Calcium in PDB 3ko2: I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7C)

The structure of I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7C), PDB code: 3ko2 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)	33.56 / 2.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.031, 70.006, 72.258, 81.66, 70.00, 89.48
R / Rfree (%)	24.8 / 28.6

The binding sites of Calcium atom in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7C) (pdb code 3ko2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7C), PDB code: 3ko2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7C)


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 (-7C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca171 b:56.8 occ:1.00 OP1 C:DA14 2.5 30.4 1.0 O A:GLY21 2.6 29.2 1.0 O A:HOH173 2.7 55.8 1.0 OD1 B:ASP22 2.8 22.6 1.0 OP2 D:DG15 2.8 31.3 1.0 CG B:ASP22 3.5 21.9 1.0 OD2 B:ASP22 3.5 21.5 1.0 O A:ASP20 3.7 31.6 1.0 C A:GLY21 3.7 30.4 1.0 P C:DA14 3.9 31.4 1.0 P D:DG15 4.0 33.8 1.0 OE1 B:GLN50 4.1 32.7 1.0 C5' D:DG15 4.2 31.8 1.0 CA A:GLY21 4.3 30.1 1.0 NE2 B:GLN50 4.3 28.8 1.0 O3' C:DG13 4.4 33.4 1.0 O5' D:DG15 4.4 29.0 1.0 CA C:CA25 4.5 0.5 1.0 OP2 C:DA14 4.6 27.6 1.0 CD B:GLN50 4.6 32.0 1.0 C A:ASP20 4.7 36.0 1.0 OP1 D:DG15 4.8 33.9 1.0 N A:ASP22 4.8 29.4 1.0 N A:GLY21 5.0 27.1 1.0 O5' C:DA14 5.0 29.6 1.0 CB B:ASP22 5.0 21.0 1.0 C5' C:DA14 5.0 26.5 1.0

Calcium binding site 2 out of 6 in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7C)


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 (-7C) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca172 b:46.4 occ:1.00 O B:GLY21 2.5 23.7 1.0 OP1 D:DC14 2.5 27.0 1.0 OD2 A:ASP22 2.6 31.1 1.0 OP2 C:DG15 2.8 29.8 1.0 OD1 A:ASP22 3.3 34.7 1.0 CG A:ASP22 3.3 30.0 1.0 C B:GLY21 3.4 24.2 1.0 CA B:GLY21 3.7 23.4 1.0 OE1 A:GLN50 3.8 22.5 1.0 O B:ASP20 3.9 20.6 1.0 P D:DC14 3.9 24.2 1.0 NE2 A:GLN50 4.0 17.4 1.0 P C:DG15 4.2 32.5 1.0 CA C:CA25 4.2 0.5 1.0 CD A:GLN50 4.3 22.0 1.0 O3' D:DA13 4.5 35.1 1.0 N B:ASP22 4.6 21.5 1.0 C5' C:DG15 4.6 30.1 1.0 N B:GLY21 4.6 20.3 1.0 C B:ASP20 4.7 22.1 1.0 C5' D:DC14 4.7 23.0 1.0 O5' C:DG15 4.7 30.0 1.0 OP2 D:DC14 4.8 23.7 1.0 CB A:ASP22 4.8 31.3 1.0 OP1 C:DG15 4.8 34.2 1.0 O5' D:DC14 4.8 23.1 1.0 NZ A:LYS54 5.0 41.3 1.0

Calcium binding site 3 out of 6 in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7C)


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 (-7C) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca25 b:0.5 occ:1.00 OP2 C:DG15 2.5 29.8 1.0 OD1 A:ASP22 2.5 34.7 1.0 OP2 D:DG15 2.6 31.3 1.0 OD2 B:ASP22 2.6 21.5 1.0 O3' D:DC14 2.7 23.6 1.0 O3' C:DA14 2.8 28.4 1.0 P C:DG15 3.2 32.5 1.0 P D:DG15 3.3 33.8 1.0 O B:GLY21 3.5 23.7 1.0 C3' D:DC14 3.7 22.3 1.0 CG A:ASP22 3.7 30.0 1.0 CG B:ASP22 3.9 21.9 1.0 C3' C:DA14 3.9 27.6 1.0 C4' D:DC14 4.0 22.9 1.0 O A:GLY21 4.0 29.2 1.0 C4' C:DA14 4.2 27.1 1.0 CA A:CA172 4.2 46.4 1.0 O5' D:DG15 4.2 29.0 1.0 OP1 C:DG15 4.3 34.2 1.0 O5' C:DG15 4.3 30.0 1.0 C B:GLY21 4.4 24.2 1.0 OP1 D:DG15 4.4 33.9 1.0 OD2 A:ASP22 4.4 31.1 1.0 CA A:CA171 4.5 56.8 1.0 CA A:ASP22 4.6 32.1 1.0 CA B:ASP22 4.6 22.6 1.0 C5' D:DC14 4.6 23.0 1.0 OD1 B:ASP22 4.6 22.6 1.0 C A:GLY21 4.6 30.4 1.0 OP1 D:DC14 4.7 27.0 1.0 CB A:ASP22 4.7 31.3 1.0 N B:ASP22 4.8 21.5 1.0 CB B:ASP22 4.9 21.0 1.0 OP1 C:DA14 4.9 30.4 1.0 N A:ASP22 5.0 29.4 1.0

Calcium binding site 4 out of 6 in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7C)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7C) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca171 b:80.2 occ:1.00 OP1 H:DA14 2.7 46.5 1.0 O F:GLY21 2.8 40.0 1.0 OD1 G:ASP22 2.9 53.3 1.0 O F:ASP20 3.2 35.5 1.0 OP2 I:DG15 3.3 35.9 1.0 OE1 G:GLN50 3.6 45.1 1.0 C F:GLY21 3.7 41.2 1.0 CG G:ASP22 3.8 51.3 1.0 OD2 G:ASP22 4.0 48.8 1.0 CA F:GLY21 4.0 39.4 1.0 P H:DA14 4.0 48.2 1.0 C F:ASP20 4.2 39.7 1.0 NE2 G:GLN50 4.3 40.3 1.0 CD G:GLN50 4.3 44.0 1.0 NZ G:LYS54 4.5 62.5 0.0 OP2 H:DA14 4.5 45.5 1.0 C5' I:DG15 4.5 34.9 1.0 P I:DG15 4.6 39.3 1.0 N F:GLY21 4.6 34.4 1.0 O3' H:DG13 4.6 53.7 1.0 N F:ASP22 4.8 42.4 1.0 CE F:LYS104 4.8 43.3 1.0 O5' I:DG15 4.8 33.3 1.0 NZ F:LYS104 4.8 52.1 1.0

Calcium binding site 5 out of 6 in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7C)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7C) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca172 b:64.0 occ:1.00 O G:GLY21 2.7 33.7 1.0 OP1 I:DC14 2.7 52.1 1.0 OP2 H:DG15 2.8 45.1 1.0 OD2 F:ASP22 2.8 49.3 1.0 OD1 F:ASP22 3.4 50.9 1.0 CG F:ASP22 3.5 46.9 1.0 C G:GLY21 3.6 36.1 1.0 O G:ASP20 3.8 28.7 1.0 OE1 F:GLN50 3.8 58.9 1.0 CA G:GLY21 3.9 35.6 1.0 P I:DC14 4.0 50.3 1.0 P H:DG15 4.2 48.3 1.0 C5' H:DG15 4.3 45.7 1.0 NE2 F:GLN50 4.3 54.9 1.0 O3' I:DA13 4.5 45.2 1.0 CD F:GLN50 4.5 58.9 1.0 CA H:CA25 4.5 88.4 1.0 O5' H:DG15 4.6 46.1 1.0 C G:ASP20 4.6 32.1 1.0 N G:GLY21 4.7 33.6 1.0 N G:ASP22 4.8 50.8 1.0 NZ F:LYS54 4.8 43.4 0.0 OP2 I:DC14 4.8 50.3 1.0 C4' H:DG15 4.8 44.0 1.0 CB F:ASP22 5.0 47.7 1.0

Calcium binding site 6 out of 6 in the I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7C)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of I-Msoi Re-Designed For Altered Dna Cleavage Specificity (-7C) within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca25 b:88.4 occ:1.00 OD1 F:ASP22 2.6 50.9 1.0 OD2 G:ASP22 2.7 48.8 1.0 O3' H:DA14 2.7 42.0 1.0 OP2 I:DG15 2.8 35.9 1.0 O3' I:DC14 2.8 47.4 1.0 OP2 H:DG15 2.9 45.1 1.0 P I:DG15 3.4 39.3 1.0 P H:DG15 3.4 48.3 1.0 O G:GLY21 3.5 33.7 1.0 O F:GLY21 3.6 40.0 1.0 C3' I:DC14 3.7 46.0 1.0 C3' H:DA14 3.8 42.1 1.0 CG F:ASP22 3.8 46.9 1.0 CG G:ASP22 3.9 51.3 1.0 C4' I:DC14 3.9 47.7 1.0 C4' H:DA14 4.0 42.3 1.0 O5' I:DG15 4.4 33.3 1.0 C F:GLY21 4.4 41.2 1.0 O5' H:DG15 4.4 46.1 1.0 C G:GLY21 4.4 36.1 1.0 CA F:ASP22 4.5 46.6 1.0 OP1 H:DG15 4.5 49.9 1.0 OP1 I:DG15 4.5 40.5 1.0 CA F:CA172 4.5 64.0 1.0 OD2 F:ASP22 4.6 49.3 1.0 OD1 G:ASP22 4.6 53.3 1.0 OP1 H:DA14 4.7 46.5 1.0 CA G:ASP22 4.7 51.8 1.0 CB F:ASP22 4.7 47.7 1.0 OP1 I:DC14 4.8 52.1 1.0 N F:ASP22 4.8 42.4 1.0 C5' I:DC14 4.9 47.3 1.0 CB G:ASP22 4.9 51.5 1.0 O4' I:DC14 4.9 47.1 1.0 N G:ASP22 4.9 50.8 1.0 C5' H:DA14 5.0 42.0 1.0 O4' H:DA14 5.0 42.2 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