Cobalt in PDB 4djd: Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr)

The structure of Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr), PDB code: 4djd was solved by Y.Kung, T.I.Doukov, L.C.Blasiak, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.83 / 2.38
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	125.614, 242.843, 79.665, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.9

The structure of Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr) also contains other interesting chemical elements:

Iron	(Fe)	8 atoms
Calcium	(Ca)	2 atoms

The binding sites of Cobalt atom in the Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr) (pdb code 4djd). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr), PDB code: 4djd:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr) within 5.0Å range: probe atom residue distance (Å) B Occ C:Co502 b:91.2 occ:1.00 CO C:B12502 0.0 91.2 1.0 N21 C:B12502 1.9 0.1 1.0 N22 C:B12502 1.9 0.4 1.0 N24 C:B12502 1.9 65.5 1.0 N23 C:B12502 1.9 96.5 1.0 C9 C:B12502 2.8 98.0 1.0 C4 C:B12502 2.9 0.5 1.0 C19 C:B12502 2.9 57.9 1.0 C1 C:B12502 2.9 0.2 1.0 C11 C:B12502 2.9 97.0 1.0 C16 C:B12502 3.0 76.2 1.0 C6 C:B12502 3.0 0.2 1.0 C14 C:B12502 3.0 87.8 1.0 C10 C:B12502 3.2 96.2 1.0 OG1 C:THR375 3.3 87.4 1.0 C5 C:B12502 3.4 0.5 1.0 C20 C:B12502 3.4 0.2 1.0 C15 C:B12502 3.4 79.6 1.0 C18 C:B12502 4.1 79.8 1.0 C8 C:B12502 4.2 96.0 1.0 C2 C:B12502 4.2 0.0 1.0 C3 C:B12502 4.2 0.5 1.0 C17 C:B12502 4.3 77.4 1.0 C13 C:B12502 4.3 90.5 1.0 C12 C:B12502 4.3 91.3 1.0 CB C:THR375 4.3 93.8 1.0 C7 C:B12502 4.3 0.0 1.0 CG2 C:THR375 4.3 92.3 1.0 C26 C:B12502 4.6 0.7 1.0 C46 C:B12502 4.8 60.6 1.0 CA C:THR375 4.8 0.5 1.0 C35 C:B12502 4.9 73.7 1.0 C48 C:B12502 4.9 76.2 1.0 C41 C:B12502 5.0 97.0 1.0 C53 C:B12502 5.0 80.2 1.0 C37 C:B12502 5.0 0.7 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Folate-Free Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr) within 5.0Å range: probe atom residue distance (Å) B Occ E:Co502 b:0.8 occ:1.00 CO E:B12502 0.0 0.8 1.0 N21 E:B12502 1.9 0.3 1.0 N22 E:B12502 1.9 0.9 1.0 N24 E:B12502 1.9 0.9 1.0 N23 E:B12502 1.9 0.7 1.0 C9 E:B12502 2.8 0.3 1.0 C19 E:B12502 2.9 0.3 1.0 C4 E:B12502 2.9 0.8 1.0 C1 E:B12502 2.9 0.1 1.0 C11 E:B12502 2.9 0.1 1.0 C16 E:B12502 3.0 0.1 1.0 C6 E:B12502 3.0 0.8 1.0 C14 E:B12502 3.0 0.3 1.0 C10 E:B12502 3.2 1.0 1.0 C5 E:B12502 3.4 0.7 1.0 C20 E:B12502 3.4 0.5 1.0 C15 E:B12502 3.4 0.1 1.0 OG1 E:THR375 3.7 0.1 1.0 C18 E:B12502 4.1 0.9 1.0 C8 E:B12502 4.2 0.6 1.0 C2 E:B12502 4.2 0.2 1.0 C3 E:B12502 4.2 0.7 1.0 C17 E:B12502 4.3 0.8 1.0 C13 E:B12502 4.3 0.7 1.0 C12 E:B12502 4.3 0.1 1.0 C7 E:B12502 4.3 0.6 1.0 CG2 E:THR375 4.3 0.2 1.0 CB E:THR375 4.5 0.3 1.0 C26 E:B12502 4.6 0.4 1.0 CA E:THR375 4.7 0.3 1.0 C46 E:B12502 4.8 0.5 1.0 C35 E:B12502 4.9 0.1 1.0 C48 E:B12502 4.9 81.8 1.0 C41 E:B12502 5.0 0.3 1.0 C53 E:B12502 5.0 0.9 1.0 C37 E:B12502 5.0 0.2 1.0

Y.Kung, N.Ando, T.I.Doukov, L.C.Blasiak, G.Bender, J.Seravalli, S.W.Ragsdale, C.L.Drennan. Visualizing Molecular Juggling Within A B12-Dependent Methyltransferase Complex. Nature V. 484 265 2012.
ISSN: ISSN 0028-0836
PubMed: 22419154
DOI: 10.1038/NATURE10916