Magnesium in PDB 4lox: Crystal Structure of the I-Smami Laglidadg Homing Endonuclease Bound to Cleaved Dna

The structure of Crystal Structure of the I-Smami Laglidadg Homing Endonuclease Bound to Cleaved Dna, PDB code: 4lox was solved by J.Chik, B.Shen, B.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.56 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.284, 67.429, 98.090, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 27.7

The binding sites of Magnesium atom in the Crystal Structure of the I-Smami Laglidadg Homing Endonuclease Bound to Cleaved Dna (pdb code 4lox). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the I-Smami Laglidadg Homing Endonuclease Bound to Cleaved Dna, PDB code: 4lox:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the I-Smami Laglidadg Homing Endonuclease Bound to Cleaved Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the I-Smami Laglidadg Homing Endonuclease Bound to Cleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:18.8 occ:1.00 OP1 C:DT15 2.0 41.0 1.0 O D:HOH101 2.1 28.9 1.0 O A:ALA19 2.2 21.7 1.0 OP1 D:DT15 2.2 29.2 1.0 OD2 A:ASP179 2.3 23.3 1.0 O A:HOH501 2.3 23.1 1.0 OD1 A:ASP179 3.0 26.1 1.0 CG A:ASP179 3.0 22.3 1.0 C A:ALA19 3.3 22.9 1.0 P C:DT15 3.5 41.3 1.0 P D:DT15 3.7 30.6 1.0 CA A:ALA19 3.8 21.6 1.0 MG A:MG402 3.9 23.3 1.0 OE2 A:GLU20 4.0 35.8 1.0 O A:HOH507 4.1 37.2 1.0 NE2 A:GLN206 4.2 21.4 1.0 C5' C:DT15 4.2 37.4 1.0 OP3 C:DT15 4.3 39.3 1.0 O5' C:DT15 4.3 37.4 1.0 O3' D:DA14 4.3 30.9 1.0 N A:GLU20 4.4 22.9 1.0 C5' D:DT15 4.4 31.4 1.0 CB A:ASP179 4.5 22.8 1.0 C4' D:DT15 4.5 31.9 1.0 O A:ASP18 4.5 21.6 1.0 O5' D:DT15 4.5 30.1 1.0 CB A:ALA19 4.6 20.0 1.0 OP2 C:DT15 4.6 45.9 1.0 OE1 A:GLN206 4.6 26.4 1.0 OP2 D:DT15 4.6 29.5 1.0 CA A:GLU20 4.8 26.3 1.0 O3' D:DT15 4.8 31.9 1.0 CD A:GLN206 4.8 23.6 1.0 CD A:GLU20 4.8 30.2 1.0 N A:ALA19 5.0 21.8 1.0 C3' D:DT15 5.0 32.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the I-Smami Laglidadg Homing Endonuclease Bound to Cleaved Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the I-Smami Laglidadg Homing Endonuclease Bound to Cleaved Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:23.3 occ:1.00 OE2 A:GLU20 2.1 35.8 1.0 OD1 A:ASP179 2.2 26.1 1.0 OP3 E:DC16 2.4 61.9 1.0 O3' D:DT15 2.4 31.9 1.0 OP2 C:DT15 2.6 45.9 1.0 OP1 C:DT15 2.8 41.0 1.0 O A:GLY178 2.9 29.2 1.0 CD A:GLU20 2.9 30.2 1.0 OE1 A:GLU20 3.1 35.3 1.0 P C:DT15 3.1 41.3 1.0 O5' E:DC16 3.3 55.5 1.0 CG A:ASP179 3.4 22.3 1.0 C3' D:DT15 3.5 32.1 1.0 P E:DC16 3.5 61.0 1.0 O3' B:DA14 3.5 47.8 0.5 C A:GLY178 3.7 23.9 1.0 O C:HOH110 3.8 43.8 1.0 MG A:MG401 3.9 18.8 1.0 O5' C:DT15 4.1 37.4 1.0 C4' B:DA14 4.1 48.9 0.5 CA A:ASP179 4.2 24.1 1.0 OD2 A:ASP179 4.2 23.3 1.0 C4' D:DT15 4.2 31.9 1.0 N A:ASP179 4.3 23.1 1.0 O A:ALA19 4.3 21.7 1.0 OP3 C:DT15 4.4 39.3 1.0 CG A:GLU20 4.4 27.4 1.0 CB A:ASP179 4.4 22.8 1.0 OP2 E:DC16 4.4 59.3 1.0 C3' B:DA14 4.4 50.5 0.5 OP1 E:DC16 4.5 69.0 1.0 CA A:GLY178 4.5 22.6 1.0 C5' E:DC16 4.6 50.4 1.0 C2' D:DT15 4.8 33.3 1.0 O4' B:DA14 4.8 48.1 0.5 C A:ALA19 5.0 22.9 1.0 OP1 D:DT15 5.0 29.2 1.0

J.Chik, B.Shen, B.Stoddard. Crystal Structure of A Laglidadg Endonuclease From the Sordaria Macrospore. To Be Published.