Magnesium in PDB 3e54: Archaeal Intron-Encoded Homing Endonuclease I-VDI141I Complexed with Dna

The structure of Archaeal Intron-Encoded Homing Endonuclease I-VDI141I Complexed with Dna, PDB code: 3e54 was solved by N.Nomura, Y.Nomura, D.Sussman, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.16 / 2.50
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	66.580, 66.580, 217.910, 90.00, 90.00, 120.00
R / Rfree (%)	23.1 / 25

The binding sites of Magnesium atom in the Archaeal Intron-Encoded Homing Endonuclease I-VDI141I Complexed with Dna (pdb code 3e54). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Archaeal Intron-Encoded Homing Endonuclease I-VDI141I Complexed with Dna, PDB code: 3e54:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Archaeal Intron-Encoded Homing Endonuclease I-VDI141I Complexed with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Archaeal Intron-Encoded Homing Endonuclease I-VDI141I Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:44.4 occ:1.00 O B:ALA218 1.8 30.0 1.0 OP3 D:DG503 1.9 28.3 1.0 OE2 A:GLU19 2.3 36.4 1.0 OP1 E:DA613 2.3 20.1 1.0 C B:ALA218 2.9 30.6 1.0 OE1 A:GLU19 2.9 40.5 1.0 CD A:GLU19 2.9 44.2 1.0 O D:EOH801 3.2 46.6 1.0 P D:DG503 3.3 32.9 1.0 CA B:ALA218 3.5 27.9 1.0 C1 D:EOH801 3.6 49.0 1.0 P E:DA613 3.8 25.7 1.0 OP2 D:DG503 3.8 32.4 1.0 NE2 A:GLN46 3.8 30.4 1.0 O B:GLU217 3.9 39.9 1.0 N B:GLU219 4.0 35.0 1.0 O5' D:DG503 4.1 24.0 1.0 O3' E:DA612 4.2 30.5 1.0 OE1 A:GLN46 4.3 34.5 1.0 CG A:GLU19 4.3 31.0 1.0 C2 D:EOH801 4.3 38.9 1.0 OP1 D:DG503 4.4 40.1 1.0 CA B:GLU219 4.4 35.1 1.0 CB B:ALA218 4.4 36.0 1.0 CD A:GLN46 4.5 27.3 1.0 C5' D:DG503 4.5 23.9 1.0 N B:ALA218 4.6 31.4 1.0 OP2 E:DA613 4.6 33.6 1.0 MG B:MG701 4.6 49.3 1.0 C B:GLU217 4.7 35.9 1.0 C5' E:DA613 4.8 26.7 1.0 CG B:GLU219 4.8 29.4 1.0 O5' E:DA613 4.8 32.2 1.0 C4' E:DA613 4.9 30.4 1.0 O E:HOH1062 5.0 43.3 1.0

Magnesium binding site 2 out of 5 in the Archaeal Intron-Encoded Homing Endonuclease I-VDI141I Complexed with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Archaeal Intron-Encoded Homing Endonuclease I-VDI141I Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:41.0 occ:1.00 OD2 A:ASP39 2.1 36.1 1.0 OD1 A:ASP39 2.6 37.5 1.0 CG A:ASP39 2.7 30.7 1.0 N7 C:DA493 3.4 37.7 1.0 CB A:ASP39 4.2 32.0 1.0 OD2 A:ASP79 4.2 30.1 1.0 C8 C:DA493 4.3 36.9 1.0 OP2 C:DG492 4.3 45.7 1.0 N6 C:DA493 4.4 50.4 1.0 C8 C:DG492 4.4 33.8 1.0 N7 C:DG492 4.4 33.4 1.0 C5 C:DA493 4.5 29.8 1.0 NH1 A:ARG37 4.5 34.7 1.0 O A:HOH1070 4.7 41.5 1.0 O A:PRO40 4.8 35.2 1.0 CG A:ASP79 4.8 34.8 1.0 CB A:ASP79 4.8 35.3 1.0 NZ A:LYS27 4.9 42.8 1.0 CA A:ASP39 4.9 29.7 1.0 C6 C:DA493 4.9 39.8 1.0

Magnesium binding site 3 out of 5 in the Archaeal Intron-Encoded Homing Endonuclease I-VDI141I Complexed with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Archaeal Intron-Encoded Homing Endonuclease I-VDI141I Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:49.3 occ:1.00 O3' C:DA502 1.9 28.2 1.0 OP2 D:DG503 2.7 32.4 1.0 O3' E:DA613 2.7 35.0 1.0 OE2 B:GLU219 2.7 35.3 1.0 OE2 A:GLU19 2.8 36.4 1.0 C3' C:DA502 3.0 18.7 1.0 OP2 F:DG614 3.0 39.9 1.0 CG B:GLU219 3.3 29.4 1.0 CD B:GLU219 3.4 41.6 1.0 C4' C:DA502 3.4 30.3 1.0 CD A:GLU19 3.6 44.2 1.0 O5' D:DG503 3.7 24.0 1.0 P D:DG503 3.7 32.9 1.0 CG A:GLU19 3.7 31.0 1.0 O D:HOH1007 3.7 23.1 1.0 C3' E:DA613 3.8 28.6 1.0 C4' E:DA613 4.0 30.4 1.0 P F:DG614 4.2 30.0 1.0 OP3 D:DG503 4.2 28.3 1.0 C2' C:DA502 4.2 14.8 1.0 O4' C:DA502 4.2 23.4 1.0 CB B:GLU219 4.3 27.0 1.0 O5' F:DG614 4.4 26.4 1.0 C1' C:DA502 4.4 25.4 1.0 OP3 F:DG614 4.4 28.7 1.0 O B:ALA218 4.5 30.0 1.0 OE1 B:GLU219 4.5 36.7 1.0 C5' C:DA502 4.6 26.8 1.0 MG A:MG702 4.6 44.4 1.0 O4' E:DA613 4.8 31.1 1.0 O A:ALA18 4.8 24.7 1.0 OE1 A:GLU19 4.8 40.5 1.0 CB A:GLU19 4.9 28.6 1.0 CA B:GLU219 4.9 35.1 1.0 C5' D:DG503 4.9 23.9 1.0 C2' E:DA613 5.0 20.8 1.0 MG C:MG703 5.0 54.5 1.0 OP1 D:DG503 5.0 40.1 1.0

Magnesium binding site 4 out of 5 in the Archaeal Intron-Encoded Homing Endonuclease I-VDI141I Complexed with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Archaeal Intron-Encoded Homing Endonuclease I-VDI141I Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg705 b:42.2 occ:1.00 OD2 B:ASP239 2.3 38.8 1.0 OD1 B:ASP239 2.9 36.9 1.0 CG B:ASP239 3.0 30.9 1.0 N7 E:DG604 3.4 38.2 1.0 OD2 B:ASP279 4.0 30.4 1.0 OP2 E:DG603 4.2 46.6 1.0 C8 E:DG604 4.2 31.2 1.0 C8 E:DG603 4.4 29.7 1.0 CB B:ASP239 4.4 33.8 1.0 N7 E:DG603 4.5 24.3 1.0 C5 E:DG604 4.6 28.9 1.0 CG B:ASP279 4.6 30.4 1.0 CB B:ASP279 4.6 36.6 1.0 O6 E:DG604 4.6 56.1 1.0 O B:PRO240 4.7 36.3 1.0 O B:HOH1024 4.7 36.3 1.0 O B:ASP279 4.8 49.2 1.0 NH1 B:ARG237 4.8 34.5 1.0

Magnesium binding site 5 out of 5 in the Archaeal Intron-Encoded Homing Endonuclease I-VDI141I Complexed with Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Archaeal Intron-Encoded Homing Endonuclease I-VDI141I Complexed with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg703 b:54.5 occ:1.00 OP1 C:DA502 1.6 19.0 1.0 OE1 B:GLU219 2.3 36.7 1.0 OP3 F:DG614 2.4 28.7 1.0 OE2 B:GLU219 2.4 35.3 1.0 O A:ALA18 2.5 24.7 1.0 CD B:GLU219 2.7 41.6 1.0 NE2 B:GLN246 3.0 22.3 1.0 P C:DA502 3.1 28.8 1.0 OE1 B:GLN246 3.3 29.2 1.0 C A:ALA18 3.4 29.4 1.0 CD B:GLN246 3.5 23.6 1.0 CA A:ALA18 3.7 27.1 1.0 P F:DG614 3.8 30.0 1.0 O3' C:DA501 3.8 33.3 1.0 OP2 C:DA502 3.9 35.8 1.0 C5' C:DA502 4.0 26.8 1.0 O5' C:DA502 4.0 35.3 1.0 O F:EOH802 4.1 45.2 1.0 OP2 F:DG614 4.2 39.9 1.0 CG B:GLU219 4.2 29.4 1.0 O A:GLU17 4.2 37.2 1.0 C1 F:EOH802 4.4 46.2 1.0 O B:HOH1063 4.4 42.4 1.0 C4' C:DA502 4.4 30.3 1.0 CB A:ALA18 4.5 37.6 1.0 N A:GLU19 4.7 35.3 1.0 OP1 F:DG614 4.7 39.6 1.0 C2 F:EOH802 4.7 30.0 1.0 O5' F:DG614 4.8 26.4 1.0 N A:ALA18 4.9 32.6 1.0 CG B:GLN246 4.9 24.0 1.0 MG B:MG701 5.0 49.3 1.0 C A:GLU17 5.0 35.5 1.0

N.Nomura, Y.Nomura, D.Sussman, D.Klein, B.L.Stoddard. Recognition of A Common Rdna Target Site in Archaea and Eukarya By Analogous Laglidadg and His-Cys Box Homing Endonucleases Nucleic Acids Res. V. 36 6988 2008.
ISSN: ISSN 0305-1048
PubMed: 18984620
DOI: 10.1093/NAR/GKN846