Magnesium in PDB 5e5s: I-Smami K103A Mutant

The structure of I-Smami K103A Mutant, PDB code: 5e5s was solved by B.W.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.589, 68.199, 97.652, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 25.1

The binding sites of Magnesium atom in the I-Smami K103A Mutant (pdb code 5e5s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the I-Smami K103A Mutant, PDB code: 5e5s:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the I-Smami K103A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of I-Smami K103A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:34.4 occ:1.00 O A:ALA19 2.0 37.3 1.0 OP1 C:DT15 2.1 39.4 1.0 O C:HOH101 2.3 42.4 1.0 OD2 A:ASP179 2.4 40.1 1.0 O A:HOH502 2.6 33.2 1.0 OP1 B:DT15 2.6 80.5 1.0 OD1 A:ASP179 2.8 35.6 1.0 CG A:ASP179 2.9 34.6 1.0 C A:ALA19 3.2 39.3 1.0 P C:DT15 3.5 40.5 1.0 P B:DT15 3.9 82.4 1.0 CA A:ALA19 4.0 39.4 1.0 O3' C:DA14 4.1 43.0 1.0 N A:GLU20 4.2 43.5 1.0 C4' C:DT15 4.4 44.3 1.0 O A:HOH501 4.4 38.3 1.0 CB A:ASP179 4.4 36.1 1.0 O5' C:DT15 4.4 39.5 1.0 NE2 A:GLN206 4.5 38.1 1.0 OP2 B:DT15 4.5 81.7 1.0 CA A:GLU20 4.5 44.9 1.0 C5' C:DT15 4.5 42.3 1.0 O5' B:DT15 4.5 79.1 1.0 OE1 A:GLN206 4.6 47.1 1.0 CB A:ALA19 4.6 34.6 1.0 OP2 C:DT15 4.6 36.6 1.0 C5' B:DT15 4.6 73.8 1.0 O3' C:DT15 4.7 45.5 1.0 C3' C:DT15 4.8 40.8 1.0 O3' B:DA14 4.9 78.5 1.0 O A:ASP18 4.9 37.0 1.0 CD A:GLN206 5.0 43.8 1.0

Magnesium binding site 2 out of 3 in the I-Smami K103A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of I-Smami K103A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:49.2 occ:1.00 OP3 D:DC16 1.8 40.5 1.0 O D:HOH101 2.1 47.6 1.0 O B:HOH202 2.2 48.9 1.0 OE2 A:GLU20 2.2 71.8 1.0 O A:HOH501 2.2 38.3 1.0 O A:GLY178 2.3 41.6 1.0 P D:DC16 3.0 48.3 1.0 OP1 D:DC16 3.0 50.6 1.0 CD A:GLU20 3.3 62.6 1.0 C A:GLY178 3.4 40.5 1.0 O D:HOH102 3.5 36.6 1.0 O5' D:DC16 3.7 45.5 1.0 OE1 A:GLU20 3.8 72.9 1.0 CA A:GLY178 3.8 41.0 1.0 OP2 D:DC16 4.1 53.7 1.0 C5' D:DC16 4.3 52.5 1.0 OD1 A:ASP179 4.4 35.6 1.0 CG A:GLU20 4.5 57.7 1.0 N A:ASP179 4.5 37.1 1.0 O3' C:DT15 4.5 45.5 1.0 OP2 B:DA14 4.6 83.8 1.0 O A:SER177 4.7 39.1 1.0 O5' B:DA14 4.8 75.8 1.0 NZ A:LYS262 4.8 52.4 1.0 CA A:ASP179 5.0 39.2 1.0 N A:GLY178 5.0 37.0 1.0

Magnesium binding site 3 out of 3 in the I-Smami K103A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of I-Smami K103A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:53.2 occ:1.00 O C:HOH102 2.0 52.6 1.0 O B:HOH206 2.1 41.7 1.0 O D:HOH103 2.1 41.6 1.0 OP1 B:DA14 2.2 73.1 1.0 O B:HOH203 2.3 43.4 1.0 O D:HOH102 2.5 36.6 1.0 P B:DA14 3.4 64.8 1.0 O4' B:DA13 3.6 52.7 1.0 OP2 B:DA14 3.8 83.8 1.0 C1' B:DA13 4.1 55.4 1.0 C4' B:DA13 4.1 62.0 1.0 N3 B:DA13 4.2 46.5 1.0 O4' B:DA14 4.2 77.0 1.0 O2 B:DT12 4.2 55.0 1.0 O5' B:DA14 4.3 75.8 1.0 C4' B:DA14 4.4 78.1 1.0 O2 C:DT15 4.4 43.2 1.0 OP3 D:DC16 4.6 40.5 1.0 O3' B:DA13 4.6 66.0 1.0 OP2 D:DC16 4.6 53.7 1.0 C5' B:DA14 4.7 72.7 1.0 O3' C:DT15 4.8 45.5 1.0 C3' B:DA13 4.8 59.6 1.0 O4' D:DC16 4.9 48.5 1.0 C4 B:DA13 4.9 48.5 1.0 N9 B:DA13 4.9 55.8 1.0 C4' D:DC16 4.9 50.2 1.0 O B:HOH202 5.0 48.9 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