Iron in PDB 2ycl: Complete Structure of the Corrinoid,Iron-Sulfur Protein Including the N-Terminal Domain with A 4FE-4S Cluster

The structure of Complete Structure of the Corrinoid,Iron-Sulfur Protein Including the N-Terminal Domain with A 4FE-4S Cluster, PDB code: 2ycl was solved by S.Goetzl, J.H.Jeoung, S.E.Hennig, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.745 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	172.219, 43.476, 101.855, 90.00, 119.39, 90.00
R / Rfree (%)	19.15 / 25.14

The structure of Complete Structure of the Corrinoid,Iron-Sulfur Protein Including the N-Terminal Domain with A 4FE-4S Cluster also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Iron atom in the Complete Structure of the Corrinoid,Iron-Sulfur Protein Including the N-Terminal Domain with A 4FE-4S Cluster (pdb code 2ycl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Complete Structure of the Corrinoid,Iron-Sulfur Protein Including the N-Terminal Domain with A 4FE-4S Cluster, PDB code: 2ycl:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Complete Structure of the Corrinoid,Iron-Sulfur Protein Including the N-Terminal Domain with 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 Complete Structure of the Corrinoid,Iron-Sulfur Protein Including the N-Terminal Domain with A 4FE-4S Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1443 b:37.7 occ:0.99 FE1 A:SF41443 0.0 37.7 1.0 S4 A:SF41443 2.2 42.5 1.0 S2 A:SF41443 2.2 39.0 1.0 S3 A:SF41443 2.4 33.7 1.0 SG A:CYS20 2.5 44.3 1.0 FE3 A:SF41443 2.5 43.6 1.0 FE2 A:SF41443 2.6 32.1 1.0 FE4 A:SF41443 2.9 34.9 1.0 CB A:CYS20 3.3 44.3 1.0 S1 A:SF41443 3.9 35.2 1.0 N A:CYS20 4.1 50.7 1.0 CB A:PHE28 4.1 44.5 1.0 CG A:PHE28 4.2 49.4 1.0 CA A:CYS20 4.4 50.3 1.0 CD1 A:PHE28 4.5 49.2 1.0 CD2 A:PHE28 4.6 43.2 1.0 CB A:CYS42 4.6 30.4 1.0 N A:LYS18 4.6 58.2 1.0 N A:GLU19 4.7 60.6 1.0 SG A:CYS42 4.8 32.6 1.0 CA A:CYS25 4.8 36.7 1.0 CA A:LYS18 4.9 57.9 1.0 SG A:CYS25 4.9 31.4 1.0 C A:LYS18 4.9 60.1 1.0

Iron binding site 2 out of 4 in the Complete Structure of the Corrinoid,Iron-Sulfur Protein Including the N-Terminal Domain with 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 Complete Structure of the Corrinoid,Iron-Sulfur Protein Including the N-Terminal Domain with A 4FE-4S Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1443 b:32.1 occ:0.99 FE2 A:SF41443 0.0 32.1 1.0 S3 A:SF41443 2.3 33.7 1.0 S1 A:SF41443 2.3 35.2 1.0 S4 A:SF41443 2.3 42.5 1.0 SG A:CYS25 2.4 31.4 1.0 FE3 A:SF41443 2.6 43.6 1.0 FE1 A:SF41443 2.6 37.7 1.0 FE4 A:SF41443 2.8 34.9 1.0 CB A:CYS25 3.6 40.5 1.0 CA A:CYS25 3.7 36.7 1.0 S2 A:SF41443 3.7 39.0 1.0 N A:ASN16 4.0 42.7 1.0 N A:CYS25 4.1 41.8 1.0 N A:LYS15 4.4 41.9 1.0 CA A:ASN16 4.4 45.7 1.0 N A:CYS17 4.6 50.6 1.0 N A:LYS14 4.7 34.7 1.0 SG A:CYS42 4.8 32.6 1.0 C A:THR24 4.9 45.7 1.0 C A:LYS15 4.9 46.8 1.0

Iron binding site 3 out of 4 in the Complete Structure of the Corrinoid,Iron-Sulfur Protein Including the N-Terminal Domain with 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 Complete Structure of the Corrinoid,Iron-Sulfur Protein Including the N-Terminal Domain with A 4FE-4S Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1443 b:43.6 occ:0.99 FE3 A:SF41443 0.0 43.6 1.0 S2 A:SF41443 2.2 39.0 1.0 S4 A:SF41443 2.2 42.5 1.0 S1 A:SF41443 2.4 35.2 1.0 FE1 A:SF41443 2.5 37.7 1.0 FE2 A:SF41443 2.6 32.1 1.0 SG A:CYS17 2.7 55.6 1.0 FE4 A:SF41443 2.8 34.9 1.0 N A:CYS17 3.4 50.6 1.0 N A:LYS18 3.7 58.2 1.0 S3 A:SF41443 3.8 33.7 1.0 CB A:CYS17 3.9 54.3 1.0 CA A:CYS17 4.0 53.4 1.0 C A:CYS17 4.1 63.7 1.0 N A:GLU19 4.1 60.6 1.0 N A:ASN16 4.4 42.7 1.0 C A:ASN16 4.4 48.2 1.0 CA A:LYS18 4.6 57.9 1.0 CA A:ASN16 4.6 45.7 1.0 CB A:LYS15 4.6 40.0 1.0 SG A:CYS20 4.7 44.3 1.0 C A:LYS18 4.7 60.1 1.0 CD2 A:TYR44 4.7 49.3 1.0 SG A:CYS25 4.8 31.4 1.0 N A:CYS20 4.8 50.7 1.0 CB A:GLU19 4.9 57.9 1.0 C A:LYS15 5.0 46.8 1.0 CA A:GLU19 5.0 55.3 1.0 O A:CYS17 5.0 62.4 1.0 SG A:CYS42 5.0 32.6 1.0

Iron binding site 4 out of 4 in the Complete Structure of the Corrinoid,Iron-Sulfur Protein Including the N-Terminal Domain with 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 Complete Structure of the Corrinoid,Iron-Sulfur Protein Including the N-Terminal Domain with A 4FE-4S Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1443 b:34.9 occ:0.99 FE4 A:SF41443 0.0 34.9 1.0 S2 A:SF41443 2.2 39.0 1.0 SG A:CYS42 2.3 32.6 1.0 S3 A:SF41443 2.3 33.7 1.0 S1 A:SF41443 2.4 35.2 1.0 FE2 A:SF41443 2.8 32.1 1.0 FE3 A:SF41443 2.8 43.6 1.0 FE1 A:SF41443 2.9 37.7 1.0 CB A:CYS42 3.1 30.4 1.0 CA A:CYS42 3.9 33.8 1.0 S4 A:SF41443 4.1 42.5 1.0 CG A:PRO13 4.2 37.7 1.0 CD A:PRO13 4.3 35.5 1.0 CD2 A:TYR44 4.5 49.3 1.0 C A:CYS42 4.5 41.4 1.0 CD A:PRO43 4.6 43.9 1.0 CB A:PRO13 4.7 35.6 1.0 N A:PRO43 4.8 39.8 1.0 N A:TYR44 4.9 46.9 1.0 SG A:CYS17 4.9 55.6 1.0 SG A:CYS25 4.9 31.4 1.0 CB A:TYR44 4.9 47.6 1.0 CB A:CYS20 5.0 44.3 1.0

S.Goetzl, J.H.Jeoung, S.E.Hennig, H.Dobbek. Structural Basis For Electron and Methyl-Group Transfer in A Methyltransferase System Operating in the Reductive Acetyl-Coa Pathway J.Mol.Biol. V. 411 96 2011.
ISSN: ISSN 0022-2836
PubMed: 21640123
DOI: 10.1016/J.JMB.2011.05.025