Calcium in PDB 2aor: Crystal Structure of Muth-Hemimethylated Dna Complex

The structure of Crystal Structure of Muth-Hemimethylated Dna Complex, PDB code: 2aor 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)	19.58 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.397, 89.045, 75.092, 90.00, 105.70, 90.00
R / Rfree (%)	19.6 / 22.6

The binding sites of Calcium atom in the Crystal Structure of Muth-Hemimethylated Dna Complex (pdb code 2aor). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Muth-Hemimethylated Dna Complex, PDB code: 2aor:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Muth-Hemimethylated 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-Hemimethylated Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:46.9 occ:1.00 O A:HOH466 2.2 36.6 1.0 O D:HOH70 2.3 39.7 1.0 OD1 A:ASP70 2.3 22.3 1.0 O A:HOH469 2.4 31.3 1.0 OE2 A:GLU56 2.7 32.5 1.0 OP1 D:DG16 2.9 27.2 1.0 O3' D:DG15 3.5 27.4 1.0 CG A:ASP70 3.6 16.5 1.0 CD A:GLU56 3.7 31.0 1.0 P D:DG16 3.8 26.7 1.0 C5' D:DG16 4.0 20.2 1.0 O A:HOH403 4.0 19.6 1.0 O A:HOH427 4.1 50.5 1.0 CA A:CA402 4.1 21.0 1.0 O A:HOH416 4.2 30.9 1.0 O A:SER65 4.2 42.5 1.0 OE1 A:GLU56 4.3 30.7 1.0 OD2 A:ASP70 4.4 19.8 1.0 O A:THR62 4.4 45.4 1.0 O5' D:DG16 4.4 25.5 1.0 CB A:ASP70 4.5 22.3 1.0 CA A:ASP70 4.6 23.7 1.0 CG A:GLU56 4.7 28.0 1.0 C3' D:DG15 4.8 31.6 1.0 O A:HOH491 4.8 39.0 1.0 CB A:SER65 4.9 45.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Muth-Hemimethylated 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-Hemimethylated Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:21.0 occ:1.00 OP1 D:DG16 2.3 27.2 1.0 O A:LEU78 2.3 18.0 1.0 OD2 A:ASP70 2.3 19.8 1.0 O A:HOH403 2.3 19.6 1.0 OE1 A:GLU77 2.4 27.9 1.0 O A:HOH461 2.5 23.4 1.0 OD1 A:ASP70 3.0 22.3 1.0 CG A:ASP70 3.0 16.5 1.0 CD A:GLU77 3.3 29.9 1.0 C A:LEU78 3.4 19.7 1.0 P D:DG16 3.5 26.7 1.0 OE2 A:GLU77 3.8 30.8 1.0 N A:LEU78 4.0 21.2 1.0 OP2 D:DG16 4.0 28.5 1.0 O5' D:DG16 4.0 25.5 1.0 O A:HOH416 4.1 30.9 1.0 CA A:CA401 4.1 46.9 1.0 CA A:LEU78 4.2 21.4 1.0 CG A:GLU77 4.3 26.4 1.0 CG A:LYS79 4.3 27.3 1.0 OE2 A:GLU56 4.3 32.5 1.0 C5' D:DG16 4.3 20.2 1.0 CB A:LEU78 4.4 22.3 1.0 NZ A:LYS79 4.4 36.2 1.0 CB A:ASP70 4.5 22.3 1.0 N A:LYS79 4.5 22.0 1.0 O D:HOH25 4.7 25.9 1.0 CA A:LYS79 4.7 23.3 1.0 O3' D:DG15 4.7 27.4 1.0 O D:HOH70 4.8 39.7 1.0 OP2 D:DA17 4.9 21.7 1.0 C A:GLU77 5.0 23.5 1.0 O3' D:DG16 5.0 18.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Muth-Hemimethylated Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Muth-Hemimethylated Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:23.3 occ:1.00 OE1 B:GLU77 2.2 27.6 1.0 O C:HOH63 2.2 22.7 1.0 O B:LEU78 2.3 23.0 1.0 OD2 B:ASP70 2.3 32.6 1.0 OP1 C:DG16 2.4 28.9 1.0 O B:HOH508 2.4 21.1 1.0 CG B:ASP70 3.1 33.3 1.0 OD1 B:ASP70 3.1 34.5 1.0 CD B:GLU77 3.1 30.6 1.0 C B:LEU78 3.5 23.0 1.0 P C:DG16 3.6 28.5 1.0 OE2 B:GLU77 3.8 31.4 1.0 N B:LEU78 3.9 23.0 1.0 O B:HOH420 4.1 29.7 1.0 O5' C:DG16 4.1 28.0 1.0 CG B:GLU77 4.1 26.1 1.0 OP2 C:DG16 4.2 29.6 1.0 CA B:LEU78 4.2 22.8 1.0 O C:HOH54 4.2 44.1 1.0 C5' C:DG16 4.3 22.8 1.0 CA B:CA404 4.4 77.7 1.0 CB B:LEU78 4.5 20.4 1.0 CB B:ASP70 4.5 31.4 1.0 CG B:LYS79 4.5 29.1 1.0 N B:LYS79 4.5 22.8 1.0 OE2 B:GLU56 4.6 30.9 1.0 NZ B:LYS79 4.7 36.9 1.0 O C:HOH24 4.7 21.2 1.0 CA B:LYS79 4.8 25.2 1.0 OP2 C:DA17 4.8 21.0 1.0 O3' C:DG15 4.8 28.7 1.0 C B:GLU77 4.9 23.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Muth-Hemimethylated Dna Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Muth-Hemimethylated Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:77.7 occ:1.00 O C:HOH54 2.3 44.1 1.0 O B:HOH457 2.3 47.6 1.0 OE2 B:GLU56 2.4 30.9 1.0 O B:HOH489 2.5 40.9 1.0 OD1 B:ASP70 2.7 34.5 1.0 OP1 C:DG16 3.1 28.9 1.0 CD B:GLU56 3.5 29.0 1.0 C5' C:DG16 3.6 22.8 1.0 O3' C:DG15 3.6 28.7 1.0 O B:HOH513 3.7 41.5 1.0 O B:HOH508 3.9 21.1 1.0 P C:DG16 3.9 28.5 1.0 CG B:ASP70 3.9 33.3 1.0 OE1 B:GLU56 4.0 30.7 1.0 O5' C:DG16 4.2 28.0 1.0 O B:THR62 4.3 52.1 1.0 O B:SER65 4.3 61.3 1.0 CA B:CA403 4.4 23.3 1.0 O B:HOH420 4.5 29.7 1.0 CG B:GLU56 4.5 27.0 1.0 OD2 B:ASP70 4.6 32.6 1.0 O B:HOH469 4.7 49.9 1.0 CB B:ASP70 4.8 31.4 1.0 O B:HOH455 4.8 37.1 1.0 C4' C:DG16 4.9 22.8 1.0 C3' C:DG15 4.9 30.6 1.0 CB B:SER65 4.9 61.5 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