Magnesium in PDB 5e67: K103A/K262A Double Mutant of I-Smami

The structure of K103A/K262A Double Mutant of I-Smami, PDB code: 5e67 was solved by B.W.Shen, B.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.518, 67.326, 98.572, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 25.4

The binding sites of Magnesium atom in the K103A/K262A Double Mutant of I-Smami (pdb code 5e67). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the K103A/K262A Double Mutant of I-Smami, PDB code: 5e67:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the K103A/K262A Double Mutant of I-Smami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of K103A/K262A Double Mutant of I-Smami within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:41.9 occ:1.00 O B:HOH203 1.6 35.2 1.0 O A:HOH525 2.1 38.6 1.0 O A:ALA19 2.2 24.4 1.0 OD1 A:ASP179 2.2 23.6 1.0 MG A:MG402 2.6 48.1 1.0 OP2 C:DC16 2.6 40.4 1.0 CG A:ASP179 2.9 24.9 1.0 OD2 A:ASP179 3.0 25.0 1.0 C A:ALA19 3.3 25.1 1.0 P C:DC16 3.7 40.0 1.0 OP1 B:DT15 3.7 38.5 1.0 O A:HOH558 3.8 41.5 1.0 OP1 C:DC16 3.9 39.3 1.0 CA A:ALA19 4.0 23.2 1.0 O C:HOH101 4.0 39.5 1.0 N A:GLU20 4.3 26.5 1.0 OE2 A:GLU20 4.3 50.7 1.0 CB A:ALA19 4.3 22.1 1.0 CB A:ASP179 4.4 24.3 1.0 CA A:GLU20 4.6 29.8 1.0 OE1 A:GLN206 4.7 29.2 1.0 O5' C:DC16 4.7 38.8 1.0 O A:GLY178 4.7 24.6 1.0 O3' C:DT15 4.9 41.3 1.0 CA A:ASP179 4.9 23.8 1.0 O C:HOH115 4.9 43.6 1.0 P B:DT15 5.0 38.8 1.0 CG A:GLU20 5.0 37.9 1.0 O3' B:DA14 5.0 39.6 1.0

Magnesium binding site 2 out of 2 in the K103A/K262A Double Mutant of I-Smami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of K103A/K262A Double Mutant of I-Smami within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:48.1 occ:1.00 OE2 A:GLU20 2.4 50.7 1.0 O C:HOH115 2.4 43.6 1.0 OD1 A:ASP179 2.6 23.6 1.0 MG A:MG401 2.6 41.9 1.0 OP1 C:DC16 2.8 39.3 1.0 O B:HOH203 2.8 35.2 1.0 O A:GLY178 2.9 24.6 1.0 CD A:GLU20 3.5 43.1 1.0 OP2 C:DC16 3.6 40.4 1.0 P C:DC16 3.6 40.0 1.0 C A:GLY178 3.6 21.9 1.0 O A:ALA19 3.8 24.4 1.0 CG A:ASP179 3.8 24.9 1.0 CG A:GLU20 4.0 37.9 1.0 N A:ASP179 4.3 22.0 1.0 C5' C:DC16 4.3 38.0 1.0 O5' C:DC16 4.4 38.8 1.0 CA A:ASP179 4.4 23.8 1.0 C A:ALA19 4.4 25.1 1.0 C1 A:MXE403 4.4 51.8 1.0 CA A:GLY178 4.4 20.9 1.0 O3' B:DA14 4.5 39.6 1.0 OP1 B:DT15 4.5 38.5 1.0 OE1 A:GLU20 4.6 45.5 1.0 O A:HOH525 4.6 38.6 1.0 OD2 A:ASP179 4.7 25.0 1.0 CB A:ASP179 4.7 24.3 1.0 CB A:ALA19 4.8 22.1 1.0 CA A:GLU20 4.8 29.8 1.0 CB A:GLU20 4.9 33.4 1.0 N A:GLU20 4.9 26.5 1.0 O3' C:DT15 5.0 41.3 1.0

B.W.Shen, A.Lambert, B.C.Walker, B.L.Stoddard, B.K.Kaiser. The Structural Basis of Asymmetry in Dna Binding and Cleavage As Exhibited By the I-Smami Laglidadg Meganuclease. J.Mol.Biol. V. 428 206 2016.
ISSN: ESSN 1089-8638
PubMed: 26705195
DOI: 10.1016/J.JMB.2015.12.005