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Calcium 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:

Cobalt (Co) 2 atoms
Iron (Fe) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4dje

Go back to Calcium Binding Sites List in 4dje
Calcium 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 Calcium with other atoms in the Ca 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
A:Ca301

b:30.0
occ:1.00
O A:GLY222 3.3 0.3 1.0
OD2 A:ASP224 3.4 71.9 1.0
OD1 A:ASP224 3.6 71.9 1.0
O A:HOH401 3.6 30.0 1.0
CA A:GLY222 3.8 0.3 1.0
CG A:ASP224 3.8 71.9 1.0
C A:GLY222 3.9 0.3 1.0
CE A:LYS184 4.0 0.8 1.0
CG A:LYS184 4.7 0.8 1.0
CD A:LYS184 4.8 0.8 1.0
NZ A:LYS184 4.9 0.8 1.0

Calcium binding site 2 out of 2 in 4dje

Go back to Calcium Binding Sites List in 4dje
Calcium 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 Calcium with other atoms in the Ca 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
B:Ca301

b:30.0
occ:1.00
O B:GLY222 3.3 91.4 1.0
O B:HOH402 3.3 30.0 1.0
OD2 B:ASP224 3.3 89.2 1.0
O B:HOH401 3.4 30.0 1.0
O B:PRO191 3.7 0.2 1.0
OD1 B:ASP224 3.8 89.2 1.0
CG B:ASP224 3.9 89.2 1.0
CB B:LYS184 4.0 0.5 1.0
C B:GLY222 4.2 91.4 1.0
CA B:GLY222 4.5 91.4 1.0
CB B:ALA190 4.6 0.6 1.0
CD B:LYS184 4.7 0.5 1.0
CA B:LYS184 4.7 0.4 1.0
C B:PRO191 4.8 0.2 1.0
CG B:LYS184 4.8 0.5 1.0
CG2 B:THR193 4.9 0.5 1.0
CA B:LYS192 4.9 0.8 1.0
OG1 B:THR193 5.0 0.5 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: Sat Jul 13 23:27:15 2024

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