Calcium in PDB 3mxb: 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: 3mxb 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)	35.84 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.050, 89.360, 86.340, 90.00, 99.51, 90.00
R / Rfree (%)	18 / 23.1

The binding sites of Calcium atom in the Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus (pdb code 3mxb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus, PDB code: 3mxb:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca175 b:19.5 occ:1.00 OP1 C:DC514 2.3 18.1 1.0 O B:SER19 2.4 22.2 1.0 OP2 E:DC615 2.4 22.6 1.0 OD2 A:ASP20 2.6 29.9 1.0 O B:HOH202 2.6 21.3 1.0 O B:HOH176 2.6 18.1 1.0 OD1 A:ASP20 2.9 20.4 1.0 CG A:ASP20 3.1 23.7 1.0 C B:SER19 3.4 20.6 1.0 P E:DC615 3.6 23.4 1.0 O A:HOH199 3.6 9.8 1.0 P C:DC514 3.6 20.8 1.0 CA B:SER19 3.9 15.8 1.0 O3' C:DA513 4.0 20.6 0.8 O5' E:DC615 4.1 21.7 1.0 NE2 A:GLN47 4.2 15.0 1.0 OP1 E:DC615 4.2 30.7 1.0 OE1 A:GLN47 4.3 17.9 1.0 C5' E:DC615 4.3 22.9 1.0 O B:ASP18 4.4 20.0 1.0 OP2 C:DC514 4.5 28.7 1.0 C4' C:DC514 4.5 19.6 1.0 C5' C:DC514 4.6 20.9 1.0 N B:ASP20 4.6 29.4 1.0 CB A:ASP20 4.6 18.5 1.0 O5' C:DC514 4.6 21.5 1.0 CD A:GLN47 4.7 17.8 1.0 CB B:SER19 4.7 25.6 1.0 O3' E:DC614 4.7 16.9 1.0 OD1 B:ASP20 4.8 24.0 1.0 O4 B:PO4175 4.9 73.8 1.0 CA B:ASP20 4.9 19.8 1.0 N B:SER19 5.0 26.1 1.0

Calcium binding site 2 out of 4 in the Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 B:Ca173 b:23.8 occ:1.00 OP1 E:DC614 2.3 21.9 1.0 OP2 C:DC515 2.4 31.3 1.0 O A:GLY19 2.5 19.7 1.0 OD2 B:ASP20 2.5 24.6 1.0 O C:HOH87 2.6 29.9 1.0 O A:HOH201 2.6 16.1 1.0 OD1 B:ASP20 3.0 24.0 1.0 CG B:ASP20 3.1 24.3 1.0 C A:GLY19 3.5 23.5 1.0 O A:HOH199 3.5 9.8 1.0 P C:DC515 3.6 33.8 1.0 P E:DC614 3.7 20.3 1.0 CA A:GLY19 4.0 24.7 1.0 O3' E:DA613 4.0 19.8 1.0 O5' C:DC515 4.1 35.1 0.9 NE2 B:GLN47 4.3 12.4 1.0 C5' C:DC515 4.3 36.8 1.0 O A:ASP18 4.3 28.6 1.0 OP1 C:DC515 4.4 38.3 1.0 OE1 B:GLN47 4.4 22.4 1.0 C4' E:DC614 4.5 21.4 0.9 C5' E:DC614 4.5 23.0 1.0 OP2 E:DC614 4.6 27.6 1.0 CB B:ASP20 4.6 21.3 1.0 N A:ASP20 4.6 27.0 1.0 O5' E:DC614 4.7 23.4 1.0 CD B:GLN47 4.8 15.8 1.0 O3' C:DC514 4.8 32.4 1.0 OD1 A:ASP20 4.9 20.4 1.0 CA A:ASP20 5.0 21.5 1.0

Calcium binding site 3 out of 4 in the Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 R:Ca175 b:20.8 occ:1.00 O S:SER19 2.3 21.3 1.0 OP1 T:DC514 2.4 21.1 1.0 OP2 V:DC615 2.4 25.9 1.0 O S:HOH195 2.4 24.7 1.0 OD2 R:ASP20 2.6 23.6 1.0 O S:HOH189 2.6 16.8 1.0 OD1 R:ASP20 3.0 20.8 1.0 CG R:ASP20 3.1 22.9 1.0 C S:SER19 3.3 18.8 1.0 O S:HOH196 3.5 9.8 1.0 P V:DC615 3.6 28.4 1.0 P T:DC514 3.7 21.9 1.0 CA S:SER19 3.8 18.5 1.0 O3' T:DA513 4.1 27.7 0.9 O5' V:DC615 4.1 20.7 0.9 NE2 R:GLN47 4.2 18.2 1.0 OP1 V:DC615 4.3 33.8 0.9 C5' V:DC615 4.3 23.4 1.0 OE1 R:GLN47 4.4 21.6 1.0 O S:ASP18 4.5 22.3 1.0 C5' T:DC514 4.5 17.9 1.0 N S:ASP20 4.5 21.1 1.0 C4' T:DC514 4.6 20.9 1.0 OP2 T:DC514 4.6 26.2 1.0 CB S:SER19 4.6 36.1 1.0 CB R:ASP20 4.6 16.7 1.0 O5' T:DC514 4.7 28.6 1.0 CD R:GLN47 4.7 23.1 1.0 O3' V:DC614 4.7 23.3 1.0 O1 S:PO4174 4.8 81.2 1.0 OD1 S:ASP20 4.8 16.4 1.0 CA S:ASP20 4.9 19.7 1.0 N S:SER19 4.9 19.3 1.0 O S:HOH182 5.0 32.6 1.0

Calcium binding site 4 out of 4 in the Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Molecular Basis of Engineered Meganuclease Targeting of the Endogenous Human RAG1 Locus within 5.0Å range: probe atom residue distance (Å) B Occ S:Ca173 b:23.1 occ:1.00 OP1 V:DC614 2.3 24.9 1.0 OP2 T:DC515 2.4 26.8 1.0 O R:GLY19 2.5 17.7 1.0 O T:HOH145 2.5 25.4 1.0 O S:HOH211 2.6 12.5 1.0 OD2 S:ASP20 2.6 27.3 1.0 OD1 S:ASP20 2.9 16.4 1.0 CG S:ASP20 3.1 24.4 1.0 C R:GLY19 3.5 21.6 1.0 O S:HOH196 3.5 9.8 1.0 P T:DC515 3.6 33.9 1.0 P V:DC614 3.7 24.5 1.0 CA R:GLY19 4.0 16.9 1.0 O5' T:DC515 4.0 25.4 0.6 O3' V:DA613 4.1 24.5 1.0 C5' T:DC515 4.2 31.0 0.8 OP1 T:DC515 4.3 32.4 1.0 O R:ASP18 4.3 32.6 1.0 OE1 S:GLN47 4.3 24.1 1.0 NE2 S:GLN47 4.4 18.1 1.0 OP2 V:DC614 4.6 28.1 0.9 C4' V:DC614 4.6 21.9 0.9 C5' V:DC614 4.6 16.0 1.0 CB S:ASP20 4.6 19.8 1.0 N R:ASP20 4.6 25.6 1.0 O5' V:DC614 4.7 20.4 1.0 CD S:GLN47 4.7 20.9 1.0 OD1 R:ASP20 4.8 20.8 1.0 O3' T:DC514 4.8 25.2 0.9 CA R:ASP20 4.9 13.1 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