Magnesium in PDB 1u0c: Y33C Mutant of Homing Endonuclease I-Crei

The structure of Y33C Mutant of Homing Endonuclease I-Crei, PDB code: 1u0c was solved by D.Sussman, M.Chadsey, S.Fauce, A.Engel, A.Bruett, R.Monnat, B.L.Stoddard, L.M.Seligman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.089, 68.021, 87.182, 90.00, 92.00, 90.00
R / Rfree (%)	21.4 / 27.7

The binding sites of Magnesium atom in the Y33C Mutant of Homing Endonuclease I-Crei (pdb code 1u0c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Y33C Mutant of Homing Endonuclease I-Crei, PDB code: 1u0c:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Y33C Mutant of Homing Endonuclease I-Crei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Y33C Mutant of Homing Endonuclease I-Crei within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:22.2 occ:1.00 OD1 B:ASP320 2.1 20.1 1.0 OP2 C:DG515 2.3 14.2 0.5 OP2 D:DG565 2.4 26.6 0.5 OD2 A:ASP20 2.5 24.0 1.0 O3' D:DC564 2.9 25.9 0.5 O3' C:DA514 2.9 12.4 0.5 P C:DG515 3.2 15.0 0.5 P D:DG565 3.2 26.1 0.5 CG B:ASP320 3.3 17.2 1.0 MG B:MG601 3.4 4.5 1.0 O A:GLY19 3.5 16.8 1.0 O B:GLY319 3.6 18.9 1.0 MG A:MG602 3.6 9.1 1.0 CG A:ASP20 3.7 23.0 1.0 C3' C:DA514 3.9 11.2 0.5 C3' D:DC564 3.9 25.5 0.5 C A:GLY19 4.0 20.5 1.0 O5' C:DG515 4.0 15.3 0.5 OD2 B:ASP320 4.1 15.9 1.0 CA B:ASP320 4.2 19.1 1.0 C B:GLY319 4.2 21.0 1.0 OP1 D:DG565 4.2 26.4 0.5 C4' D:DC564 4.3 25.2 0.5 CA A:ASP20 4.3 21.5 1.0 CB B:ASP320 4.3 18.9 1.0 O5' D:DG565 4.4 28.2 0.5 N A:ASP20 4.4 20.1 1.0 OP1 D:DC564 4.4 21.3 0.5 C4' C:DA514 4.4 13.1 0.5 OP1 C:DG515 4.4 15.4 0.5 N B:ASP320 4.5 19.5 1.0 OD1 A:ASP20 4.5 23.4 1.0 CB A:ASP20 4.6 22.1 1.0 O C:HOH36 4.9 20.4 1.0 CA A:GLY19 4.9 18.4 1.0 O C:HOH10 4.9 32.5 1.0 O D:HOH6 5.0 18.1 1.0

Magnesium binding site 2 out of 3 in the Y33C Mutant of Homing Endonuclease I-Crei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Y33C Mutant of Homing Endonuclease I-Crei within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:9.1 occ:1.00 OP1 C:DA514 2.3 10.8 0.5 O B:GLY319 2.3 18.9 1.0 O A:HOH619 2.4 17.3 1.0 O D:HOH7 2.4 22.2 1.0 OP2 D:DG565 2.4 26.6 0.5 OD1 A:ASP20 2.5 23.4 1.0 OD2 A:ASP20 2.6 24.0 1.0 CG A:ASP20 2.9 23.0 1.0 C B:GLY319 3.5 21.0 1.0 P C:DA514 3.6 11.4 0.5 MG C:MG603 3.6 22.2 1.0 P D:DG565 3.7 26.1 0.5 O3' C:DG513 3.8 10.6 0.5 CA B:GLY319 4.1 20.0 1.0 OP1 D:DG565 4.2 26.4 0.5 OE2 A:GLU47 4.2 21.6 1.0 OE1 A:GLU47 4.3 18.6 1.0 C5' C:DA514 4.4 11.5 0.5 O B:ASP318 4.4 18.8 1.0 C4' C:DA514 4.4 13.1 0.5 CB A:ASP20 4.4 22.1 1.0 O5' C:DA514 4.5 9.9 0.5 N B:ASP320 4.6 19.5 1.0 C5' D:DG565 4.6 26.3 0.5 O5' D:DG565 4.6 28.2 0.5 O B:HOH76 4.7 33.4 1.0 CD A:GLU47 4.7 20.8 1.0 OP2 C:DA514 4.7 6.8 0.5 OD1 B:ASP320 4.7 20.1 1.0 CA B:ASP320 4.8 19.1 1.0 O3' D:DC564 4.9 25.9 0.5 O3' C:DA514 5.0 12.4 0.5

Magnesium binding site 3 out of 3 in the Y33C Mutant of Homing Endonuclease I-Crei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Y33C Mutant of Homing Endonuclease I-Crei within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:4.5 occ:1.00 OP1 D:DC564 2.2 21.3 0.5 O A:GLY19 2.3 16.8 1.0 OP2 C:DG515 2.3 14.2 0.5 O C:HOH10 2.4 32.5 1.0 OD2 B:ASP320 2.5 15.9 1.0 O A:HOH606 2.5 30.9 1.0 OD1 B:ASP320 2.7 20.1 1.0 CG B:ASP320 2.9 17.2 1.0 C A:GLY19 3.3 20.5 1.0 MG C:MG603 3.4 22.2 1.0 P D:DC564 3.6 22.4 0.5 P C:DG515 3.7 15.0 0.5 OE1 B:GLU347 3.7 25.6 1.0 CA A:GLY19 3.7 18.4 1.0 O3' D:DA563 4.1 22.3 0.5 O A:ASP18 4.2 22.4 1.0 O5' C:DG515 4.3 15.3 0.5 C5' C:DG515 4.4 15.1 0.5 CB B:ASP320 4.4 18.9 1.0 N A:ASP20 4.4 20.1 1.0 OP2 D:DC564 4.4 20.1 0.5 OP1 C:DG515 4.5 15.4 0.5 C4' D:DC564 4.6 25.2 0.5 CD B:GLU347 4.6 25.7 1.0 O5' D:DC564 4.7 22.8 0.5 C5' D:DC564 4.7 23.8 0.5 OE2 B:GLU347 4.7 24.1 1.0 O3' C:DA514 4.8 12.4 0.5 N A:GLY19 4.8 18.2 1.0 OD2 A:ASP20 4.8 24.0 1.0 CA A:ASP20 4.9 21.5 1.0 C A:ASP18 4.9 20.8 1.0 O3' D:DC564 5.0 25.9 0.5

D.Sussman, M.Chadsey, S.Fauce, A.Engel, A.Bruett, R.Monnat, B.L.Stoddard, L.M.Seligman. Isolation and Characterization of New Homing Endonuclease Specificities at Individual Target Site Positions. J.Mol.Biol. V. 342 31 2004.
ISSN: ISSN 0022-2836
PubMed: 15313605
DOI: 10.1016/J.JMB.2004.07.031