Magnesium in PDB 2vbl: Molecular Basis of Human Xpc Gene Recognition and Cleavage By Engineered Homing Endonuclease Heterodimers

The structure of Molecular Basis of Human Xpc Gene Recognition and Cleavage By Engineered Homing Endonuclease Heterodimers, PDB code: 2vbl was solved by P.Redondo, J.Prieto, I.G.Munoz, A.Alibes, F.Stricher, L.Serrano, S.Arnould, C.Perez, J.P.Cabaniols, P.Duchateau, F.Paques, F.J.Blanco, G.Montoya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.92 / 1.8
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.612, 69.209, 88.671, 90.00, 95.46, 90.00
R / Rfree (%)	14.7 / 19.7

The binding sites of Magnesium atom in the Molecular Basis of Human Xpc Gene Recognition and Cleavage By Engineered Homing Endonuclease Heterodimers (pdb code 2vbl). 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 Human Xpc Gene Recognition and Cleavage By Engineered Homing Endonuclease Heterodimers, PDB code: 2vbl:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Molecular Basis of Human Xpc Gene Recognition and Cleavage By Engineered Homing Endonuclease Heterodimers


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 Human Xpc Gene Recognition and Cleavage By Engineered Homing Endonuclease Heterodimers within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1025 b:17.6 occ:1.00 OP1 E:DA14 2.1 21.5 1.0 O A:GLY19 2.2 24.9 1.0 OP2 T:DA15 2.3 25.4 1.0 O A:HOH2012 2.3 28.4 1.0 O T:HOH2005 2.3 30.0 1.0 OD2 B:ASP20 2.4 25.2 1.0 OP3 T:DA15 2.4 46.2 1.0 OD1 B:ASP20 2.9 26.5 1.0 CG B:ASP20 3.0 21.1 1.0 P T:DA15 3.2 30.1 1.0 C A:GLY19 3.2 23.1 1.0 P E:DA14 3.5 23.2 1.0 MG C:MG1026 3.6 23.5 1.0 CA A:GLY19 3.7 22.1 1.0 O5' T:DA15 3.9 25.8 1.0 O3' E:DA13 4.0 25.5 1.0 NE2 B:GLN47 4.1 25.1 1.0 O A:HOH2075 4.2 44.7 1.0 OP1 T:DA15 4.2 27.5 1.0 O A:ASP18 4.2 23.4 1.0 OE1 B:GLN47 4.3 26.2 1.0 C5' E:DA14 4.3 21.6 1.0 N A:ASP20 4.4 21.2 1.0 C5' T:DA15 4.4 23.5 1.0 C4' E:DA14 4.4 21.0 1.0 O5' E:DA14 4.4 22.0 1.0 CB B:ASP20 4.5 21.1 1.0 O3' C:DA14 4.5 23.2 1.0 OP2 E:DA14 4.5 22.9 1.0 CD B:GLN47 4.6 24.9 1.0 OD1 A:ASP20 4.7 23.5 1.0 CA A:ASP20 4.8 20.5 1.0 N A:GLY19 4.9 22.7 1.0 C A:ASP18 5.0 22.5 1.0

Magnesium binding site 2 out of 3 in the Molecular Basis of Human Xpc Gene Recognition and Cleavage By Engineered Homing Endonuclease Heterodimers


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 Human Xpc Gene Recognition and Cleavage By Engineered Homing Endonuclease Heterodimers within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1026 b:23.5 occ:1.00 OP1 S:DA15 1.9 24.7 1.0 OP2 T:DA15 2.0 25.4 1.0 OD1 A:ASP20 2.2 23.5 1.0 OD1 B:ASP20 2.2 26.5 1.0 O3' C:DA14 2.5 23.2 1.0 O3' E:DA14 2.6 23.1 1.0 P T:DA15 3.0 30.1 1.0 P S:DA15 3.2 30.4 1.0 CG A:ASP20 3.4 22.2 1.0 CG B:ASP20 3.5 21.1 1.0 C3' C:DA14 3.5 21.0 1.0 C3' E:DA14 3.6 19.9 1.0 MG C:MG1025 3.6 17.6 1.0 MG E:MG1025 3.6 17.4 1.0 O A:GLY19 3.7 24.9 1.0 O5' T:DA15 3.8 25.8 1.0 O B:ALA19 3.8 24.4 1.0 O5' S:DA15 3.9 23.3 1.0 C4' C:DA14 3.9 24.8 1.0 OP3 T:DA15 4.0 46.2 1.0 C4' E:DA14 4.0 21.0 1.0 OD2 B:ASP20 4.1 25.2 1.0 OP1 T:DA15 4.1 27.5 1.0 OP3 S:DA15 4.1 26.2 1.0 OP2 S:DA15 4.2 48.8 1.0 OD2 A:ASP20 4.2 24.0 1.0 C A:GLY19 4.3 23.1 1.0 CA A:ASP20 4.3 20.5 1.0 C B:ALA19 4.3 20.9 1.0 CB A:ASP20 4.4 22.3 1.0 CA B:ASP20 4.4 19.9 1.0 CB B:ASP20 4.5 21.1 1.0 O T:HOH2006 4.5 27.9 1.0 O S:HOH2005 4.6 30.8 1.0 N A:ASP20 4.6 21.2 1.0 OP1 C:DA14 4.7 23.7 1.0 OP1 E:DA14 4.7 21.5 1.0 N B:ASP20 4.7 20.2 1.0 C5' C:DA14 4.8 22.4 1.0 C5' E:DA14 4.9 21.6 1.0 C2' C:DA14 4.9 24.6 1.0 C2' E:DA14 5.0 24.6 1.0

Magnesium binding site 3 out of 3 in the Molecular Basis of Human Xpc Gene Recognition and Cleavage By Engineered Homing Endonuclease Heterodimers


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 Human Xpc Gene Recognition and Cleavage By Engineered Homing Endonuclease Heterodimers within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1025 b:17.4 occ:1.00 OP1 C:DA14 2.1 23.7 1.0 O B:ALA19 2.2 24.4 1.0 O B:HOH2023 2.3 20.5 1.0 OD2 A:ASP20 2.4 24.0 1.0 O S:HOH2004 2.4 25.7 1.0 OP1 S:DA15 2.5 24.7 1.0 OP2 S:DA15 2.5 48.8 1.0 OD1 A:ASP20 2.8 23.5 1.0 CG A:ASP20 3.0 22.2 1.0 P S:DA15 3.1 30.4 1.0 C B:ALA19 3.2 20.9 1.0 P C:DA14 3.6 25.0 1.0 MG C:MG1026 3.6 23.5 1.0 CA B:ALA19 3.7 20.6 1.0 O5' S:DA15 4.0 23.3 1.0 O3' C:DG13 4.0 23.8 1.0 OE1 A:GLN47 4.1 29.0 1.0 O B:ASP18 4.2 24.2 1.0 NE2 A:GLN47 4.3 19.5 1.0 OP3 S:DA15 4.3 26.2 1.0 C5' C:DA14 4.3 22.4 1.0 O B:HOH2099 4.3 51.9 1.0 O B:HOH2098 4.4 81.1 1.0 N B:ASP20 4.4 20.2 1.0 C5' S:DA15 4.4 19.2 1.0 C4' C:DA14 4.5 24.8 1.0 CB A:ASP20 4.5 22.3 1.0 O5' C:DA14 4.5 23.0 1.0 OP2 C:DA14 4.5 24.5 1.0 O3' E:DA14 4.6 23.1 1.0 CB B:ALA19 4.6 25.8 1.0 CD A:GLN47 4.6 21.8 1.0 OD1 B:ASP20 4.7 26.5 1.0 CA B:ASP20 4.8 19.9 1.0 N B:ALA19 4.9 20.3 1.0 C B:ASP18 5.0 21.9 1.0

P.Redondo, J.Prieto, I.G.Munoz, A.Alibes, F.Stricher, L.Serrano, J.P.Cabaniols, F.Daboussi, S.Arnould, C.Perez, P.Duchateau, F.Paques, F.J.Blanco, G.Montoya. Molecular Basis of Xeroderma Pigmentosum Group C Dna Recognition By Engineered Meganucleases Nature V. 456 107 2008.
ISSN: ISSN 0028-0836
PubMed: 18987743
DOI: 10.1038/NATURE07343