Magnesium in PDB 4f0q: Mspji Restriction Endonuclease - P21 Form

The structure of Mspji Restriction Endonuclease - P21 Form, PDB code: 4f0q was solved by J.R.Horton, M.Mabuchi, D.Cohen-Karni, X.Zhang, R.Griggs, M.Samaranayake, R.J.Roberts, Y.Zheng, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.57 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.764, 144.284, 87.842, 90.00, 116.27, 90.00
R / Rfree (%)	21 / 24.6

The binding sites of Magnesium atom in the Mspji Restriction Endonuclease - P21 Form (pdb code 4f0q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Mspji Restriction Endonuclease - P21 Form, PDB code: 4f0q:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Mspji Restriction Endonuclease - P21 Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mspji Restriction Endonuclease - P21 Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:21.3 occ:1.00 OD2 A:ASP334 2.1 26.1 1.0 O A:ALA356 2.1 19.7 1.0 O A:HOH705 2.1 19.3 1.0 O A:HOH795 2.1 23.8 1.0 OE1 A:GLN355 2.1 22.6 1.0 O A:HOH700 2.1 26.5 1.0 CG A:ASP334 2.9 21.5 1.0 OD1 A:ASP334 3.2 27.8 1.0 CD A:GLN355 3.2 18.0 1.0 C A:ALA356 3.2 18.9 1.0 NZ A:LYS297 3.5 24.9 1.0 N A:ALA356 3.6 20.3 1.0 NE2 A:GLN355 3.7 20.9 1.0 CA A:ALA356 3.9 19.3 1.0 OE2 A:GLU301 4.2 21.5 1.0 N A:LYS357 4.2 16.1 1.0 OD1 A:ASP330 4.3 26.6 1.0 CB A:ASP334 4.3 21.0 1.0 O A:HOH698 4.4 19.9 1.0 CG A:GLN355 4.4 20.2 1.0 CA A:LYS357 4.4 20.8 1.0 CB A:ALA356 4.5 18.4 1.0 CE A:LYS297 4.5 21.9 1.0 O A:HOH801 4.6 28.1 1.0 CB A:LYS357 4.7 24.2 1.0 C A:GLN355 4.7 18.0 1.0 CG A:GLU301 4.9 21.6 1.0 O A:HOH636 5.0 19.7 1.0 CD A:GLU301 5.0 23.7 1.0

Magnesium binding site 2 out of 3 in the Mspji Restriction Endonuclease - P21 Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mspji Restriction Endonuclease - P21 Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:19.6 occ:1.00 O B:ALA356 2.0 19.6 1.0 O B:HOH870 2.1 24.0 1.0 OD2 B:ASP334 2.1 19.1 1.0 O B:HOH621 2.1 22.2 1.0 O B:HOH648 2.1 22.2 1.0 OE1 B:GLN355 2.1 19.1 1.0 CG B:ASP334 3.0 16.9 1.0 CD B:GLN355 3.2 20.2 1.0 C B:ALA356 3.2 16.9 1.0 OD1 B:ASP334 3.3 17.6 1.0 NE2 B:GLN355 3.8 20.0 1.0 N B:ALA356 3.9 20.1 1.0 OE2 B:GLU301 4.1 20.6 1.0 CA B:ALA356 4.1 17.0 1.0 NZ B:LYS297 4.1 26.9 1.0 OD1 B:ASP330 4.1 26.7 1.0 N B:LYS357 4.2 17.1 1.0 O B:HOH624 4.2 18.3 1.0 CA B:LYS357 4.3 19.0 1.0 CB B:ASP334 4.4 16.3 1.0 CG B:GLN355 4.4 16.8 1.0 CB B:LYS357 4.5 21.3 1.0 O B:HOH763 4.6 23.1 1.0 CB B:ALA356 4.6 17.1 1.0 O B:HOH766 4.7 22.9 1.0 O B:HOH710 4.8 23.2 1.0 C B:GLN355 4.8 20.4 1.0 CG B:GLU301 4.9 22.9 1.0 CD B:GLU301 4.9 19.2 1.0 CG B:LYS357 4.9 23.4 1.0 O B:GLY331 4.9 24.4 1.0 CG B:ASP330 5.0 25.7 1.0

Magnesium binding site 3 out of 3 in the Mspji Restriction Endonuclease - P21 Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mspji Restriction Endonuclease - P21 Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:33.8 occ:1.00 O C:HOH778 2.1 36.2 1.0 OE1 C:GLN355 2.1 32.4 1.0 O C:ALA356 2.2 38.6 1.0 CD C:GLN355 3.3 31.1 1.0 OD2 C:ASP334 3.3 37.7 1.0 C C:ALA356 3.4 31.1 1.0 O C:HOH659 3.8 32.1 1.0 CG C:ASP334 4.1 33.1 1.0 OD1 C:ASP334 4.1 37.0 1.0 CG C:GLN355 4.1 27.2 1.0 CA C:LYS357 4.1 29.7 1.0 N C:LYS357 4.2 30.4 1.0 CB C:LYS357 4.2 29.9 1.0 NE2 C:GLN355 4.2 30.8 1.0 CE C:LYS297 4.2 29.1 1.0 N C:ALA356 4.2 25.5 1.0 CA C:ALA356 4.4 25.6 1.0 O C:HOH715 4.6 34.5 1.0 NZ C:LYS297 4.8 39.6 1.0 OE2 C:GLU301 5.0 33.7 1.0

J.R.Horton, M.Y.Mabuchi, D.Cohen-Karni, X.Zhang, R.M.Griggs, M.Samaranayake, R.J.Roberts, Y.Zheng, X.Cheng. Structure and Cleavage Activity of the Tetrameric Mspji Dna Modification-Dependent Restriction Endonuclease. Nucleic Acids Res. V. 40 9763 2012.
ISSN: ISSN 0305-1048
PubMed: 22848107
DOI: 10.1093/NAR/GKS719