Iron in PDB 5l31: Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds.

The structure of Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds., PDB code: 5l31 was solved by F.A.Tezcan, L.A.Churchfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.77 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.594, 77.534, 88.063, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 26.7

The structure of Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds. also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Iron atom in the Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds. (pdb code 5l31). 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 An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds., PDB code: 5l31:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five 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 An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds. within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:39.3 occ:1.00 FE A:HEM201 0.0 39.3 1.0 ND A:HEM201 1.9 41.5 1.0 NA A:HEM201 2.0 42.9 1.0 NC A:HEM201 2.1 38.7 1.0 NB A:HEM201 2.1 40.0 1.0 SD A:MET7 2.1 41.6 1.0 NE2 A:HIS102 2.4 32.0 1.0 C1D A:HEM201 2.9 40.0 1.0 C4D A:HEM201 2.9 41.0 1.0 C1A A:HEM201 3.0 43.9 1.0 C4A A:HEM201 3.0 42.9 1.0 C4C A:HEM201 3.1 38.5 1.0 C1B A:HEM201 3.1 40.8 1.0 C1C A:HEM201 3.1 37.8 1.0 C4B A:HEM201 3.1 40.2 1.0 CD2 A:HIS102 3.2 32.1 1.0 CG A:MET7 3.3 40.6 1.0 CE1 A:HIS102 3.4 31.1 1.0 CHD A:HEM201 3.4 39.4 1.0 CHA A:HEM201 3.4 42.1 1.0 CE A:MET7 3.4 40.8 1.0 CHB A:HEM201 3.4 41.3 1.0 CHC A:HEM201 3.5 39.6 1.0 CB A:MET7 4.2 39.4 1.0 C2D A:HEM201 4.2 38.5 1.0 C3D A:HEM201 4.2 39.9 1.0 C2A A:HEM201 4.2 47.2 1.0 C3A A:HEM201 4.2 44.3 1.0 C2C A:HEM201 4.3 37.4 1.0 C3C A:HEM201 4.3 37.0 1.0 C2B A:HEM201 4.3 40.8 1.0 C3B A:HEM201 4.4 40.8 1.0 CG A:HIS102 4.4 31.0 1.0 ND1 A:HIS102 4.5 31.5 1.0 CA A:MET7 4.9 40.6 1.0

Iron binding site 2 out of 4 in the Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five 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 An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds. within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:40.4 occ:1.00 FE B:HEM201 0.0 40.4 1.0 ND B:HEM201 1.9 42.5 1.0 NA B:HEM201 2.0 45.3 1.0 NC B:HEM201 2.1 39.0 1.0 NB B:HEM201 2.1 40.5 1.0 SD B:MET7 2.2 40.5 1.0 NE2 B:HIS102 2.4 38.6 1.0 C4D B:HEM201 2.9 43.2 1.0 C1D B:HEM201 2.9 41.1 1.0 C1A B:HEM201 3.0 47.6 1.0 C4A B:HEM201 3.0 45.2 1.0 C4B B:HEM201 3.1 38.7 1.0 C1B B:HEM201 3.1 41.4 1.0 C4C B:HEM201 3.1 39.0 1.0 C1C B:HEM201 3.1 37.4 1.0 CD2 B:HIS102 3.2 39.1 1.0 CE B:MET7 3.3 41.1 1.0 CHA B:HEM201 3.4 45.2 1.0 CHD B:HEM201 3.4 39.3 1.0 CG B:MET7 3.4 42.5 1.0 CE1 B:HIS102 3.4 39.2 1.0 CHB B:HEM201 3.4 42.0 1.0 CHC B:HEM201 3.5 38.3 1.0 C3D B:HEM201 4.2 43.8 1.0 C2D B:HEM201 4.2 41.5 1.0 C2A B:HEM201 4.2 49.8 1.0 C3A B:HEM201 4.2 48.3 1.0 CB B:MET7 4.3 42.9 1.0 C2B B:HEM201 4.3 39.7 1.0 C2C B:HEM201 4.3 36.8 1.0 C3C B:HEM201 4.3 36.5 1.0 C3B B:HEM201 4.3 38.8 1.0 CG B:HIS102 4.4 40.0 1.0 ND1 B:HIS102 4.5 39.7 1.0 NH2 B:ARG106 4.9 83.3 1.0

Iron binding site 3 out of 4 in the Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five 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 An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds. within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:62.6 occ:1.00 FE C:HEM201 0.0 62.6 1.0 ND C:HEM201 1.9 68.5 1.0 NA C:HEM201 2.0 67.9 1.0 SD C:MET7 2.1 56.1 1.0 NC C:HEM201 2.1 64.7 1.0 NB C:HEM201 2.1 61.9 1.0 NE2 C:HIS102 2.4 59.2 1.0 C4D C:HEM201 2.9 69.8 1.0 C1D C:HEM201 2.9 68.2 1.0 C1A C:HEM201 3.0 68.0 1.0 C4A C:HEM201 3.0 66.6 1.0 C4B C:HEM201 3.0 61.1 1.0 C1B C:HEM201 3.1 63.2 1.0 C4C C:HEM201 3.1 65.0 1.0 C1C C:HEM201 3.1 62.8 1.0 CE C:MET7 3.2 56.3 1.0 CD2 C:HIS102 3.3 58.7 1.0 CG C:MET7 3.4 60.0 1.0 CHA C:HEM201 3.4 69.3 1.0 CHD C:HEM201 3.4 66.5 1.0 CE1 C:HIS102 3.4 59.0 1.0 CHC C:HEM201 3.4 61.4 1.0 CHB C:HEM201 3.4 65.1 1.0 C3D C:HEM201 4.2 70.1 1.0 C2D C:HEM201 4.2 69.2 1.0 C2A C:HEM201 4.2 70.1 1.0 CB C:MET7 4.2 60.7 1.0 C3A C:HEM201 4.2 67.8 1.0 C2C C:HEM201 4.3 64.3 1.0 C2B C:HEM201 4.3 60.1 1.0 C3C C:HEM201 4.3 63.6 1.0 C3B C:HEM201 4.3 59.4 1.0 CG C:HIS102 4.5 58.9 1.0 ND1 C:HIS102 4.5 59.1 1.0 CA C:MET7 5.0 61.3 1.0

Iron binding site 4 out of 4 in the Crystal Structure of An Engineered Metal-Free RIDC1 Variant Containing Five 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 An Engineered Metal-Free RIDC1 Variant Containing Five Disulfide Bonds. within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:58.4 occ:1.00 FE D:HEM201 0.0 58.4 1.0 ND D:HEM201 1.9 64.5 1.0 NA D:HEM201 2.0 65.3 1.0 NC D:HEM201 2.1 61.6 1.0 NB D:HEM201 2.1 60.5 1.0 SD D:MET7 2.2 56.7 1.0 NE2 D:HIS102 2.4 50.6 1.0 C4D D:HEM201 2.9 65.9 1.0 C1D D:HEM201 2.9 65.4 1.0 C1A D:HEM201 3.0 66.2 1.0 C4A D:HEM201 3.0 65.7 1.0 C1B D:HEM201 3.1 61.4 1.0 C4B D:HEM201 3.1 60.3 1.0 C4C D:HEM201 3.1 62.0 1.0 C1C D:HEM201 3.1 59.7 1.0 CE1 D:HIS102 3.2 52.0 1.0 CG D:MET7 3.3 60.2 1.0 CHA D:HEM201 3.4 66.4 1.0 CE D:MET7 3.4 58.7 1.0 CHD D:HEM201 3.4 63.5 1.0 CHB D:HEM201 3.4 63.6 1.0 CD2 D:HIS102 3.5 52.1 1.0 CHC D:HEM201 3.5 60.3 1.0 CB D:MET7 4.1 61.0 1.0 C3D D:HEM201 4.2 67.2 1.0 C2D D:HEM201 4.2 66.1 1.0 C2A D:HEM201 4.2 69.4 1.0 C3A D:HEM201 4.2 68.7 1.0 C2B D:HEM201 4.3 60.9 1.0 C2C D:HEM201 4.3 59.3 1.0 C3C D:HEM201 4.3 60.8 1.0 C3B D:HEM201 4.4 60.7 1.0 ND1 D:HIS102 4.4 53.1 1.0 CG D:HIS102 4.5 54.1 1.0 CA D:MET7 4.9 62.8 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