 C2D A:HEM201 4.2 36.0 1.0 ND1 A:HIS102 4.2 36.9 1.0 C3A A:HEM201 4.2 35.5 1.0 CB A:MET7 4.2 32.0 1.0 C2B A:HEM201 4.3 31.9 1.0 C2C A:HEM201 4.3 31.4 1.0 CG A:HIS102 4.3 38.2 1.0 C3C A:HEM201 4.3 31.2 1.0 C3B A:HEM201 4.3 30.0 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds


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-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:37.4 occ:1.00 FE B:HEM201 0.0 37.4 1.0 ND B:HEM201 1.9 39.0 1.0 NA B:HEM201 2.0 37.0 1.0 NB B:HEM201 2.1 34.2 1.0 NC B:HEM201 2.1 36.5 1.0 NE2 B:HIS102 2.2 37.8 1.0 SD B:MET7 2.3 38.3 1.0 C4D B:HEM201 2.9 38.1 1.0 C1D B:HEM201 2.9 37.2 1.0 C1A B:HEM201 3.0 41.1 1.0 C4A B:HEM201 3.1 40.4 1.0 C4B B:HEM201 3.1 38.7 1.0 C1B B:HEM201 3.1 37.0 1.0 CE1 B:HIS102 3.1 38.1 1.0 C1C B:HEM201 3.1 33.4 1.0 C4C B:HEM201 3.1 37.2 1.0 CD2 B:HIS102 3.2 35.3 1.0 CE B:MET7 3.4 40.3 1.0 CHA B:HEM201 3.4 40.4 1.0 CG B:MET7 3.4 40.6 1.0 CHC B:HEM201 3.4 37.7 1.0 CHD B:HEM201 3.5 35.7 1.0 CHB B:HEM201 3.5 36.1 1.0 C3D B:HEM201 4.2 39.9 1.0 C2D B:HEM201 4.2 40.2 1.0 C2A B:HEM201 4.2 37.3 1.0 ND1 B:HIS102 4.2 38.5 1.0 C3A B:HEM201 4.2 42.0 1.0 CB B:MET7 4.3 35.6 1.0 C2C B:HEM201 4.3 39.0 1.0 C2B B:HEM201 4.3 36.6 1.0 C3C B:HEM201 4.3 39.0 1.0 CG B:HIS102 4.3 39.0 1.0 C3B B:HEM201 4.4 35.5 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds


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-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:39.8 occ:1.00 FE C:HEM201 0.0 39.8 1.0 ND C:HEM201 1.9 41.9 1.0 NA C:HEM201 2.0 44.2 1.0 NE2 C:HIS102 2.1 45.7 1.0 NB C:HEM201 2.1 39.3 1.0 NC C:HEM201 2.1 40.5 1.0 SD C:MET7 2.4 39.7 1.0 C4D C:HEM201 2.9 42.9 1.0 C1D C:HEM201 2.9 40.2 1.0 C1A C:HEM201 3.0 45.8 1.0 CE1 C:HIS102 3.1 46.1 1.0 C4B C:HEM201 3.1 40.8 1.0 C4A C:HEM201 3.1 43.4 1.0 C1B C:HEM201 3.1 37.0 1.0 C4C C:HEM201 3.1 37.7 1.0 CD2 C:HIS102 3.1 41.5 1.0 C1C C:HEM201 3.1 40.3 1.0 CE C:MET7 3.3 43.6 1.0 CHA C:HEM201 3.4 45.4 1.0 CHD C:HEM201 3.4 42.9 1.0 CHC C:HEM201 3.4 37.3 1.0 CHB C:HEM201 3.5 45.7 1.0 CG C:MET7 3.6 41.8 1.0 C3D C:HEM201 4.2 49.1 1.0 C2D C:HEM201 4.2 43.0 1.0 ND1 C:HIS102 4.2 46.4 1.0 C2A C:HEM201 4.2 49.1 1.0 CG C:HIS102 4.2 43.8 1.0 C3A C:HEM201 4.2 49.7 1.0 C2B C:HEM201 4.3 41.3 1.0 C3C C:HEM201 4.3 39.3 1.0 C2C C:HEM201 4.3 41.3 1.0 CB C:MET7 4.3 42.2 1.0 C3B C:HEM201 4.3 40.8 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Zn-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds


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-RIDC1 Complex Bearing Six Interfacial Disulfide Bonds within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:47.4 occ:1.00 FE D:HEM201 0.0 47.4 1.0 ND D:HEM201 1.9 49.5 1.0 NA D:HEM201 2.0 53.7 1.0 NE2 D:HIS102 2.1 43.5 1.0 NB D:HEM201 2.1 49.4 1.0 NC D:HEM201 2.1 51.1 1.0 SD D:MET7 2.6 52.1 1.0 C4D D:HEM201 2.9 49.5 1.0 C1D D:HEM201 2.9 54.6 1.0 CE1 D:HIS102 3.0 40.7 1.0 C1A D:HEM201 3.0 47.9 1.0 C4A D:HEM201 3.1 52.4 1.0 C4B D:HEM201 3.1 53.3 1.0 C1B D:HEM201 3.1 47.3 1.0 C1C D:HEM201 3.1 47.3 1.0 C4C D:HEM201 3.2 47.9 1.0 CD2 D:HIS102 3.2 43.6 1.0 CHA D:HEM201 3.4 46.5 1.0 CHC D:HEM201 3.4 51.2 1.0 CHB D:HEM201 3.5 48.7 1.0 CHD D:HEM201 3.5 53.4 1.0 CG D:MET7 3.6 53.5 1.0 CE D:MET7 3.7 53.4 1.0 C2D D:HEM201 4.1 53.0 1.0 ND1 D:HIS102 4.1 40.2 1.0 C3D D:HEM201 4.1 51.5 1.0 C2A D:HEM201 4.2 56.3 1.0 CB D:MET7 4.3 49.8 1.0 C3A D:HEM201 4.3 57.2 1.0 CG D:HIS102 4.3 43.5 1.0 C2B D:HEM201 4.3 48.4 1.0 C2C D:HEM201 4.3 52.4 1.0 C3B D:HEM201 4.3 55.1 1.0 C3C D:HEM201 4.4 50.2 1.0

L.A.Churchfield, A.Medina-Morales, J.D.Brodin, A.Perez, F.A.Tezcan. De Novo Design of An Allosteric Metalloprotein Assembly with Strained Disulfide Bonds. J.Am.Chem.Soc. V. 138 13163 2016.
ISSN: ESSN 1520-5126
PubMed: 27649076
DOI: 10.1021/JACS.6B08458