Magnesium in PDB 2qoj: Coevolution of A Homing Endonuclease and Its Host Target Sequence

The structure of Coevolution of A Homing Endonuclease and Its Host Target Sequence, PDB code: 2qoj was solved by M.Scalley-Kim, A.Mcconnell Smith, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.30 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.353, 72.701, 61.100, 90.00, 103.88, 90.00
R / Rfree (%)	21.6 / 27.6

The binding sites of Magnesium atom in the Coevolution of A Homing Endonuclease and Its Host Target Sequence (pdb code 2qoj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Coevolution of A Homing Endonuclease and Its Host Target Sequence, PDB code: 2qoj:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Coevolution of A Homing Endonuclease and Its Host Target Sequence


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Coevolution of A Homing Endonuclease and Its Host Target Sequence within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg601 b:22.2 occ:1.00 OP2 Y:DC517 2.0 35.5 1.0 MG Z:MG603 2.4 37.5 1.0 O3' Y:DA516 2.5 29.1 1.0 OE1 Z:GLU148 2.6 17.8 1.0 P Y:DC517 2.7 39.0 1.0 OE2 Z:GLU148 2.8 23.3 1.0 O Z:GLY15 2.9 17.1 1.0 CD Z:GLU148 3.1 18.8 1.0 OD2 Z:ASP16 3.1 16.4 1.0 OP2 X:DT417 3.1 29.9 0.5 O3' X:DC416 3.1 32.6 1.0 C4' X:DC416 3.4 30.6 1.0 OP1 X:DC416 3.5 31.5 1.0 C3' X:DC416 3.7 31.6 1.0 C3' Y:DA516 3.7 22.4 1.0 OP1 Y:DC517 3.8 37.6 1.0 P X:DT417 3.8 31.7 0.5 C Z:GLY15 3.8 16.8 1.0 O5' Y:DC517 3.9 34.9 1.0 C5' X:DC416 4.1 30.3 1.0 CG Z:ASP16 4.3 17.2 1.0 O4' X:DC416 4.4 30.5 1.0 O3' X:DT415 4.4 30.9 1.0 O X:HOH3 4.5 20.5 1.0 P X:DC416 4.5 30.7 1.0 CA Z:ASP16 4.5 17.0 1.0 C4' Y:DA516 4.5 18.4 1.0 CG Z:GLU148 4.6 16.8 1.0 N Z:ASP16 4.6 16.6 1.0 CA Z:GLY15 4.7 15.8 1.0 O5' X:DC416 4.8 31.3 1.0 C5' Y:DC517 4.8 28.7 1.0 O5' X:DT417 4.8 30.6 1.0 OP1 X:DT417 4.8 31.8 0.5 C2' Y:DA516 4.9 18.7 1.0 MG Z:MG602 5.0 47.2 1.0

Magnesium binding site 2 out of 3 in the Coevolution of A Homing Endonuclease and Its Host Target Sequence


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Coevolution of A Homing Endonuclease and Its Host Target Sequence within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg602 b:47.2 occ:1.00 OP2 X:DT417 2.2 29.9 0.5 O Z:ALA147 2.3 16.5 1.0 OP1 Y:DA516 2.3 19.6 1.0 OD1 Z:ASP16 2.6 20.1 1.0 O Y:HOH1 2.7 15.5 1.0 OD2 Z:ASP16 3.1 16.4 1.0 CG Z:ASP16 3.2 17.2 1.0 P X:DT417 3.2 31.7 0.5 C Z:ALA147 3.3 16.6 1.0 OP1 X:DT417 3.5 31.8 0.5 P Y:DA516 3.6 16.0 1.0 CA Z:ALA147 3.9 16.6 1.0 O5' X:DT417 3.9 30.6 1.0 O3' Y:DA515 4.0 20.8 1.0 C5' Y:DA516 4.0 18.0 1.0 OE1 Z:GLU148 4.2 17.8 1.0 C5' X:DT417 4.2 24.9 1.0 O5' Y:DA516 4.3 18.5 1.0 C4' Y:DA516 4.4 18.4 1.0 N Z:GLU148 4.5 16.8 1.0 O Z:GLU146 4.5 16.7 1.0 CB Z:ALA147 4.6 15.7 1.0 O3' X:DC416 4.7 32.6 1.0 CB Z:ASP16 4.7 16.9 1.0 OP2 Y:DA516 4.8 20.1 1.0 CA Z:GLU148 4.9 17.4 1.0 C4' X:DT417 4.9 24.2 1.0 MG Z:MG601 5.0 22.2 1.0

Magnesium binding site 3 out of 3 in the Coevolution of A Homing Endonuclease and Its Host Target Sequence


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Coevolution of A Homing Endonuclease and Its Host Target Sequence within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg603 b:37.5 occ:1.00 OE2 Z:GLU148 2.0 23.3 1.0 O Z:GLY15 2.1 17.1 1.0 OP1 X:DC416 2.1 31.5 1.0 OP2 Y:DC517 2.2 35.5 1.0 MG Z:MG601 2.4 22.2 1.0 CD Z:GLU148 3.1 18.8 1.0 C Z:GLY15 3.1 16.8 1.0 OE1 Z:GLU148 3.5 17.8 1.0 P X:DC416 3.5 30.7 1.0 CA Z:GLY15 3.5 15.8 1.0 P Y:DC517 3.7 39.0 1.0 OE1 Z:GLN171 3.7 20.1 1.0 NE2 Z:GLN171 3.9 19.6 1.0 O3' X:DT415 4.0 30.9 1.0 O Z:GLU14 4.1 16.8 1.0 C5' X:DC416 4.2 30.3 1.0 CD Z:GLN171 4.2 20.1 1.0 C4' X:DC416 4.3 30.6 1.0 CG Z:GLU148 4.3 16.8 1.0 N Z:ASP16 4.3 16.6 1.0 O5' X:DC416 4.4 31.3 1.0 O3' Y:DA516 4.4 29.1 1.0 O Z:HOH636 4.4 16.2 1.0 OP2 X:DC416 4.6 31.1 1.0 OD2 Z:ASP16 4.6 16.4 1.0 O5' Y:DC517 4.6 34.9 1.0 N Z:GLY15 4.7 16.1 1.0 OP1 Y:DC517 4.7 37.6 1.0 CA Z:ASP16 4.8 17.0 1.0 C Z:GLU14 4.8 16.2 1.0 C5' Y:DC517 4.8 28.7 1.0

M.Scalley-Kim, A.Mcconnell-Smith, B.L.Stoddard. Coevolution of A Homing Endonuclease and Its Host Target Sequence. J.Mol.Biol. V. 372 1305 2007.
ISSN: ISSN 0022-2836
PubMed: 17720189
DOI: 10.1016/J.JMB.2007.07.052