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Cobalt in PDB 4dje: Crystal Structure of Folate-Bound Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr), Co-Crystallized with Folate

Protein crystallography data

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

Resolution Low / High (Å) 48.46 / 3.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 136.419, 250.664, 82.427, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 28.9

Other elements in 4dje:

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

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

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Folate-Bound Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr), Co-Crystallized with Folate (pdb code 4dje). 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-Bound Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr), Co-Crystallized with Folate, PDB code: 4dje:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 4dje

Go back to Cobalt Binding Sites List in 4dje
Cobalt binding site 1 out of 2 in the Crystal Structure of Folate-Bound Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr), Co-Crystallized with Folate


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-Bound Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr), Co-Crystallized with Folate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co502

b:0.0
occ:1.00
CO C:B12502 0.0 0.0 1.0
N23 C:B12502 1.9 0.0 1.0
N22 C:B12502 1.9 0.0 1.0
N21 C:B12502 1.9 0.0 1.0
N24 C:B12502 1.9 0.0 1.0
C11 C:B12502 2.9 0.0 1.0
C9 C:B12502 2.9 0.0 1.0
C19 C:B12502 2.9 0.0 1.0
C4 C:B12502 2.9 0.0 1.0
C16 C:B12502 2.9 0.0 1.0
C14 C:B12502 2.9 0.0 1.0
C6 C:B12502 2.9 0.0 1.0
C1 C:B12502 2.9 0.0 1.0
C10 C:B12502 3.2 0.0 1.0
C5 C:B12502 3.3 0.0 1.0
C15 C:B12502 3.4 0.0 1.0
C20 C:B12502 3.6 0.0 1.0
C13 C:B12502 4.1 0.0 1.0
C18 C:B12502 4.2 0.0 1.0
C17 C:B12502 4.2 0.0 1.0
C12 C:B12502 4.2 0.0 1.0
C8 C:B12502 4.2 0.0 1.0
C2 C:B12502 4.2 0.0 1.0
C3 C:B12502 4.2 0.0 1.0
C7 C:B12502 4.2 0.0 1.0
C26 C:B12502 4.6 0.0 1.0
OG1 C:THR375 4.6 0.4 1.0
C46 C:B12502 4.7 0.0 1.0
C48 C:B12502 4.7 0.0 1.0
CG2 C:THR375 4.7 0.4 1.0
C35 C:B12502 4.8 0.0 1.0
C37 C:B12502 4.8 0.0 1.0
CA C:THR375 4.9 0.5 1.0
C53 C:B12502 5.0 0.0 1.0

Cobalt binding site 2 out of 2 in 4dje

Go back to Cobalt Binding Sites List in 4dje
Cobalt binding site 2 out of 2 in the Crystal Structure of Folate-Bound Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr), Co-Crystallized with Folate


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-Bound Corrinoid Iron-Sulfur Protein (Cfesp) in Complex with Its Methyltransferase (Metr), Co-Crystallized with Folate 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
N23 E:B12502 1.9 0.8 1.0
N21 E:B12502 1.9 0.8 1.0
N22 E:B12502 1.9 0.8 1.0
N24 E:B12502 1.9 0.8 1.0
C9 E:B12502 2.8 0.8 1.0
C11 E:B12502 2.8 0.8 1.0
C16 E:B12502 2.9 0.8 1.0
C4 E:B12502 2.9 0.8 1.0
C19 E:B12502 2.9 0.8 1.0
C1 E:B12502 2.9 0.8 1.0
C14 E:B12502 2.9 0.8 1.0
C6 E:B12502 3.0 0.8 1.0
C10 E:B12502 3.1 0.8 1.0
C5 E:B12502 3.3 0.8 1.0
C15 E:B12502 3.4 0.8 1.0
C20 E:B12502 3.6 0.8 1.0
OG1 E:THR375 4.1 0.3 1.0
C13 E:B12502 4.2 0.8 1.0
C8 E:B12502 4.2 0.8 1.0
C17 E:B12502 4.2 0.8 1.0
C3 E:B12502 4.2 0.8 1.0
C2 E:B12502 4.2 0.8 1.0
C12 E:B12502 4.2 0.8 1.0
C18 E:B12502 4.2 0.8 1.0
C7 E:B12502 4.3 0.8 1.0
C26 E:B12502 4.6 0.8 1.0
C54 E:B12502 4.7 0.8 1.0
C48 E:B12502 4.7 0.8 1.0
C35 E:B12502 4.8 0.8 1.0
C41 E:B12502 4.9 0.8 1.0
C53 E:B12502 4.9 0.8 1.0
C46 E:B12502 5.0 0.8 1.0

Reference:

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
Page generated: Sun Dec 13 10:44:04 2020

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