Magnesium in PDB 5akm: The Crystal Structure of I-Dmoi G20S in Complex with Its Target Dna in the Presence of 2MM Mg

The structure of The Crystal Structure of I-Dmoi G20S in Complex with Its Target Dna in the Presence of 2MM Mg, PDB code: 5akm was solved by R.Molina, M.J.Marcaida, P.Redondo, M.Marenchino, M.D'abramo, G.Montoya, J.Prieto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.53 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.390, 68.650, 107.340, 90.00, 119.94, 90.00
R / Rfree (%)	17.9 / 23.5

The binding sites of Magnesium atom in the The Crystal Structure of I-Dmoi G20S in Complex with Its Target Dna in the Presence of 2MM Mg (pdb code 5akm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystal Structure of I-Dmoi G20S in Complex with Its Target Dna in the Presence of 2MM Mg, PDB code: 5akm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Crystal Structure of I-Dmoi G20S in Complex with Its Target Dna in the Presence of 2MM Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of I-Dmoi G20S in Complex with Its Target Dna in the Presence of 2MM Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1190 b:63.9 occ:1.00 OP3 E:DC16 2.1 63.9 1.0 O A:ALA116 2.5 47.6 1.0 OP1 B:DA14 2.6 67.6 1.0 OD1 A:ASP21 2.7 50.0 1.0 OD2 A:ASP21 3.0 61.8 1.0 O A:HOH2002 3.0 43.2 1.0 CG A:ASP21 3.2 59.0 1.0 O3' D:DC15 3.4 44.4 1.0 P E:DC16 3.5 71.0 1.0 OE1 A:GLU117 3.5 58.3 1.0 C A:ALA116 3.7 42.1 1.0 O5' E:DC16 3.8 59.5 1.0 P B:DA14 3.9 82.5 1.0 O3' B:DA13 4.2 95.7 1.0 OP1 E:DC16 4.3 55.8 1.0 CD A:GLU117 4.3 50.0 1.0 OP2 E:DC16 4.4 77.4 1.0 C4' B:DA14 4.4 72.6 1.0 CA A:ALA116 4.5 37.1 1.0 O3' B:DA14 4.5 66.5 1.0 C5' B:DA14 4.6 64.9 1.0 N A:GLU117 4.7 41.5 1.0 C3' D:DC15 4.7 44.0 1.0 CB A:ASP21 4.7 59.2 1.0 CA A:GLU117 4.7 36.0 1.0 O5' B:DA14 4.8 75.3 1.0 CB A:ALA116 4.8 31.4 1.0 OE2 A:GLU117 4.9 52.7 1.0

Magnesium binding site 2 out of 4 in the The Crystal Structure of I-Dmoi G20S in Complex with Its Target Dna in the Presence of 2MM Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of I-Dmoi G20S in Complex with Its Target Dna in the Presence of 2MM Mg within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1181 b:59.0 occ:1.00 OP2 J:DC16 2.1 88.9 1.0 OP1 G:DA14 2.2 52.5 1.0 O F:HOH2003 2.2 51.8 1.0 OD2 F:ASP21 2.2 64.8 1.0 O F:ALA116 2.4 63.9 1.0 OP3 J:DC16 2.8 0.7 1.0 CG F:ASP21 2.9 60.1 1.0 OD1 F:ASP21 2.9 51.8 1.0 P J:DC16 3.0 0.8 1.0 C F:ALA116 3.4 58.5 1.0 P G:DA14 3.6 52.7 1.0 O F:HOH2002 3.9 48.0 1.0 CA F:ALA116 4.0 46.5 1.0 O3' G:DA13 4.0 61.5 1.0 NZ F:LYS120 4.1 89.5 1.0 OP1 J:DC16 4.1 0.9 1.0 O5' J:DC16 4.1 94.8 1.0 C4' G:DA14 4.2 51.6 1.0 C5' G:DA14 4.3 50.5 1.0 CB F:ASP21 4.4 57.3 1.0 O5' G:DA14 4.4 61.2 1.0 N F:GLU117 4.5 63.2 1.0 CB F:ALA116 4.5 38.5 1.0 CG F:GLU117 4.6 77.6 1.0 NE2 F:GLN42 4.6 78.7 1.0 O3' G:DA14 4.6 42.0 1.0 OP2 G:DA14 4.7 56.8 1.0 OE1 F:GLN42 4.7 71.2 1.0 CA F:GLU117 4.8 68.7 1.0 C3' G:DA14 4.8 45.3 1.0 O F:VAL115 4.9 46.2 1.0 CE F:LYS120 5.0 97.8 1.0 C5' J:DC16 5.0 81.2 1.0

Magnesium binding site 3 out of 4 in the The Crystal Structure of I-Dmoi G20S in Complex with Its Target Dna in the Presence of 2MM Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of I-Dmoi G20S in Complex with Its Target Dna in the Presence of 2MM Mg within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1182 b:67.5 occ:1.00 OP1 I:DC15 2.2 73.4 1.0 OE2 F:GLU117 2.3 71.8 1.0 OP2 H:DG15 2.3 61.1 1.0 O F:HOH2001 2.4 55.1 1.0 O F:SER20 2.4 53.5 1.0 OP3 H:DG15 2.6 65.9 1.0 P H:DG15 2.9 66.4 1.0 CD F:GLU117 3.1 73.2 1.0 C F:SER20 3.2 45.4 1.0 OE1 F:GLU117 3.3 75.6 1.0 CA F:SER20 3.4 43.1 1.0 P I:DC15 3.6 68.2 1.0 O5' H:DG15 3.6 59.3 1.0 O F:ILE19 3.8 60.0 1.0 O F:HOH2002 4.0 48.0 1.0 O3' I:DA14 4.0 81.1 1.0 ND2 F:ASN129 4.1 54.7 1.0 C5' H:DG15 4.1 51.6 1.0 CB F:SER20 4.2 49.7 1.0 OP1 H:DG15 4.3 74.2 1.0 CG F:GLU117 4.4 77.6 1.0 OP2 I:DC15 4.4 66.3 1.0 N F:SER20 4.5 41.5 1.0 N F:ASP21 4.5 43.4 1.0 C4' I:DC15 4.5 67.0 1.0 C F:ILE19 4.6 50.2 1.0 O5' I:DC15 4.6 77.3 1.0 C5' I:DC15 4.7 68.7 1.0 OD1 F:ASP21 5.0 51.8 1.0

Magnesium binding site 4 out of 4 in the The Crystal Structure of I-Dmoi G20S in Complex with Its Target Dna in the Presence of 2MM Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of I-Dmoi G20S in Complex with Its Target Dna in the Presence of 2MM Mg within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg1182 b:63.8 occ:1.00 OP3 O:DC16 2.3 66.7 1.0 O K:ALA116 2.3 50.6 1.0 O K:HOH2003 2.6 42.1 1.0 OP1 L:DA14 2.6 59.0 1.0 OD1 K:ASP21 2.8 42.2 1.0 OD2 K:ASP21 3.0 59.8 1.0 CG K:ASP21 3.3 53.9 1.0 C K:ALA116 3.4 49.3 1.0 O3' N:DC15 3.5 79.6 1.0 P O:DC16 3.6 56.5 1.0 O K:HOH2002 3.8 55.7 1.0 O5' O:DC16 3.9 71.0 1.0 P L:DA14 4.0 55.0 1.0 CB K:GLU117 4.1 56.3 1.0 OE1 K:GLU117 4.1 87.3 1.0 CA K:GLU117 4.2 50.3 1.0 OP1 O:DC16 4.2 51.3 1.0 N K:GLU117 4.3 46.0 1.0 O3' L:DA13 4.3 50.6 1.0 CA K:ALA116 4.4 44.3 1.0 C4' L:DA14 4.4 46.0 1.0 OP2 O:DC16 4.6 65.7 1.0 O3' L:DA14 4.7 45.7 1.0 CB K:ALA116 4.7 30.7 1.0 C5' L:DA14 4.8 48.1 1.0 CG K:GLU117 4.8 74.8 1.0 C3' N:DC15 4.8 77.3 1.0 CB K:ASP21 4.8 48.6 1.0 CD K:GLU117 4.9 89.3 1.0 O5' L:DA14 4.9 59.1 1.0 OP2 L:DA14 5.0 48.6 1.0

R.Molina, M.J.Marcaida, P.Redondo, M.Marenchino, P.Duchateau, M.D'abramo, G.Montoya, J.Prieto. Engineering A Nickase on the Homing Endonuclease I-Dmoi Scaffold. J.Biol.Chem. V. 290 18534 2015.
ISSN: ISSN 0021-9258
PubMed: 26045557
DOI: 10.1074/JBC.M115.658666