Magnesium in PDB 5e63: K262A Mutant of I-Smami

The structure of K262A Mutant of I-Smami, PDB code: 5e63 was solved by B.Shen, B.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.835, 67.694, 97.780, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 27.9

The binding sites of Magnesium atom in the K262A Mutant of I-Smami (pdb code 5e63). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the K262A Mutant of I-Smami, PDB code: 5e63:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the K262A 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 K262A Mutant of I-Smami within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:32.0 occ:1.00 OP3 C:DT15 1.8 50.5 1.0 OD1 A:ASP179 2.2 19.7 1.0 OP1 E:DC16 2.3 62.4 1.0 O3' B:DA14 2.4 65.1 1.0 O3' D:DT15 2.7 32.5 1.0 OE1 A:GLU20 2.7 29.7 1.0 OE2 A:GLU20 2.9 30.1 1.0 CD A:GLU20 3.1 27.4 1.0 P C:DT15 3.1 48.4 1.0 CG A:ASP179 3.2 19.4 1.0 O5' C:DT15 3.4 46.5 1.0 MG A:MG402 3.4 22.3 1.0 C3' B:DA14 3.5 67.0 1.0 OD2 A:ASP179 3.6 19.1 1.0 C3' D:DT15 3.6 32.9 1.0 O A:ALA19 3.7 20.3 1.0 P E:DC16 3.8 62.3 1.0 OP2 C:DT15 4.0 48.1 1.0 C4' B:DA14 4.0 66.9 1.0 OP1 C:DT15 4.1 46.9 1.0 C4' D:DT15 4.1 33.4 1.0 O A:GLY178 4.3 19.6 1.0 O C:HOH102 4.3 41.3 1.0 CG A:GLU20 4.4 25.4 1.0 C A:ALA19 4.4 20.1 1.0 CB A:ASP179 4.5 19.7 1.0 OP2 E:DC16 4.5 64.3 1.0 CA A:GLU20 4.6 22.6 1.0 OP3 E:DC16 4.6 62.1 1.0 CA A:ASP179 4.6 19.8 1.0 C A:GLY178 4.6 19.7 1.0 OP1 D:DT15 4.7 33.5 1.0 C5' C:DT15 4.7 43.4 1.0 O5' D:DT15 4.8 33.9 1.0 O5' E:DC16 4.8 56.7 1.0 C2' B:DA14 4.8 67.9 1.0 N A:ASP179 4.9 19.6 1.0 N A:GLU20 4.9 21.3 1.0 CB A:GLU20 4.9 24.2 1.0 C2' D:DT15 4.9 34.2 1.0

Magnesium binding site 2 out of 3 in the K262A 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 K262A Mutant of I-Smami within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:22.3 occ:1.00 OP1 D:DT15 1.8 33.5 1.0 OP3 C:DT15 2.0 50.5 1.0 OP1 C:DT15 2.1 46.9 1.0 OD2 A:ASP179 2.1 19.1 1.0 O A:ALA19 2.2 20.3 1.0 O D:HOH101 2.2 18.9 1.0 P C:DT15 2.5 48.4 1.0 CG A:ASP179 3.0 19.4 1.0 P D:DT15 3.1 34.2 1.0 O5' D:DT15 3.3 33.9 1.0 C A:ALA19 3.3 20.1 1.0 OD1 A:ASP179 3.3 19.7 1.0 MG A:MG401 3.4 32.0 1.0 O C:HOH101 3.5 18.2 1.0 O5' C:DT15 3.7 46.5 1.0 OP2 C:DT15 3.7 48.1 1.0 O3' D:DA14 3.8 34.5 1.0 CA A:ALA19 3.9 19.1 1.0 NE2 A:GLN206 4.1 17.9 1.0 C4' D:DT15 4.3 33.4 1.0 OP2 D:DT15 4.3 36.1 1.0 CB A:ASP179 4.4 19.7 1.0 C5' D:DT15 4.4 34.3 1.0 N A:GLU20 4.5 21.3 1.0 C5' C:DT15 4.5 43.4 1.0 OE1 A:GLN206 4.5 18.8 1.0 O A:ASP18 4.5 18.6 1.0 CD A:GLN206 4.7 18.6 1.0 O3' D:DT15 4.7 32.5 1.0 CB A:ALA19 4.7 18.6 1.0 O3' B:DA14 4.8 65.1 1.0 C3' D:DT15 4.8 32.9 1.0 CA A:GLU20 4.8 22.6 1.0

Magnesium binding site 3 out of 3 in the K262A Mutant of I-Smami


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of K262A Mutant of I-Smami within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:33.6 occ:1.00 OP2 E:DC16 1.9 64.3 1.0 O A:GLY178 2.4 19.6 1.0 OE2 A:GLU20 3.1 30.1 1.0 P E:DC16 3.2 62.3 1.0 OP1 B:DA14 3.2 67.6 1.0 C A:GLY178 3.2 19.7 1.0 O A:SER177 3.3 19.2 1.0 CA A:GLY178 3.4 19.5 1.0 O5' E:DC16 3.5 56.7 1.0 OP1 E:DC16 3.8 62.4 1.0 O B:HOH101 3.9 30.9 1.0 CD A:GLU20 4.0 27.4 1.0 O5' B:DA14 4.0 69.2 1.0 P B:DA14 4.0 69.2 1.0 C A:SER177 4.2 19.1 1.0 N A:GLY178 4.3 19.2 1.0 OP3 E:DC16 4.4 62.1 1.0 OP2 B:DA14 4.5 71.3 1.0 N A:ASP179 4.5 19.6 1.0 O A:HOH522 4.6 36.2 1.0 OE1 A:GLU20 4.6 29.7 1.0 CG A:GLU20 4.7 25.4 1.0 O A:HOH519 4.8 18.9 1.0 CE1 A:PHE16 4.9 17.0 1.0 C5' E:DC16 4.9 51.9 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