Iron in PDB 5dii: Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster

The structure of Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster, PDB code: 5dii was solved by M.Sutter, C.Aussignargues, A.Turmo, C.A.Kerfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.63 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.897, 55.558, 117.930, 83.45, 81.22, 86.95
R / Rfree (%)	18.8 / 21.8

The binding sites of Iron atom in the Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster (pdb code 5dii). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster, PDB code: 5dii:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:24.2 occ:0.74 FE1 A:SF4301 0.0 24.2 0.7 S4 A:SF4301 2.2 29.8 0.7 S2 A:SF4301 2.2 29.1 0.7 S3 A:SF4301 2.2 32.4 0.7 SG A:CYS55 2.3 27.6 1.0 HB3 A:CYS55 2.3 31.5 1.0 CB A:CYS55 2.7 26.3 1.0 FE3 A:SF4301 2.8 23.3 0.7 FE2 A:SF4301 2.8 24.2 0.7 FE4 A:SF4301 2.9 36.1 0.7 HA A:CYS55 3.3 39.5 1.0 H A:GLY155 3.5 31.8 1.0 HB2 A:CYS55 3.5 31.5 1.0 CA A:CYS55 3.6 32.9 1.0 HA2 C:GLY155 3.8 41.9 1.0 S1 A:SF4301 3.8 29.2 0.7 H A:SER56 3.8 42.2 1.0 HA2 A:GLY155 3.9 35.3 1.0 H A:ALA157 4.0 31.6 1.0 N A:GLY155 4.2 26.5 1.0 HA A:ALA157 4.4 34.2 1.0 N A:SER56 4.4 35.1 1.0 CA A:GLY155 4.5 29.4 1.0 C A:CYS55 4.5 33.8 1.0 CA C:GLY155 4.6 35.0 1.0 H A:CYS55 4.6 26.9 1.0 N A:CYS55 4.7 22.4 1.0 O C:GLY155 4.7 31.4 1.0 H C:ALA157 4.8 36.1 1.0 SG B:CYS55 4.8 28.4 1.0 N A:ALA157 4.8 26.3 1.0 O B:HOH381 4.8 40.0 1.0 C C:GLY155 4.8 30.1 1.0 SG C:CYS55 4.8 28.7 1.0 HB3 C:CYS55 4.8 32.1 1.0 H C:GLY155 4.9 34.2 1.0 HA A:ILE154 4.9 32.1 1.0 HB3 B:CYS55 4.9 33.8 1.0 C A:GLY155 5.0 30.9 1.0 O C:HOH327 5.0 36.1 1.0

Iron binding site 2 out of 8 in the Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:24.2 occ:0.74 FE2 A:SF4301 0.0 24.2 0.7 S4 A:SF4301 2.1 29.8 0.7 S3 A:SF4301 2.2 32.4 0.7 S1 A:SF4301 2.2 29.2 0.7 SG B:CYS55 2.3 28.4 1.0 HB3 B:CYS55 2.3 33.8 1.0 CB B:CYS55 2.8 28.1 1.0 FE3 A:SF4301 2.8 23.3 0.7 FE1 A:SF4301 2.8 24.2 0.7 FE4 A:SF4301 2.9 36.1 0.7 H B:GLY155 3.4 32.5 1.0 HA B:CYS55 3.4 39.4 1.0 HB2 B:CYS55 3.5 33.8 1.0 CA B:CYS55 3.7 32.9 1.0 HA2 B:GLY155 3.7 33.6 1.0 S2 A:SF4301 3.8 29.1 0.7 HA2 A:GLY155 3.8 35.3 1.0 H B:SER56 3.9 42.7 1.0 H B:ALA157 4.0 29.8 1.0 N B:GLY155 4.2 27.1 1.0 HA B:ALA157 4.2 28.7 1.0 CA B:GLY155 4.3 28.0 1.0 N B:SER56 4.5 35.6 1.0 C B:CYS55 4.6 27.1 1.0 O B:HOH381 4.6 40.0 1.0 CA A:GLY155 4.6 29.4 1.0 HB3 A:CYS55 4.7 31.5 1.0 O A:GLY155 4.7 31.1 1.0 H A:ALA157 4.7 31.6 1.0 H B:CYS55 4.7 33.3 1.0 N B:CYS55 4.7 27.7 1.0 N B:ALA157 4.8 24.8 1.0 C A:GLY155 4.8 30.9 1.0 SG A:CYS55 4.8 27.6 1.0 SG C:CYS55 4.8 28.7 1.0 H A:GLY155 4.8 31.8 1.0 C B:GLY155 4.9 28.7 1.0 HA B:ILE154 4.9 38.9 1.0 CA B:ALA157 5.0 23.9 1.0

Iron binding site 3 out of 8 in the Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:23.3 occ:0.74 FE3 A:SF4301 0.0 23.3 0.7 S4 A:SF4301 2.2 29.8 0.7 S1 A:SF4301 2.2 29.2 0.7 S2 A:SF4301 2.2 29.1 0.7 SG C:CYS55 2.3 28.7 1.0 HB3 C:CYS55 2.4 32.1 1.0 FE2 A:SF4301 2.8 24.2 0.7 FE1 A:SF4301 2.8 24.2 0.7 CB C:CYS55 2.8 26.7 1.0 FE4 A:SF4301 2.9 36.1 0.7 HA C:CYS55 3.5 30.6 1.0 H C:GLY155 3.5 34.2 1.0 HB2 C:CYS55 3.6 32.1 1.0 HA2 B:GLY155 3.6 33.6 1.0 S3 A:SF4301 3.8 32.4 0.7 CA C:CYS55 3.8 25.5 1.0 HA2 C:GLY155 3.9 41.9 1.0 H C:ALA157 4.0 36.1 1.0 H C:SER56 4.0 36.8 1.0 HA C:ALA157 4.2 37.1 1.0 N C:GLY155 4.2 28.5 1.0 CA C:GLY155 4.5 35.0 1.0 CA B:GLY155 4.5 28.0 1.0 N C:SER56 4.6 30.6 1.0 O B:GLY155 4.7 25.5 1.0 C C:CYS55 4.7 22.9 1.0 C B:GLY155 4.7 28.7 1.0 HB3 B:CYS55 4.7 33.8 1.0 N C:ALA157 4.7 30.1 1.0 H B:ALA157 4.7 29.8 1.0 SG B:CYS55 4.8 28.4 1.0 H C:CYS55 4.8 31.1 1.0 O B:HOH381 4.8 40.0 1.0 N C:CYS55 4.8 25.9 1.0 O B:HOH333 4.8 34.7 1.0 SG A:CYS55 4.8 27.6 1.0 H B:GLY155 4.8 32.5 1.0 C C:GLY155 4.9 30.1 1.0 HA C:ILE154 4.9 36.0 1.0 HB3 A:CYS55 4.9 31.5 1.0 CA C:ALA157 5.0 30.9 1.0

Iron binding site 4 out of 8 in the Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:36.1 occ:0.74 FE4 A:SF4301 0.0 36.1 0.7 O B:HOH381 2.1 40.0 1.0 S3 A:SF4301 2.2 32.4 0.7 S2 A:SF4301 2.2 29.1 0.7 S1 A:SF4301 2.2 29.2 0.7 FE3 A:SF4301 2.9 23.3 0.7 FE2 A:SF4301 2.9 24.2 0.7 FE1 A:SF4301 2.9 24.2 0.7 S4 A:SF4301 3.8 29.8 0.7 HB3 A:CYS55 3.9 31.5 1.0 HB3 B:CYS55 3.9 33.8 1.0 HB3 C:CYS55 4.0 32.1 1.0 H A:SER56 4.0 42.2 1.0 HA A:ALA157 4.0 34.2 1.0 HA C:ALA157 4.0 37.1 1.0 HA B:ALA157 4.1 28.7 1.0 H B:SER56 4.2 42.7 1.0 H C:SER56 4.2 36.8 1.0 HB2 B:ALA157 4.3 31.9 1.0 HB2 C:ALA157 4.4 35.3 1.0 HB2 A:ALA157 4.4 35.2 1.0 H A:ALA157 4.5 31.6 1.0 H B:ALA157 4.6 29.8 1.0 H C:ALA157 4.6 36.1 1.0 N A:SER56 4.7 35.1 1.0 HA A:SER56 4.7 39.6 1.0 CB A:CYS55 4.7 26.3 1.0 CB B:CYS55 4.8 28.1 1.0 CA A:ALA157 4.8 28.5 1.0 CB C:CYS55 4.8 26.7 1.0 CA C:ALA157 4.8 30.9 1.0 CA B:ALA157 4.8 23.9 1.0 HA B:SER56 4.9 39.3 1.0 N B:SER56 4.9 35.6 1.0 HA A:CYS55 4.9 39.5 1.0 N C:SER56 4.9 30.6 1.0 CB B:ALA157 4.9 26.6 1.0 HA C:SER56 5.0 40.2 1.0 CB C:ALA157 5.0 29.4 1.0 CB A:ALA157 5.0 29.4 1.0

Iron binding site 5 out of 8 in the Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:23.1 occ:0.72 FE1 D:SF4301 0.0 23.1 0.7 S4 D:SF4301 2.2 29.2 0.7 S2 D:SF4301 2.2 30.9 0.7 S3 D:SF4301 2.2 28.0 0.7 SG E:CYS55 2.3 26.5 1.0 HB3 E:CYS55 2.4 35.3 1.0 CB E:CYS55 2.8 29.4 1.0 FE2 D:SF4301 2.9 23.1 0.7 FE3 D:SF4301 2.9 22.6 0.7 FE4 D:SF4301 2.9 34.0 0.7 HA E:CYS55 3.4 35.7 1.0 H E:GLY155 3.4 32.9 1.0 HB2 E:CYS55 3.5 35.3 1.0 HA2 D:GLY155 3.7 32.3 1.0 CA E:CYS55 3.7 29.7 1.0 HA2 E:GLY155 3.8 32.5 1.0 S1 D:SF4301 3.8 26.0 0.7 H E:SER56 3.9 43.8 1.0 H E:ALA157 4.0 29.5 1.0 N E:GLY155 4.2 27.4 1.0 HA E:ALA157 4.2 29.8 1.0 CA E:GLY155 4.4 27.1 1.0 N E:SER56 4.5 36.5 1.0 CA D:GLY155 4.5 26.9 1.0 C E:CYS55 4.6 25.7 1.0 O D:GLY155 4.7 32.2 1.0 H E:CYS55 4.7 29.6 1.0 H D:ALA157 4.7 25.7 1.0 N E:CYS55 4.7 24.7 1.0 C D:GLY155 4.7 30.7 1.0 N E:ALA157 4.7 24.6 1.0 O F:HOH368 4.8 51.3 1.0 SG D:CYS55 4.8 26.1 1.0 SG F:CYS55 4.8 25.9 1.0 H D:GLY155 4.8 32.1 1.0 HB3 D:CYS55 4.8 34.5 1.0 C E:GLY155 4.9 27.4 1.0 HB3 F:CYS55 4.9 32.2 1.0 HA E:ILE154 4.9 37.2 1.0 CA E:ALA157 5.0 24.8 1.0

Iron binding site 6 out of 8 in the Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:23.1 occ:0.72 FE2 D:SF4301 0.0 23.1 0.7 S4 D:SF4301 2.2 29.2 0.7 S3 D:SF4301 2.2 28.0 0.7 S1 D:SF4301 2.2 26.0 0.7 SG F:CYS55 2.3 25.9 1.0 HB3 F:CYS55 2.3 32.2 1.0 CB F:CYS55 2.7 26.8 1.0 FE3 D:SF4301 2.8 22.6 0.7 FE1 D:SF4301 2.9 23.1 0.7 FE4 D:SF4301 2.9 34.0 0.7 HA F:CYS55 3.4 29.5 1.0 H F:GLY155 3.5 30.5 1.0 HB2 F:CYS55 3.5 32.2 1.0 HA2 E:GLY155 3.7 32.5 1.0 CA F:CYS55 3.7 24.6 1.0 S2 D:SF4301 3.8 30.9 0.7 H F:SER56 3.8 31.6 1.0 HA2 F:GLY155 3.9 35.9 1.0 H F:ALA157 4.0 29.4 1.0 N F:GLY155 4.2 25.4 1.0 HA F:ALA157 4.3 31.5 1.0 N F:SER56 4.4 26.3 1.0 O F:HOH368 4.4 51.3 1.0 CA F:GLY155 4.5 29.9 1.0 C F:CYS55 4.5 20.0 1.0 CA E:GLY155 4.6 27.1 1.0 O E:GLY155 4.7 22.8 1.0 H F:CYS55 4.7 29.0 1.0 H E:ALA157 4.7 29.5 1.0 SG D:CYS55 4.7 26.1 1.0 N F:CYS55 4.7 24.2 1.0 C E:GLY155 4.7 27.4 1.0 N F:ALA157 4.8 24.5 1.0 HA F:ILE154 4.8 32.6 1.0 SG E:CYS55 4.8 26.5 1.0 HB3 E:CYS55 4.8 35.3 1.0 H E:GLY155 4.8 32.9 1.0 C F:GLY155 4.9 27.5 1.0

Iron binding site 7 out of 8 in the Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:22.6 occ:0.72 FE3 D:SF4301 0.0 22.6 0.7 S4 D:SF4301 2.1 29.2 0.7 S1 D:SF4301 2.2 26.0 0.7 S2 D:SF4301 2.2 30.9 0.7 SG D:CYS55 2.3 26.1 1.0 HB3 D:CYS55 2.4 34.5 1.0 FE2 D:SF4301 2.8 23.1 0.7 FE4 D:SF4301 2.8 34.0 0.7 CB D:CYS55 2.8 28.7 1.0 FE1 D:SF4301 2.9 23.1 0.7 HA D:CYS55 3.4 35.7 1.0 H D:GLY155 3.4 32.1 1.0 HB2 D:CYS55 3.6 34.5 1.0 CA D:CYS55 3.7 29.8 1.0 S3 D:SF4301 3.8 28.0 0.7 HA2 D:GLY155 3.8 32.3 1.0 HA2 F:GLY155 3.8 35.9 1.0 H D:SER56 3.9 36.7 1.0 H D:ALA157 3.9 25.7 1.0 N D:GLY155 4.2 26.8 1.0 HA D:ALA157 4.2 27.1 1.0 CA D:GLY155 4.4 26.9 1.0 N D:SER56 4.5 30.6 1.0 C D:CYS55 4.6 25.0 1.0 CA F:GLY155 4.7 29.9 1.0 H F:ALA157 4.7 29.4 1.0 HB3 F:CYS55 4.7 32.2 1.0 N D:ALA157 4.7 21.4 1.0 H D:CYS55 4.7 27.7 1.0 N D:CYS55 4.7 23.1 1.0 O F:GLY155 4.8 26.3 1.0 O F:HOH368 4.8 51.3 1.0 SG F:CYS55 4.8 25.9 1.0 C F:GLY155 4.8 27.5 1.0 SG E:CYS55 4.8 26.5 1.0 O F:HOH325 4.8 35.7 1.0 H F:GLY155 4.9 30.5 1.0 C D:GLY155 4.9 30.7 1.0 HA D:ILE154 4.9 33.5 1.0 CA D:ALA157 5.0 22.6 1.0 HB3 E:CYS55 5.0 35.3 1.0

Iron binding site 8 out of 8 in the Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of An Engineered Bacterial Microcompartment Shell Protein Binding A [4FE-4S] Cluster within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:34.0 occ:0.72 FE4 D:SF4301 0.0 34.0 0.7 O F:HOH368 2.1 51.3 1.0 S2 D:SF4301 2.2 30.9 0.7 S3 D:SF4301 2.2 28.0 0.7 S1 D:SF4301 2.2 26.0 0.7 FE3 D:SF4301 2.8 22.6 0.7 FE1 D:SF4301 2.9 23.1 0.7 FE2 D:SF4301 2.9 23.1 0.7 S4 D:SF4301 3.8 29.2 0.7 HB3 F:CYS55 3.9 32.2 1.0 HB3 D:CYS55 4.0 34.5 1.0 HB3 E:CYS55 4.0 35.3 1.0 HA F:ALA157 4.0 31.5 1.0 HA D:ALA157 4.0 27.1 1.0 HA E:ALA157 4.1 29.8 1.0 H F:SER56 4.1 31.6 1.0 H D:SER56 4.1 36.7 1.0 H E:SER56 4.2 43.8 1.0 HB2 D:ALA157 4.3 30.0 1.0 HB2 E:ALA157 4.3 28.2 1.0 HB2 F:ALA157 4.4 26.5 1.0 H D:ALA157 4.6 25.7 1.0 HA F:SER56 4.6 31.9 1.0 H E:ALA157 4.6 29.5 1.0 H F:ALA157 4.6 29.4 1.0 N F:SER56 4.7 26.3 1.0 CB F:CYS55 4.8 26.8 1.0 CB D:CYS55 4.8 28.7 1.0 CA F:ALA157 4.8 26.2 1.0 CA D:ALA157 4.8 22.6 1.0 N D:SER56 4.8 30.6 1.0 CB E:CYS55 4.8 29.4 1.0 CA E:ALA157 4.8 24.8 1.0 HA D:SER56 4.8 36.1 1.0 N E:SER56 4.9 36.5 1.0 HA E:SER56 4.9 39.1 1.0 CB D:ALA157 4.9 25.0 1.0 HA D:CYS55 5.0 35.7 1.0 CB F:ALA157 5.0 22.1 1.0 CB E:ALA157 5.0 23.5 1.0 SG D:CYS55 5.0 26.1 1.0

C.Aussignargues, M.E.Pandelia, M.Sutter, J.S.Plegaria, J.Zarzycki, A.Turmo, J.Huang, D.C.Ducat, E.L.Hegg, B.R.Gibney, C.A.Kerfeld. Structure and Function of A Bacterial Microcompartment Shell Protein Engineered to Bind A [4FE-4S] Cluster. J.Am.Chem.Soc. V. 138 5262 2016.
ISSN: ESSN 1520-5126
PubMed: 26704697
DOI: 10.1021/JACS.5B11734