Magnesium in PDB 2xe0: Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus

The structure of Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus, PDB code: 2xe0 was solved by I.G.Munoz, J.Prieto, S.Subramanian, J.Coloma, P.Redondo, M.Villate, N.Merino, M.Marenchino, M.D'abramo, F.L.Gervasio, S.Grizot, F.Daboussi, J.Smith, I.Chion-Sotine, F.Paques, P.Duchateau, A.Alibes, F.Stricher, L.Serrano, F.J.Blanco, G.Montoya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.769 / 2.31
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	177.857, 71.538, 45.005, 90.00, 90.00, 90.00
R / Rfree (%)	21.31 / 25.57

The binding sites of Magnesium atom in the Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus (pdb code 2xe0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus, PDB code: 2xe0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1525 b:20.8 occ:1.00 OP1 D:DC614 2.3 39.0 1.0 O A:GLY19 2.4 37.1 1.0 O A:HOH2002 2.4 34.7 1.0 OP3 C:DC515 2.4 29.1 1.0 OD2 B:ASP20 2.5 33.7 1.0 OP1 C:DC515 2.5 38.1 1.0 OD1 B:ASP20 2.8 32.3 1.0 CG B:ASP20 3.0 33.8 1.0 P C:DC515 3.1 34.8 0.7 C A:GLY19 3.3 35.2 1.0 MG C:MG1526 3.6 33.4 1.0 P D:DC614 3.7 36.8 1.0 CA A:GLY19 3.8 33.9 1.0 O5' C:DC515 4.0 32.5 1.0 O3' D:DA613 4.2 39.1 1.0 O A:ASP18 4.3 36.9 1.0 OP2 C:DC515 4.3 37.4 1.0 C5' D:DC614 4.3 31.3 1.0 NE2 B:GLN47 4.4 33.6 1.0 CB B:ASP20 4.4 34.5 1.0 C4' D:DC614 4.5 34.4 0.9 N A:ASP20 4.5 32.7 1.0 O5' D:DC614 4.5 34.2 1.0 C5' C:DC515 4.5 30.9 0.9 OD1 A:ASP20 4.6 31.8 1.0 OE1 B:GLN47 4.6 34.8 1.0 OP2 D:DC614 4.7 37.3 1.0 O3' C:DC514 4.8 32.0 1.0 CD B:GLN47 4.9 37.2 1.0 N A:GLY19 4.9 34.0 1.0 CA A:ASP20 4.9 34.7 1.0 OXT A:ACT1155 5.0 51.2 1.0

Magnesium binding site 2 out of 3 in the Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1526 b:33.4 occ:1.00 OP3 D:DC615 2.1 25.5 1.0 OP3 C:DC515 2.1 29.1 1.0 OD1 A:ASP20 2.1 31.8 1.0 OD1 B:ASP20 2.4 32.3 1.0 O3' D:DC614 2.8 28.6 1.0 O3' C:DC514 2.8 32.0 1.0 CG A:ASP20 3.3 34.0 1.0 P C:DC515 3.5 34.8 0.7 P D:DC615 3.5 28.6 0.4 MG D:MG1625 3.6 22.9 1.0 CG B:ASP20 3.6 33.8 1.0 MG C:MG1525 3.6 20.8 1.0 O B:GLY19 3.6 34.9 1.0 O A:GLY19 3.7 37.1 1.0 C3' D:DC614 3.8 32.4 0.7 C3' C:DC514 3.8 32.6 1.0 O5' C:DC515 3.9 32.5 1.0 O5' D:DC615 3.9 30.0 1.0 OD2 A:ASP20 3.9 34.9 1.0 OP2 C:DC515 4.0 37.4 1.0 C4' D:DC614 4.1 34.4 0.9 OP2 D:DC615 4.1 28.7 1.0 C4' C:DC514 4.1 33.8 0.9 C B:GLY19 4.2 36.1 1.0 C A:GLY19 4.2 35.2 1.0 CA B:ASP20 4.3 32.2 1.0 CA A:ASP20 4.3 34.7 1.0 OD2 B:ASP20 4.3 33.7 1.0 CB A:ASP20 4.4 32.4 1.0 OP1 D:DC615 4.4 36.0 1.0 N B:ASP20 4.5 36.1 1.0 OP1 C:DC515 4.5 38.1 1.0 N A:ASP20 4.5 32.7 1.0 CB B:ASP20 4.5 34.5 1.0 O D:HOH2004 4.5 39.1 1.0 O C:HOH2014 4.6 36.5 1.0 OP1 C:DC514 4.8 31.7 1.0 OP1 D:DC614 4.9 39.0 1.0

Magnesium binding site 3 out of 3 in the Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1625 b:22.9 occ:1.00 O B:GLY19 2.2 34.9 1.0 OD2 A:ASP20 2.2 34.9 1.0 OP1 D:DC615 2.3 36.0 1.0 OP1 C:DC514 2.3 31.7 1.0 O B:HOH2001 2.5 33.7 1.0 OP3 D:DC615 2.6 25.5 1.0 CG A:ASP20 3.0 34.0 1.0 OD1 A:ASP20 3.0 31.8 1.0 P D:DC615 3.0 28.6 0.4 C B:GLY19 3.2 36.1 1.0 MG C:MG1526 3.6 33.4 1.0 CA B:GLY19 3.7 31.8 1.0 P C:DC514 3.7 33.3 1.0 O5' D:DC615 3.9 30.0 1.0 O3' C:DA513 4.2 35.2 1.0 O B:ASP18 4.2 33.2 1.0 OP2 D:DC615 4.2 28.7 1.0 N B:ASP20 4.3 36.1 1.0 NE2 A:GLN47 4.3 32.0 1.0 CB A:ASP20 4.4 32.4 1.0 C5' D:DC615 4.5 29.2 0.7 OE1 A:GLN47 4.5 36.1 1.0 C3 B:PGO1155 4.5 34.4 1.0 C4' C:DC514 4.6 33.8 0.9 C5' C:DC514 4.6 32.1 0.8 O3' D:DC614 4.7 28.6 1.0 O5' C:DC514 4.7 29.5 1.0 OP2 C:DC514 4.7 33.8 1.0 OD1 B:ASP20 4.8 32.3 1.0 CA B:ASP20 4.8 32.2 1.0 N B:GLY19 4.8 28.7 1.0 CD A:GLN47 4.8 33.4 1.0 C B:ASP18 4.9 32.2 1.0

I.G.Munoz, J.Prieto, S.Subramanian, J.Coloma, P.Redondo, M.Villate, N.Merino, M.Marenchino, M.D'abramo, F.L.Gervasio, S.Grizot, F.Daboussi, J.Smith, I.Chion-Sotine, F.Paques, P.Duchateau, A.Alibes, F.Stricher, L.Serrano, F.J.Blanco, G.Montoya. Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus Nucleic Acids Res. V. 39 729 2011.
ISSN: ISSN 0305-1048
PubMed: 20846960
DOI: 10.1093/NAR/GKQ801