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

The structure of I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-8GCG), PDB code: 3mip 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)	22.96 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.539, 42.611, 71.524, 96.45, 107.04, 108.56
R / Rfree (%)	22.6 / 28.5

The binding sites of Calcium atom in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-8GCG) (pdb code 3mip). 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 (-8GCG), PDB code: 3mip:
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 (-8GCG)


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 (-8GCG) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:38.2 occ:1.00 OP1 D:DC2 2.5 39.9 1.0 OP2 C:DG3 2.6 19.6 1.0 OD1 A:ASP22 2.6 30.4 1.0 O B:GLY21 2.7 22.6 1.0 OD2 A:ASP22 2.8 26.8 1.0 CG A:ASP22 3.1 22.4 1.0 O B:HOH169 3.1 52.3 1.0 C B:GLY21 3.6 25.5 1.0 P C:DG3 3.8 37.0 1.0 CA D:CA13 3.8 66.0 1.0 P D:DC2 3.9 44.5 1.0 CA B:GLY21 4.0 16.9 1.0 NE2 A:GLN50 4.0 32.4 1.0 O B:ASP20 4.0 22.3 1.0 OE1 A:GLN50 4.1 40.6 1.0 O5' C:DG3 4.3 26.8 1.0 C5' C:DG3 4.3 28.9 1.0 O3' D:DA1 4.3 41.3 1.0 OP1 C:DG3 4.4 34.2 1.0 CD A:GLN50 4.5 40.5 1.0 CB A:ASP22 4.5 27.4 1.0 OP2 D:DC2 4.6 34.9 1.0 C5' D:DC2 4.7 32.1 1.0 N B:ASP22 4.8 22.3 1.0 C4' D:DC2 4.8 35.3 1.0 NZ A:LYS54 4.9 65.2 1.0 O5' D:DC2 4.9 34.4 1.0 C B:ASP20 4.9 23.7 1.0 N B:GLY21 5.0 16.8 1.0 O3' C:DA2 5.0 31.3 1.0

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


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 (-8GCG) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3 b:34.0 occ:1.00 O B:HOH168 2.3 52.3 1.0 OP1 C:DA2 2.4 34.2 1.0 OP2 D:DG3 2.5 20.3 1.0 OD1 B:ASP22 2.6 27.5 1.0 OD2 B:ASP22 2.8 29.3 1.0 O A:GLY21 2.8 23.5 1.0 O B:HOH190 2.8 53.5 1.0 CG B:ASP22 3.1 22.4 1.0 CA D:CA13 3.5 66.0 1.0 C A:GLY21 3.7 26.5 1.0 P C:DA2 3.8 35.9 1.0 P D:DG3 3.8 32.7 1.0 NE2 B:GLN50 4.0 36.1 1.0 OE1 B:GLN50 4.1 44.8 1.0 CA A:GLY21 4.1 19.7 1.0 O A:ASP20 4.2 20.9 1.0 O3' C:DG1 4.2 38.6 1.0 C5' D:DG3 4.3 19.0 1.0 O5' D:DG3 4.3 24.3 1.0 C4' C:DA2 4.5 27.1 1.0 CD B:GLN50 4.5 42.2 1.0 C5' C:DA2 4.6 27.3 1.0 CB B:ASP22 4.6 30.4 1.0 OP1 D:DG3 4.6 32.6 1.0 OP2 C:DA2 4.7 32.8 1.0 O5' C:DA2 4.8 29.4 1.0 O3' D:DC2 4.8 26.6 1.0 N A:ASP22 4.8 20.5 1.0 NZ B:LYS54 4.9 61.0 1.0

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


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 (-8GCG) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca13 b:66.0 occ:1.00 OP2 C:DG3 2.4 19.6 1.0 OP2 D:DG3 2.5 20.3 1.0 OD2 A:ASP22 2.6 26.8 1.0 OD2 B:ASP22 2.6 29.3 1.0 O3' D:DC2 3.0 26.6 1.0 O3' C:DA2 3.4 31.3 1.0 P D:DG3 3.4 32.7 1.0 CA B:CA3 3.5 34.0 1.0 P C:DG3 3.5 37.0 1.0 CG A:ASP22 3.7 22.4 1.0 O A:GLY21 3.7 23.5 1.0 CG B:ASP22 3.7 22.4 1.0 CA A:CA2 3.8 38.2 1.0 C3' D:DC2 4.0 33.0 1.0 O B:GLY21 4.0 22.6 1.0 C3' C:DA2 4.0 26.0 1.0 C A:GLY21 4.1 26.5 1.0 CA A:ASP22 4.2 23.2 1.0 O5' D:DG3 4.2 24.3 1.0 C4' C:DA2 4.2 27.1 1.0 C B:GLY21 4.3 25.5 1.0 C4' D:DC2 4.3 35.3 1.0 N A:ASP22 4.4 20.5 1.0 OD1 B:ASP22 4.4 27.5 1.0 CA B:ASP22 4.4 24.6 1.0 O5' C:DG3 4.4 26.8 1.0 OD1 A:ASP22 4.5 30.4 1.0 CB A:ASP22 4.6 27.4 1.0 N B:ASP22 4.6 22.3 1.0 OP1 D:DG3 4.6 32.6 1.0 OP1 D:DC2 4.7 39.9 1.0 CB B:ASP22 4.7 30.4 1.0 OP1 C:DG3 4.7 34.2 1.0 OP1 C:DA2 4.7 34.2 1.0 CA A:GLY21 4.9 19.7 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