Magnesium in PDB 4aab: Crystal Structure of the Mutant D75N I-Crei in Complex with Its Wild-Type Target (the Four Central Bases, 2NN Region, Are Composed By Gtac From 5' to 3')

The structure of Crystal Structure of the Mutant D75N I-Crei in Complex with Its Wild-Type Target (the Four Central Bases, 2NN Region, Are Composed By Gtac From 5' to 3'), PDB code: 4aab was solved by R.Molina, P.Redondo, S.Stella, M.Marenchino, M.D'abramo, F.L.Gervasio, J.C.Epinat, J.Valton, S.Grizot, P.Duchateau, J.Prieto, G.Montoya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.814 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	171.970, 71.100, 46.920, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 22.51

The structure of Crystal Structure of the Mutant D75N I-Crei in Complex with Its Wild-Type Target (the Four Central Bases, 2NN Region, Are Composed By Gtac From 5' to 3') also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Mutant D75N I-Crei in Complex with Its Wild-Type Target (the Four Central Bases, 2NN Region, Are Composed By Gtac From 5' to 3') (pdb code 4aab). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Mutant D75N I-Crei in Complex with Its Wild-Type Target (the Four Central Bases, 2NN Region, Are Composed By Gtac From 5' to 3'), PDB code: 4aab:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Mutant D75N I-Crei in Complex with Its Wild-Type Target (the Four Central Bases, 2NN Region, Are Composed By Gtac From 5' to 3')


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Mutant D75N I-Crei in Complex with Its Wild-Type Target (the Four Central Bases, 2NN Region, Are Composed By Gtac From 5' to 3') within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1156 b:35.2 occ:1.00 OP1 G:DG615 1.9 32.5 1.0 OD1 B:ASP20 2.1 29.5 1.0 OP2 E:DG515 2.1 27.4 1.0 OD1 A:ASP20 2.2 28.8 1.0 O3' F:DC614 2.3 29.9 1.0 O3' D:DC514 2.5 29.1 1.0 P G:DG615 3.0 36.0 1.0 CG A:ASP20 3.2 28.5 1.0 C3' F:DC614 3.2 29.3 1.0 CG B:ASP20 3.2 33.0 1.0 O5' G:DG615 3.3 25.1 1.0 P E:DG515 3.4 35.1 1.0 OD2 A:ASP20 3.5 27.4 1.0 C3' D:DC514 3.5 26.7 0.9 OP3 G:DG615 3.6 28.0 1.0 MG E:MG1527 3.8 20.7 1.0 O B:GLY19 3.8 28.0 1.0 C4' F:DC614 3.8 26.5 1.0 OD2 B:ASP20 3.9 23.4 1.0 MG B:MG1157 3.9 19.6 1.0 O5' E:DG515 4.0 28.5 1.0 C4' D:DC514 4.0 27.6 1.0 O D:HOH2013 4.0 27.6 1.0 O D:HOH2014 4.0 22.8 1.0 OP1 E:DG515 4.1 42.0 1.0 O A:GLY19 4.2 28.4 1.0 OP2 G:DG615 4.3 42.1 1.0 CB B:ASP20 4.4 24.8 1.0 CA B:ASP20 4.4 27.6 1.0 OP3 E:DG515 4.4 19.4 1.0 CB A:ASP20 4.5 28.1 1.0 C B:GLY19 4.5 27.7 1.0 OP1 D:DC514 4.5 34.3 1.0 C2' F:DC614 4.5 26.9 1.0 C5' G:DG615 4.7 18.7 1.0 CA A:ASP20 4.7 32.9 1.0 C5' F:DC614 4.7 27.1 1.0 C A:GLY19 4.7 24.4 1.0 OP1 F:DC614 4.8 32.8 1.0 N B:ASP20 4.8 25.2 1.0 C2' D:DC514 4.9 26.5 1.0 O4' F:DC614 4.9 31.9 1.0 C5' D:DC514 4.9 25.6 1.0 C1' F:DC614 5.0 25.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Mutant D75N I-Crei in Complex with Its Wild-Type Target (the Four Central Bases, 2NN Region, Are Composed By Gtac From 5' to 3')


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Mutant D75N I-Crei in Complex with Its Wild-Type Target (the Four Central Bases, 2NN Region, Are Composed By Gtac From 5' to 3') within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1157 b:19.6 occ:1.00 OP1 D:DC514 2.0 34.3 1.0 O A:HOH2007 2.1 33.1 1.0 OD2 A:ASP20 2.1 27.4 1.0 OP1 G:DG615 2.3 32.5 1.0 O B:GLY19 2.4 28.0 1.0 OP2 G:DG615 2.4 42.1 1.0 P G:DG615 2.8 36.0 1.0 O1 B:PGO1154 3.2 42.6 1.0 CG A:ASP20 3.3 28.5 1.0 P D:DC514 3.4 31.4 1.0 C B:GLY19 3.4 27.7 1.0 C1 B:PGO1154 3.6 48.5 1.0 OD1 A:ASP20 3.8 28.8 1.0 O5' G:DG615 3.8 25.1 1.0 MG B:MG1156 3.9 35.2 1.0 CA B:GLY19 3.9 27.2 1.0 O3' D:DA513 3.9 34.8 1.0 OP3 G:DG615 4.0 28.0 1.0 O B:ASP18 4.0 29.1 1.0 OE1 A:GLN47 4.1 28.0 1.0 NE2 A:GLN47 4.1 27.9 1.0 OP2 D:DC514 4.3 32.8 1.0 C5' G:DG615 4.4 18.7 1.0 C5' D:DC514 4.4 25.6 1.0 O5' D:DC514 4.5 33.0 1.0 CB A:ASP20 4.5 28.1 1.0 OD1 B:ASP20 4.5 29.5 1.0 CD A:GLN47 4.5 31.1 1.0 C4' D:DC514 4.5 27.6 1.0 N B:ASP20 4.6 25.2 1.0 O B:HOH2044 4.8 40.0 1.0 C B:ASP18 4.9 26.6 1.0 N B:GLY19 4.9 27.2 1.0 CA B:ASP20 5.0 27.6 1.0 C2 B:PGO1154 5.0 51.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Mutant D75N I-Crei in Complex with Its Wild-Type Target (the Four Central Bases, 2NN Region, Are Composed By Gtac From 5' to 3')


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Mutant D75N I-Crei in Complex with Its Wild-Type Target (the Four Central Bases, 2NN Region, Are Composed By Gtac From 5' to 3') within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1527 b:20.7 occ:1.00 OP3 E:DG515 1.9 19.4 1.0 OD2 B:ASP20 2.0 23.4 1.0 OP1 F:DC614 2.1 32.8 1.0 O A:HOH2005 2.1 28.4 1.0 O A:GLY19 2.2 28.4 1.0 OP2 E:DG515 2.2 27.4 1.0 P E:DG515 2.6 35.1 1.0 CG B:ASP20 2.9 33.0 1.0 OD1 B:ASP20 3.2 29.5 1.0 C A:GLY19 3.2 24.4 1.0 P F:DC614 3.5 28.2 1.0 O5' E:DG515 3.7 28.5 1.0 CA A:GLY19 3.7 21.2 1.0 OP1 E:DG515 3.7 42.0 1.0 MG B:MG1156 3.8 35.2 1.0 O1 E:PGO1525 3.9 47.5 1.0 OD1 A:ASP20 4.0 28.8 1.0 O3' F:DA613 4.1 23.0 1.0 NE2 B:GLN47 4.2 29.4 1.0 C5' F:DC614 4.2 27.1 1.0 O A:ASP18 4.3 35.6 1.0 N A:ASP20 4.3 28.0 1.0 CB B:ASP20 4.3 24.8 1.0 C4' F:DC614 4.3 26.5 1.0 C5' E:DG515 4.3 28.0 1.0 O5' F:DC614 4.4 33.0 1.0 OE1 B:GLN47 4.4 35.7 1.0 OP2 F:DC614 4.5 25.8 1.0 CA A:ASP20 4.7 32.9 1.0 C1 E:PGO1525 4.7 46.6 1.0 CD B:GLN47 4.7 34.5 1.0 O3' D:DC514 4.7 29.1 1.0 O3' F:DC614 4.8 29.9 1.0 N A:GLY19 4.9 26.0 1.0 C3' F:DC614 4.9 29.3 1.0

R.Molina, P.Redondo, S.Stella, M.Marenchino, M.D'abramo, F.L.Gervasio, J.Charles Epinat, J.Valton, S.Grizot, P.Duchateau, J.Prieto, G.Montoya. Non-Specific Protein-Dna Interactions Control I-Crei Target Binding and Cleavage. Nucleic Acids Res. V. 40 6936 2012.
ISSN: ISSN 0305-1048
PubMed: 22495931
DOI: 10.1093/NAR/GKS320