Manganese in PDB 3mxa: 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: 3mxa was solved by I.G.Munoz, J.Prieto, S.Subramanian, J.Coloma, G.Montoya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.95 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	72.000, 172.390, 46.530, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 22.4

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

Manganese 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 Manganese with other atoms in the Mn 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 A:Mn363 b:27.4 occ:1.00 OP1 C:DC514 2.1 23.6 1.0 OD2 A:ASP20 2.2 25.0 1.0 OP3 F:DC615 2.2 23.3 1.0 O A:SER210 2.3 25.2 1.0 O A:HOH395 2.3 20.7 1.0 OP1 F:DC615 2.3 33.5 1.0 P F:DC615 2.8 26.6 1.0 CG A:ASP20 3.1 30.7 1.0 C A:SER210 3.2 30.5 1.0 OD1 A:ASP20 3.4 32.1 1.0 P C:DC514 3.5 30.2 1.0 CA A:SER210 3.6 28.9 1.0 O5' F:DC615 3.7 22.1 1.0 MN A:MN365 3.8 26.2 1.0 O A:HOH385 4.0 23.4 1.0 OP2 F:DC615 4.0 28.1 1.0 NE2 A:GLN47 4.0 24.1 1.0 O3' C:DA513 4.1 30.8 1.0 OE1 A:GLN47 4.1 29.1 1.0 C5' C:DC514 4.3 29.4 1.0 O A:ASP209 4.3 32.8 1.0 C4' C:DC514 4.4 27.9 1.0 CB A:SER210 4.4 25.2 1.0 O5' C:DC514 4.4 33.4 1.0 N A:ASP211 4.4 21.8 1.0 OD1 A:ASP211 4.5 22.2 1.0 C5' F:DC615 4.5 29.0 1.0 CB A:ASP20 4.5 25.6 1.0 CD A:GLN47 4.5 29.6 1.0 OP2 C:DC514 4.5 31.2 1.0 N A:SER210 4.8 25.0 1.0 CA A:ASP211 4.9 23.8 1.0 O A:HOH398 4.9 31.6 1.0 C3' C:DC514 4.9 25.9 1.0 O3' C:DC514 5.0 29.3 1.0

Manganese 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 Manganese with other atoms in the Mn 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 A:Mn364 b:26.7 occ:1.00 O A:HOH396 2.1 20.0 1.0 OP1 E:DC614 2.1 32.1 1.0 OP3 D:DC515 2.1 22.1 1.0 OD2 A:ASP211 2.2 27.4 1.0 O A:GLY19 2.3 29.5 1.0 OP1 D:DC515 2.5 29.0 1.0 P D:DC515 2.8 27.2 1.0 CG A:ASP211 3.0 26.2 1.0 OD1 A:ASP211 3.2 22.2 1.0 C A:GLY19 3.3 28.4 1.0 P E:DC614 3.5 29.6 1.0 CA A:GLY19 3.7 24.8 1.0 O A:HOH450 3.9 29.3 1.0 O5' D:DC515 3.9 26.3 0.9 MN A:MN365 3.9 26.2 1.0 OP2 D:DC515 4.0 31.1 1.0 O3' E:DA613 4.0 27.6 0.9 NE2 A:GLN238 4.1 25.9 1.0 OE1 A:GLN238 4.2 28.3 1.0 O A:ASP18 4.2 33.6 1.0 C5' E:DC614 4.2 27.8 1.0 C4' E:DC614 4.4 25.1 1.0 O5' E:DC614 4.4 32.9 1.0 C5' D:DC515 4.4 22.3 1.0 OD1 A:ASP20 4.4 32.1 1.0 N A:ASP20 4.5 24.0 1.0 CB A:ASP211 4.5 23.9 1.0 OP2 E:DC614 4.5 30.6 1.0 CD A:GLN238 4.6 30.2 1.0 N A:GLY19 4.8 33.0 1.0 CA A:ASP20 4.9 24.1 1.0 C3' E:DC614 4.9 17.9 1.0 O3' E:DC614 4.9 25.7 1.0 O A:HOH390 4.9 30.8 1.0 C A:ASP18 5.0 23.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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 A:Mn365 b:26.2 occ:1.00 OP3 F:DC615 2.1 23.3 1.0 OD1 A:ASP20 2.2 32.1 1.0 OD1 A:ASP211 2.3 22.2 1.0 OP3 D:DC515 2.3 22.1 1.0 O3' E:DC614 2.4 25.7 1.0 O3' C:DC514 2.5 29.3 1.0 C3' C:DC514 3.3 25.9 1.0 C3' E:DC614 3.3 17.9 1.0 CG A:ASP20 3.3 30.7 1.0 P F:DC615 3.4 26.6 1.0 CG A:ASP211 3.4 26.2 1.0 P D:DC515 3.5 27.2 1.0 O5' F:DC615 3.7 22.1 1.0 O5' D:DC515 3.8 26.3 0.9 MN A:MN363 3.8 27.4 1.0 OP2 D:DC515 3.9 31.1 1.0 OD2 A:ASP20 3.9 25.0 1.0 OP2 F:DC615 3.9 28.1 1.0 MN A:MN364 3.9 26.7 1.0 C4' C:DC514 3.9 27.9 1.0 C4' E:DC614 4.0 25.1 1.0 O A:SER210 4.0 25.2 1.0 O C:HOH33 4.0 23.2 1.0 OD2 A:ASP211 4.0 27.4 1.0 O A:GLY19 4.2 29.5 1.0 O D:HOH27 4.2 31.8 1.0 OP1 F:DC615 4.5 33.5 1.0 CA A:ASP211 4.5 23.8 1.0 CB A:ASP20 4.6 25.6 1.0 C A:SER210 4.6 30.5 1.0 CB A:ASP211 4.6 23.9 1.0 CA A:ASP20 4.7 24.1 1.0 C2' E:DC614 4.7 18.3 1.0 OP1 D:DC515 4.7 29.0 1.0 C A:GLY19 4.7 28.4 1.0 C2' C:DC514 4.7 21.4 1.0 OP1 C:DC514 4.9 23.6 1.0 C5' C:DC514 4.9 29.4 1.0 N A:ASP211 4.9 21.8 1.0 C5' E:DC614 4.9 27.8 1.0 OP1 E:DC614 4.9 32.1 1.0 N A:ASP20 5.0 24.0 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-Sotinel, 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