Calcium in PDB 2d0p: Strcuture of Diol Dehydratase-Reactivating Factor in Nucleotide Free Form

The structure of Strcuture of Diol Dehydratase-Reactivating Factor in Nucleotide Free Form, PDB code: 2d0p was solved by N.Shibata, K.Mori, N.Hieda, Y.Higuchi, M.Yamanishi, T.Toraya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.58 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.920, 85.370, 296.990, 90.00, 90.00, 90.00
R / Rfree (%)	23.8 / 31.3

The binding sites of Calcium atom in the Strcuture of Diol Dehydratase-Reactivating Factor in Nucleotide Free Form (pdb code 2d0p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Strcuture of Diol Dehydratase-Reactivating Factor in Nucleotide Free Form, PDB code: 2d0p:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Strcuture of Diol Dehydratase-Reactivating Factor in Nucleotide Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Strcuture of Diol Dehydratase-Reactivating Factor in Nucleotide Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:66.8 occ:1.00 OG1 A:THR105 2.1 85.9 1.0 OE1 B:GLU31 2.2 56.2 1.0 OD2 A:ASP166 2.4 87.2 1.0 OD1 A:ASP183 2.5 71.9 1.0 O A:THR105 2.5 68.3 1.0 OD2 A:ASP183 2.7 57.4 1.0 CB A:THR105 2.8 74.8 1.0 CG A:ASP183 2.8 71.3 1.0 C A:THR105 3.2 65.1 1.0 CD B:GLU31 3.3 58.4 1.0 OE2 A:GLU184 3.4 91.1 1.0 CA A:THR105 3.5 71.7 1.0 CG A:ASP166 3.5 84.8 1.0 CG B:GLU31 4.0 45.5 1.0 N A:THR105 4.1 68.5 1.0 CG2 A:THR105 4.1 59.7 1.0 OD1 A:ASP166 4.1 89.0 1.0 CB A:ASP183 4.2 65.4 1.0 CG2 A:VAL169 4.2 66.6 1.0 N A:PRO106 4.2 52.6 1.0 N A:GLY168 4.3 70.1 1.0 C A:ASP166 4.3 76.9 1.0 CA A:ASP166 4.4 79.5 1.0 OE2 B:GLU31 4.4 53.2 1.0 O A:ASP166 4.4 66.2 1.0 CB A:ASP166 4.4 79.1 1.0 N A:VAL169 4.5 68.1 1.0 CD A:GLU184 4.5 88.2 1.0 CA A:GLY168 4.7 72.2 1.0 CA A:PRO106 4.8 40.1 1.0 N A:ASP167 4.8 80.0 1.0

Calcium binding site 2 out of 2 in the Strcuture of Diol Dehydratase-Reactivating Factor in Nucleotide Free Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Strcuture of Diol Dehydratase-Reactivating Factor in Nucleotide Free Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1006 b:72.2 occ:1.00 OD1 C:ASP183 2.0 81.0 1.0 OD2 C:ASP166 2.3 78.8 1.0 OE1 D:GLU31 2.3 51.9 1.0 O C:THR105 2.5 70.9 1.0 OG1 C:THR105 2.5 83.8 1.0 CB C:THR105 2.6 74.6 1.0 CG C:ASP183 2.9 75.1 1.0 C C:THR105 3.0 67.3 1.0 OD2 C:ASP183 3.1 75.8 1.0 CA C:THR105 3.2 72.8 1.0 OE2 C:GLU184 3.4 84.9 1.0 CG C:ASP166 3.5 73.1 1.0 CD D:GLU31 3.5 70.6 1.0 N C:THR105 3.8 66.0 1.0 CG2 C:THR105 3.9 48.7 1.0 N C:PRO106 4.1 52.6 1.0 OD1 C:ASP166 4.2 75.7 1.0 CG D:GLU31 4.2 65.2 1.0 CD C:GLU184 4.3 83.2 1.0 CB C:ASP183 4.3 64.0 1.0 CG C:GLU184 4.3 85.5 1.0 CA C:ASP166 4.5 80.5 1.0 C C:ASP166 4.5 78.5 1.0 OE2 D:GLU31 4.5 60.7 1.0 CB C:ASP166 4.5 75.6 1.0 N C:GLY168 4.6 71.6 1.0 O C:ASP166 4.6 69.8 1.0 CA C:PRO106 4.7 45.9 1.0 CG2 C:VAL169 4.7 68.8 1.0 N C:VAL169 4.7 70.2 1.0 CA C:GLY168 4.9 73.1 1.0

N.Shibata, K.Mori, N.Hieda, Y.Higuchi, M.Yamanishi, T.Toraya. Release of A Damaged Cofactor From A Coenzyme B12-Dependent Enzyme: X-Ray Structures of Diol Dehydratase-Reactivating Factor Structure V. 13 1745 2005.
ISSN: ISSN 0969-2126
PubMed: 16338403
DOI: 10.1016/J.STR.2005.08.011