Magnesium in PDB 1mow: E-Drei

The structure of E-Drei, PDB code: 1mow was solved by B.S.Chevalier, T.Kortemme, M.S.Chadsey, D.Baker, R.J.Monnat Jr., B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.86 / 2.40
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	131.760, 131.760, 120.910, 90.00, 90.00, 120.00
R / Rfree (%)	23.1 / 25.7

The binding sites of Magnesium atom in the E-Drei (pdb code 1mow). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the E-Drei, PDB code: 1mow:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the E-Drei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E-Drei within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg375 b:33.7 occ:1.00 OD1 D:ASP617 2.2 32.6 1.0 OD2 D:ASP521 2.3 31.4 1.0 OP2 E:DG815 2.4 39.8 1.0 OP2 F:DG914 2.5 29.4 1.0 O3' E:DA814 2.5 33.8 1.0 O3' F:DA913 2.6 32.2 1.0 P E:DG815 3.0 37.1 1.0 MG D:MG376 3.0 16.8 1.0 P F:DG914 3.1 36.0 1.0 O D:GLY520 3.2 31.6 1.0 CG D:ASP617 3.4 42.8 1.0 C3' E:DA814 3.5 31.9 1.0 CG D:ASP521 3.5 38.4 1.0 C3' F:DA913 3.5 40.9 1.0 C4' F:DA913 3.7 36.5 1.0 O D:GLY616 3.8 23.2 1.0 O5' E:DG815 3.8 42.7 1.0 O5' F:DG914 3.8 42.5 1.0 MG D:MG374 3.8 20.5 1.0 C4' E:DA814 3.9 30.9 1.0 C D:GLY520 4.0 32.0 1.0 OD2 D:ASP617 4.1 32.8 1.0 OP1 F:DA913 4.2 27.7 1.0 CA D:ASP521 4.2 29.7 1.0 C D:GLY616 4.3 28.4 1.0 OP1 E:DG815 4.3 51.4 1.0 OD1 D:ASP521 4.3 34.6 1.0 CA D:ASP617 4.3 31.5 1.0 OP1 F:DG914 4.4 32.3 1.0 CB D:ASP617 4.4 31.5 1.0 CB D:ASP521 4.5 34.3 1.0 N D:ASP521 4.5 28.9 1.0 C5' F:DA913 4.5 36.4 1.0 O F:HOH2331 4.5 32.7 1.0 N D:ASP617 4.5 25.7 1.0 O F:HOH2022 4.7 27.9 1.0 C5' E:DA814 4.7 24.4 1.0 C2' E:DA814 4.9 35.5 1.0 O4' F:DA913 4.9 41.2 1.0 C2' F:DA913 4.9 42.2 1.0 O F:HOH2410 4.9 48.7 1.0 OP1 E:DA814 5.0 23.1 1.0 O4' E:DA814 5.0 37.2 1.0

Magnesium binding site 2 out of 6 in the E-Drei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E-Drei within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg371 b:13.6 occ:1.00 O A:HOH2058 1.9 21.9 1.0 OP1 B:DA314 2.0 23.7 1.0 OP2 C:DG414 2.1 40.9 1.0 OD1 A:ASP21 2.4 33.3 1.0 O A:GLY116 2.4 26.0 1.0 O C:HOH2411 2.5 46.5 1.0 OD2 A:ASP21 2.8 32.2 1.0 CG A:ASP21 2.9 38.0 1.0 P C:DG414 3.3 39.4 1.0 C A:GLY116 3.4 32.8 1.0 P B:DA314 3.5 33.0 1.0 O5' C:DG414 3.5 41.9 1.0 MG A:MG372 3.6 37.8 1.0 CA A:GLY116 3.9 27.1 1.0 O3' B:DA313 4.0 39.1 1.0 C5' B:DA314 4.0 28.7 1.0 OP1 C:DG414 4.0 27.6 1.0 O A:HOH2063 4.1 52.8 1.0 C4' B:DA314 4.3 26.9 1.0 O5' B:DA314 4.3 30.4 1.0 O A:HOH2334 4.3 53.0 1.0 O A:ASP115 4.3 28.8 1.0 CB A:ASP21 4.4 32.9 1.0 O3' C:DA413 4.5 38.2 1.0 N A:ASP117 4.6 29.7 1.0 OP2 B:DA314 4.6 21.6 1.0 O A:HOH2261 4.8 43.7 1.0 C5' C:DG414 4.8 42.2 1.0 O3' B:DA314 4.9 35.8 1.0 NE2 A:GLN42 5.0 26.9 1.0 N A:GLY116 5.0 23.7 1.0 CA A:ASP117 5.0 32.2 1.0

Magnesium binding site 3 out of 6 in the E-Drei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E-Drei within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg372 b:37.8 occ:1.00 OD2 A:ASP21 2.1 32.2 1.0 OD1 A:ASP117 2.1 34.7 1.0 OP2 C:DG414 2.4 40.9 1.0 O3' B:DA314 2.6 35.8 1.0 OP2 B:DG315 2.6 41.9 1.0 O3' C:DA413 2.8 38.2 1.0 O A:GLY20 2.9 42.6 1.0 MG A:MG373 3.1 32.7 1.0 P C:DG414 3.2 39.4 1.0 P B:DG315 3.2 40.0 1.0 CG A:ASP117 3.3 45.6 1.0 CG A:ASP21 3.3 38.0 1.0 O A:GLY116 3.5 26.0 1.0 C3' B:DA314 3.6 31.9 1.0 MG A:MG371 3.6 13.6 1.0 C A:GLY20 3.7 37.4 1.0 C3' C:DA413 3.7 42.2 1.0 O5' C:DG414 3.8 41.9 1.0 O5' B:DG315 3.8 47.6 1.0 C A:GLY116 3.9 32.8 1.0 C4' B:DA314 4.0 26.9 1.0 CA A:ASP21 4.0 30.4 1.0 C4' C:DA413 4.0 44.1 1.0 OD2 A:ASP117 4.1 40.9 1.0 CA A:ASP117 4.1 32.2 1.0 OD1 A:ASP21 4.1 33.3 1.0 N A:ASP117 4.2 29.7 1.0 OP1 C:DA413 4.2 28.1 1.0 N A:ASP21 4.2 32.4 1.0 CB A:ASP21 4.3 32.9 1.0 CB A:ASP117 4.3 33.4 1.0 OP1 C:DG414 4.5 27.6 1.0 OP1 B:DG315 4.5 47.7 1.0 CA A:GLY20 4.7 33.9 1.0 C5' B:DA314 4.8 28.7 1.0 CA A:GLY116 4.8 27.1 1.0 C5' C:DA413 4.8 38.8 1.0 O C:HOH2060 4.9 26.8 1.0 O C:HOH2288 4.9 39.3 1.0 OP1 B:DA314 4.9 23.7 1.0 C2' B:DA314 5.0 36.9 1.0

Magnesium binding site 4 out of 6 in the E-Drei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E-Drei within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg373 b:32.7 occ:1.00 OP1 C:DA413 1.8 28.1 1.0 OP2 B:DG315 1.9 41.9 1.0 O A:GLY20 2.1 42.6 1.0 O C:HOH2095 2.1 38.3 1.0 OD1 A:ASP117 2.4 34.7 1.0 OD2 A:ASP117 2.4 40.9 1.0 CG A:ASP117 2.7 45.6 1.0 MG A:MG372 3.1 37.8 1.0 P B:DG315 3.2 40.0 1.0 C A:GLY20 3.2 37.4 1.0 P C:DA413 3.2 33.6 1.0 O5' B:DG315 3.3 47.6 1.0 CA A:GLY20 3.7 33.9 1.0 O3' C:DG412 3.7 32.4 1.0 O3' B:DA314 4.1 35.8 1.0 O C:HOH2252 4.1 35.2 1.0 O A:TRP19 4.1 39.5 1.0 C4' C:DA413 4.2 44.1 1.0 CB A:ASP117 4.2 33.4 1.0 C5' C:DA413 4.2 38.8 1.0 O5' C:DA413 4.2 41.2 1.0 OP2 C:DA413 4.2 30.4 1.0 OP1 B:DG315 4.3 47.7 1.0 N A:ASP21 4.3 32.4 1.0 OD2 A:ASP21 4.5 32.2 1.0 NE2 A:GLN144 4.7 40.3 1.0 C5' B:DG315 4.7 29.2 1.0 O3' C:DA413 4.7 38.2 1.0 CA A:ASP21 4.8 30.4 1.0 N A:GLY20 4.8 28.8 1.0 C3' C:DA413 4.9 42.2 1.0 C A:TRP19 4.9 35.7 1.0

Magnesium binding site 5 out of 6 in the E-Drei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of E-Drei within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg374 b:20.5 occ:1.00 OP2 F:DG914 2.1 29.4 1.0 OP1 E:DA814 2.1 23.1 1.0 O D:HOH2224 2.1 30.3 1.0 O F:HOH2410 2.2 48.7 1.0 OD1 D:ASP521 2.3 34.6 1.0 O D:GLY616 2.3 23.2 1.0 OD2 D:ASP521 2.8 31.4 1.0 CG D:ASP521 2.9 38.4 1.0 P F:DG914 3.3 36.0 1.0 C D:GLY616 3.3 28.4 1.0 P E:DA814 3.5 33.1 1.0 O5' F:DG914 3.6 42.5 1.0 CA D:GLY616 3.7 23.0 1.0 MG E:MG375 3.8 33.7 1.0 OP1 F:DG914 4.1 32.3 1.0 O3' E:DA813 4.1 29.5 1.0 C5' E:DA814 4.1 24.4 1.0 O D:ASP615 4.3 27.1 1.0 O D:HOH2284 4.3 36.2 1.0 O5' E:DA814 4.3 31.3 1.0 C4' E:DA814 4.3 30.9 1.0 CB D:ASP521 4.4 34.3 1.0 N D:ASP617 4.5 25.7 1.0 O3' F:DA913 4.5 32.2 1.0 OP2 E:DA814 4.6 20.4 1.0 O D:HOH2258 4.7 42.9 1.0 NE2 D:GLN542 4.8 24.1 1.0 C5' F:DG914 4.8 40.3 1.0 N D:GLY616 4.9 24.7 1.0 CA D:ASP617 4.9 31.5 1.0 OD1 D:ASP617 5.0 32.6 1.0

Magnesium binding site 6 out of 6 in the E-Drei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of E-Drei within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg376 b:16.8 occ:1.00 OP2 E:DG815 1.8 39.8 1.0 OP1 F:DA913 1.8 27.7 1.0 O F:HOH2173 2.1 35.8 1.0 O D:GLY520 2.1 31.6 1.0 OD2 D:ASP617 2.3 32.8 1.0 OD1 D:ASP617 2.4 32.6 1.0 CG D:ASP617 2.7 42.8 1.0 MG E:MG375 3.0 33.7 1.0 P E:DG815 3.2 37.1 1.0 P F:DA913 3.2 31.2 1.0 C D:GLY520 3.3 32.0 1.0 O5' E:DG815 3.4 42.7 1.0 O3' F:DG912 3.7 37.5 1.0 CA D:GLY520 3.8 30.4 1.0 C5' F:DA913 4.0 36.4 1.0 O D:HOH2093 4.0 42.2 1.0 O3' E:DA814 4.1 33.8 1.0 C4' F:DA913 4.1 36.5 1.0 O5' F:DA913 4.1 42.4 1.0 CB D:ASP617 4.2 31.5 1.0 OP1 E:DG815 4.2 51.4 1.0 O D:TRP519 4.2 34.8 1.0 OP2 F:DA913 4.3 29.1 1.0 OD2 D:ASP521 4.4 31.4 1.0 N D:ASP521 4.4 28.9 1.0 NE2 D:GLN644 4.7 39.3 1.0 CA D:ASP521 4.7 29.7 1.0 O3' F:DA913 4.8 32.2 1.0 C5' E:DG815 4.8 30.4 1.0 C3' F:DA913 4.9 40.9 1.0 N D:GLY520 4.9 35.2 1.0

B.S.Chevalier, T.Kortemme, M.S.Chadsey, D.Baker, R.J.Monnat Jr., B.L.Stoddard. Design, Activity and Structure of A Highly Specific Artificial Endonuclease Mol.Cell V. 10 895 2002.
ISSN: ISSN 1097-2765
PubMed: 12419232
DOI: 10.1016/S1097-2765(02)00690-1