Calcium in PDB 3mis: I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-8G)

The structure of I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-8G), PDB code: 3mis was solved by G.K.Taylor, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.25 / 2.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.589, 42.632, 71.577, 72.86, 72.83, 71.17
R / Rfree (%)	24.6 / 30.8

The binding sites of Calcium atom in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-8G) (pdb code 3mis). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-8G), PDB code: 3mis:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-8G)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-8G) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:37.3 occ:1.00 OP2 C:DG3 2.3 27.1 1.0 OP1 D:DC2 2.4 46.3 1.0 O B:GLY21 2.4 24.7 1.0 OD2 A:ASP22 2.6 27.9 1.0 OD1 A:ASP22 2.6 39.0 1.0 O B:HOH4 2.7 69.2 1.0 CG A:ASP22 3.0 32.7 1.0 C B:GLY21 3.4 28.5 1.0 CA C:CA13 3.5 83.0 1.0 P C:DG3 3.6 36.2 1.0 P D:DC2 3.7 46.1 1.0 CA B:GLY21 3.9 28.0 1.0 O3' D:DA1 4.0 55.8 1.0 NE2 A:GLN50 4.2 42.4 1.0 O5' C:DG3 4.2 31.7 1.0 OP1 C:DG3 4.3 39.2 1.0 C5' D:DC2 4.3 43.8 1.0 C5' C:DG3 4.3 25.1 1.0 O B:HOH198 4.3 41.0 1.0 OE1 A:GLN50 4.5 50.4 1.0 O5' D:DC2 4.5 45.5 1.0 CB A:ASP22 4.5 31.1 1.0 C4' D:DC2 4.5 45.1 1.0 O B:ASP20 4.5 23.2 1.0 N B:ASP22 4.6 28.5 1.0 CD A:GLN50 4.7 50.0 1.0 O3' C:DA2 4.8 57.3 1.0 OP2 D:DC2 4.8 47.8 1.0 OD2 B:ASP22 4.9 34.7 1.0 CA B:ASP22 5.0 30.8 1.0 N B:GLY21 5.0 33.4 1.0

Calcium binding site 2 out of 3 in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-8G)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-8G) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3 b:39.3 occ:1.00 OP2 D:DG3 2.2 40.4 1.0 OP1 C:DA2 2.4 35.5 1.0 O D:HOH48 2.5 41.0 1.0 O A:GLY21 2.5 22.5 1.0 OD1 B:ASP22 2.6 46.6 1.0 OD2 B:ASP22 2.8 34.7 1.0 O B:HOH5 2.8 69.2 1.0 CG B:ASP22 3.0 39.2 1.0 CA C:CA13 3.5 83.0 1.0 C A:GLY21 3.5 25.4 1.0 P D:DG3 3.6 45.0 1.0 P C:DA2 3.7 44.3 1.0 O3' C:DG1 3.9 30.5 1.0 CA A:GLY21 4.0 23.6 1.0 NE2 B:GLN50 4.2 44.5 1.0 O5' D:DG3 4.2 38.9 1.0 C5' D:DG3 4.2 41.1 1.0 OP1 D:DG3 4.4 48.2 1.0 C5' C:DA2 4.4 43.9 1.0 OE1 B:GLN50 4.5 55.7 1.0 O A:ASP20 4.5 26.5 1.0 CB B:ASP22 4.6 36.0 1.0 O5' C:DA2 4.6 47.7 1.0 C4' C:DA2 4.6 56.5 1.0 O3' D:DC2 4.6 45.3 1.0 N A:ASP22 4.7 23.1 1.0 CD B:GLN50 4.7 53.5 1.0 OP2 C:DA2 4.8 38.0 1.0 CA A:ASP22 5.0 26.2 1.0

Calcium binding site 3 out of 3 in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-8G)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-8G) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca13 b:83.0 occ:1.00 OP2 C:DG3 2.4 27.1 1.0 OP2 D:DG3 2.5 40.4 1.0 OD2 B:ASP22 2.6 34.7 1.0 OD2 A:ASP22 2.6 27.9 1.0 O3' D:DC2 2.9 45.3 1.0 O3' C:DA2 3.1 57.3 1.0 P D:DG3 3.4 45.0 1.0 P C:DG3 3.4 36.2 1.0 CA B:CA3 3.5 39.3 1.0 CA A:CA2 3.5 37.3 1.0 O A:GLY21 3.8 22.5 1.0 O B:GLY21 3.8 24.7 1.0 CG A:ASP22 3.8 32.7 1.0 CG B:ASP22 3.8 39.2 1.0 C3' D:DC2 3.9 44.0 1.0 C3' C:DA2 4.0 58.3 1.0 C4' D:DC2 4.0 45.1 1.0 C4' C:DA2 4.2 56.5 1.0 O5' C:DG3 4.3 31.7 1.0 O5' D:DG3 4.3 38.9 1.0 C B:GLY21 4.3 28.5 1.0 C A:GLY21 4.3 25.4 1.0 CA A:ASP22 4.4 26.2 1.0 CA B:ASP22 4.5 30.8 1.0 OP1 D:DG3 4.5 48.2 1.0 OD1 B:ASP22 4.5 46.6 1.0 OP1 C:DG3 4.5 39.2 1.0 OD1 A:ASP22 4.6 39.0 1.0 N A:ASP22 4.7 23.1 1.0 N B:ASP22 4.7 28.5 1.0 C5' D:DC2 4.7 43.8 1.0 CB A:ASP22 4.7 31.1 1.0 CB B:ASP22 4.8 36.0 1.0 C5' C:DA2 4.8 43.9 1.0 OP1 D:DC2 4.9 46.3 1.0 OP1 C:DA2 4.9 35.5 1.0

J.Ashworth, G.K.Taylor, J.J.Havranek, S.A.Quadri, B.L.Stoddard, D.Baker. Computational Reprogramming of Homing Endonuclease Specificity at Multiple Adjacent Base Pairs. Nucleic Acids Res. V. 38 5601 2010.
ISSN: ISSN 0305-1048
PubMed: 20435674
DOI: 10.1093/NAR/GKQ283