Calcium in PDB 1m5x: Crystal Structure of the Homing Endonuclease I-Msoi Bound to Its Dna Substrate

The structure of Crystal Structure of the Homing Endonuclease I-Msoi Bound to Its Dna Substrate, PDB code: 1m5x was solved by B.Chevalier, M.Turmel, C.Lemieux, R.J.Monnat, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.25
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.510, 42.210, 71.320, 73.34, 73.17, 71.09
R / Rfree (%)	21.9 / 25.5

The binding sites of Calcium atom in the Crystal Structure of the Homing Endonuclease I-Msoi Bound to Its Dna Substrate (pdb code 1m5x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Homing Endonuclease I-Msoi Bound to Its Dna Substrate, PDB code: 1m5x:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Homing Endonuclease I-Msoi Bound to Its Dna Substrate


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 the Homing Endonuclease I-Msoi Bound to Its Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca801 b:78.3 occ:1.00 OD1 B:ASP222 2.4 28.5 1.0 OP2 C:DG515 2.5 34.1 1.0 OP2 D:DG565 2.5 37.4 1.0 OD2 A:ASP22 2.6 21.1 1.0 O3' D:DC564 3.0 36.0 1.0 O3' C:DA514 3.1 33.9 1.0 P C:DG515 3.4 35.6 1.0 P D:DG565 3.4 39.7 1.0 CA B:CA803 3.5 39.5 1.0 CG B:ASP222 3.6 23.9 1.0 CA A:CA802 3.6 43.2 1.0 CG A:ASP22 3.8 22.4 1.0 OP1 D:DC564 3.9 37.9 1.0 C3' D:DC564 4.0 34.1 1.0 C3' C:DA514 4.1 33.2 1.0 C4' D:DC564 4.2 34.3 1.0 O A:GLY21 4.2 20.4 1.0 O B:GLY221 4.3 21.4 1.0 OD2 B:ASP222 4.3 25.1 1.0 C4' C:DA514 4.3 32.8 1.0 O C:HOH1128 4.4 36.6 1.0 OP1 C:DG515 4.4 36.1 1.0 OD1 A:ASP22 4.4 23.8 1.0 O5' D:DG565 4.4 34.6 1.0 OP1 D:DG565 4.4 40.1 1.0 O5' C:DG515 4.5 33.3 1.0 CB B:ASP222 4.6 25.1 1.0 CA B:ASP222 4.6 25.7 1.0 O C:HOH1201 4.6 49.1 1.0 OP1 C:DA514 4.7 38.2 1.0 O C:HOH1226 4.7 50.7 1.0 C A:GLY21 4.7 21.6 1.0 CA A:ASP22 4.7 22.4 1.0 C B:GLY221 4.7 22.5 1.0 CB A:ASP22 4.9 21.8 1.0 N B:ASP222 4.9 22.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Homing Endonuclease I-Msoi Bound to Its Dna Substrate


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 the Homing Endonuclease I-Msoi Bound to Its Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:43.2 occ:1.00 OP2 D:DG565 2.3 37.4 1.0 O B:GLY221 2.4 21.4 1.0 OP1 C:DA514 2.4 38.2 1.0 OD1 A:ASP22 2.4 23.8 1.0 O D:HOH1228 2.5 38.9 1.0 O B:HOH1225 2.7 28.8 1.0 OD2 A:ASP22 3.0 21.1 1.0 CG A:ASP22 3.1 22.4 1.0 C B:GLY221 3.5 22.5 1.0 CA C:CA801 3.6 78.3 1.0 P D:DG565 3.7 39.7 1.0 P C:DA514 3.8 38.3 1.0 O3' C:DG513 4.1 36.6 1.0 CA B:GLY221 4.2 21.7 1.0 OP1 D:DG565 4.2 40.1 1.0 O B:ASP220 4.4 15.0 1.0 OD1 B:ASP222 4.4 28.5 1.0 N B:ASP222 4.5 22.6 1.0 O5' D:DG565 4.5 34.6 1.0 CB A:ASP22 4.5 21.8 1.0 O B:HOH1229 4.6 49.3 1.0 NE2 A:GLN50 4.6 24.3 1.0 OE1 A:GLN50 4.7 27.6 1.0 CA B:ASP222 4.7 25.7 1.0 OP2 C:DA514 4.7 35.0 1.0 O3' D:DC564 4.8 36.0 1.0 C5' C:DA514 4.8 32.7 1.0 O5' C:DA514 4.8 35.7 1.0 C4' C:DA514 4.8 32.8 1.0 C5' D:DG565 4.9 37.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Homing Endonuclease I-Msoi Bound to Its Dna Substrate


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 the Homing Endonuclease I-Msoi Bound to Its Dna Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca803 b:39.5 occ:1.00 OP2 C:DG515 2.3 34.1 1.0 O B:HOH1227 2.3 34.1 1.0 OP1 D:DC564 2.3 37.9 1.0 O A:GLY21 2.4 20.4 1.0 OD2 B:ASP222 2.5 25.1 1.0 O C:HOH1226 2.6 50.7 1.0 OD1 B:ASP222 2.9 28.5 1.0 CG B:ASP222 3.0 23.9 1.0 CA C:CA801 3.5 78.3 1.0 C A:GLY21 3.5 21.6 1.0 P D:DC564 3.6 34.6 1.0 P C:DG515 3.6 35.6 1.0 O3' D:DA563 4.0 35.2 1.0 CA A:GLY21 4.2 20.1 1.0 OP1 C:DG515 4.2 36.1 1.0 OP2 D:DC564 4.2 33.5 1.0 NE2 B:GLN250 4.4 23.9 1.0 OE1 B:GLN250 4.4 28.6 1.0 O5' C:DG515 4.5 33.3 1.0 O A:HOH1217 4.5 38.8 1.0 CB B:ASP222 4.5 25.1 1.0 O A:ASP20 4.5 14.9 1.0 OD2 A:ASP22 4.6 21.1 1.0 N A:ASP22 4.6 20.6 1.0 C5' C:DG515 4.7 33.7 1.0 O3' C:DA514 4.7 33.9 1.0 CD B:GLN250 4.7 27.9 1.0 CA A:ASP22 4.8 22.4 1.0 O5' D:DC564 4.8 33.5 1.0 C5' D:DC564 5.0 33.9 1.0

B.Chevalier, M.Turmel, C.Lemieux, R.J.Monnat, B.L.Stoddard. Flexible Dna Target Site Recognition By Divergent Homing Endonuclease Isoschizomers I-Crei and I-Msoi J.Mol.Biol. V. 329 253 2003.
ISSN: ISSN 0022-2836
PubMed: 12758074
DOI: 10.1016/S0022-2836(03)00447-9