Calcium in PDB 2aoq: Crystal Structure of Muth-Unmethylated Dna Complex

The structure of Crystal Structure of Muth-Unmethylated Dna Complex, PDB code: 2aoq was solved by J.Y.Lee, J.Chang, N.Joseph, R.Ghirlando, D.N.Rao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.85 / 2.20
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	114.624, 114.624, 46.755, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 22

The binding sites of Calcium atom in the Crystal Structure of Muth-Unmethylated Dna Complex (pdb code 2aoq). 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 Muth-Unmethylated Dna Complex, PDB code: 2aoq:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Muth-Unmethylated Dna Complex


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 Muth-Unmethylated Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca232 b:46.0 occ:1.00 O A:HOH259 2.3 46.8 1.0 OD1 A:ASP70 2.3 42.3 1.0 OE2 A:GLU56 2.3 36.8 1.0 O A:HOH258 2.4 46.6 1.0 OP1 C:DG5 2.5 36.3 1.0 O A:THR62 2.9 66.7 1.0 O3' C:DT4 3.0 38.5 1.0 P C:DG5 3.3 36.7 1.0 CD A:GLU56 3.5 39.6 1.0 CG A:ASP70 3.5 46.9 1.0 OE1 A:GLU56 4.0 42.5 1.0 C5' C:DG5 4.0 34.9 1.0 C A:THR62 4.1 67.6 1.0 CA A:CA233 4.2 36.1 1.0 O A:HOH260 4.2 29.1 1.0 O5' C:DG5 4.2 36.2 1.0 C3' C:DT4 4.3 40.6 1.0 OD2 A:ASP70 4.3 42.9 1.0 CB A:ASP70 4.5 50.1 1.0 CA A:ASP70 4.6 53.3 1.0 OP2 C:DG5 4.6 36.8 1.0 O A:GLY64 4.6 74.3 1.0 CG A:GLU56 4.7 39.2 1.0 N A:ASP70 4.8 58.6 1.0 C4' C:DT4 4.8 40.9 1.0 CB A:THR62 4.9 67.0 1.0 C2' C:DT4 4.9 38.6 1.0 O A:ALA63 4.9 69.7 1.0 CA A:THR62 5.0 66.2 1.0 CA A:ALA63 5.0 69.9 1.0 N A:ALA63 5.0 68.5 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Muth-Unmethylated Dna Complex


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 Muth-Unmethylated Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca233 b:36.1 occ:1.00 OP1 C:DG5 2.3 36.3 1.0 OD2 A:ASP70 2.4 42.9 1.0 O A:LEU78 2.4 32.8 1.0 O A:HOH260 2.4 29.1 1.0 OE1 A:GLU77 2.5 44.4 1.0 O C:HOH20 2.5 42.9 1.0 CG A:ASP70 3.1 46.9 1.0 OD1 A:ASP70 3.1 42.3 1.0 CD A:GLU77 3.3 45.9 1.0 P C:DG5 3.4 36.7 1.0 C A:LEU78 3.5 33.7 1.0 N A:LEU78 3.8 35.7 1.0 OP2 C:DG5 3.9 36.8 1.0 OE2 A:GLU77 3.9 46.9 1.0 O5' C:DG5 4.0 36.2 1.0 CA A:LEU78 4.0 33.8 1.0 CA A:CA232 4.2 46.0 1.0 CG A:GLU77 4.2 41.3 1.0 CB A:LEU78 4.3 31.8 1.0 OE2 A:GLU56 4.3 36.8 1.0 C5' C:DG5 4.4 34.9 1.0 CB A:ASP70 4.6 50.1 1.0 CG A:LYS79 4.6 38.4 1.0 N A:LYS79 4.6 35.0 1.0 O C:HOH16 4.6 31.4 1.0 C A:GLU77 4.7 36.8 1.0 O3' C:DT4 4.8 38.5 1.0 NZ A:LYS79 4.8 44.2 1.0 O A:HOH259 4.9 46.8 1.0 CA A:LYS79 4.9 35.0 1.0 OP2 C:DA6 5.0 31.6 1.0

J.Y.Lee, J.Chang, N.Joseph, R.Ghirlando, D.N.Rao, W.Yang. Muth Complexed with Hemi- and Unmethylated Dnas: Coupling Base Recognition and Dna Cleavage. Mol.Cell V. 20 155 2005.
ISSN: ISSN 1097-2765
PubMed: 16209953
DOI: 10.1016/J.MOLCEL.2005.08.019