Magnesium in PDB 5vx0: Bak in Complex with Bim-H3GLG

The structure of Bak in Complex with Bim-H3GLG, PDB code: 5vx0 was solved by J.M.Brouwer, P.Lan, G.Lessene, P.M.Colman, P.E.Czabotar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.69 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.092, 63.231, 121.038, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20

The binding sites of Magnesium atom in the Bak in Complex with Bim-H3GLG (pdb code 5vx0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Bak in Complex with Bim-H3GLG, PDB code: 5vx0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Bak in Complex with Bim-H3GLG


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bak in Complex with Bim-H3GLG within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:30.2 occ:1.00 OD2 A:ASP30 2.6 17.5 1.0 N A:TRP177 2.9 14.6 1.0 CA A:GLY176 3.2 16.1 1.0 O A:HOH334 3.4 27.5 1.0 CG A:ASP30 3.5 19.6 1.0 C A:GLY176 3.6 15.9 1.0 SD A:MET22 3.6 20.7 1.0 CB A:ASP30 3.6 16.1 1.0 O A:HOH417 3.7 17.0 1.0 CD1 A:TRP177 3.7 16.6 1.0 CG2 A:VAL27 3.8 17.9 1.0 CA A:VAL27 3.9 16.9 1.0 CB A:TRP177 4.0 15.3 1.0 CA A:TRP177 4.1 13.6 1.0 CG A:TRP177 4.2 13.5 1.0 CB A:VAL27 4.2 14.7 1.0 CE A:MET22 4.4 19.7 1.0 N A:VAL27 4.5 14.2 1.0 O A:GLN26 4.5 15.6 1.0 SD A:MET71 4.5 18.6 1.0 CG1 A:VAL27 4.5 13.6 1.0 N A:GLY176 4.6 17.5 1.0 OD1 A:ASP30 4.7 20.3 1.0 C A:GLN26 4.7 14.2 1.0 CG2 A:ILE171 4.8 13.1 1.0 O A:GLY176 4.8 17.6 1.0 O A:VAL27 4.8 17.5 1.0 C A:VAL27 4.9 19.1 1.0 NE1 A:TRP177 4.9 20.3 1.0 CG A:GLN26 4.9 20.5 1.0 N A:VAL178 5.0 15.4 1.0 O A:GLY175 5.0 18.3 1.0

Magnesium binding site 2 out of 6 in the Bak in Complex with Bim-H3GLG


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bak in Complex with Bim-H3GLG within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:37.1 occ:1.00 O A:HOH500 2.7 55.1 1.0 O A:HOH516 2.9 30.0 1.0 N A:ALA104 3.0 19.9 1.0 O A:HOH460 3.0 37.9 1.0 CB A:THR103 3.5 23.2 1.0 CB A:ALA104 3.7 24.0 1.0 CA A:THR103 3.7 23.1 1.0 C A:THR103 3.8 22.8 1.0 CA A:ALA104 3.9 21.7 1.0 O A:HOH466 4.2 38.6 1.0 CD2 A:LEU147 4.2 18.6 1.0 O A:HOH450 4.2 50.1 1.0 CG2 A:THR103 4.4 27.4 1.0 OG1 A:THR103 4.5 24.7 1.0 N A:GLU105 4.9 24.5 1.0 O C:HOH364 4.9 23.4 1.0 CB A:LEU147 4.9 22.5 1.0 CD1 A:LEU147 4.9 22.2 1.0 CG A:LEU147 4.9 17.4 1.0 C A:ALA104 5.0 26.5 1.0

Magnesium binding site 3 out of 6 in the Bak in Complex with Bim-H3GLG


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bak in Complex with Bim-H3GLG within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:34.2 occ:1.00 N A:TRP125 3.3 16.7 1.0 O A:HOH461 3.4 43.4 1.0 OD1 B:ASN160 3.5 24.3 1.0 O A:HOH415 3.5 40.9 1.0 CB A:ASN124 3.5 19.6 1.0 CD1 A:TRP125 3.6 22.5 1.0 CA A:ASN124 3.7 16.8 1.0 CH2 A:TRP170 3.9 19.7 1.0 C A:ASN124 4.0 17.4 1.0 CZ2 A:TRP170 4.0 21.7 1.0 ND2 B:ASN160 4.0 32.7 1.0 CB A:TRP125 4.1 20.9 1.0 CG B:ASN160 4.1 27.1 1.0 CG A:TRP125 4.2 19.0 1.0 CA A:TRP125 4.3 17.2 1.0 CB B:ALA164 4.5 33.0 1.0 NE1 A:TRP125 4.6 23.2 1.0 CG A:ASN124 4.7 23.2 1.0

Magnesium binding site 4 out of 6 in the Bak in Complex with Bim-H3GLG


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bak in Complex with Bim-H3GLG within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:31.0 occ:1.00 O A:HOH308 3.1 46.4 1.0 NE A:ARG76 3.2 20.5 1.0 NH2 A:ARG76 3.4 19.2 1.0 CZ A:ARG76 3.7 23.9 1.0 CG A:GLN73 3.8 15.7 1.0 CD A:GLN73 4.2 23.6 1.0 CD A:ARG76 4.3 18.9 1.0 NE2 A:GLN73 4.3 17.6 1.0 CG A:ARG76 4.7 18.0 1.0 CB A:GLN73 4.8 15.7 1.0 OE1 A:GLN73 5.0 25.4 1.0

Magnesium binding site 5 out of 6 in the Bak in Complex with Bim-H3GLG


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Bak in Complex with Bim-H3GLG within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:18.9 occ:1.00 O C:HOH462 2.0 22.1 1.0 O A:HOH386 2.1 20.4 1.0 O A:HOH315 2.1 21.1 1.0 O A:HOH358 2.1 18.3 1.0 O A:HOH518 2.1 25.8 1.0 O A:HOH505 2.1 19.3 1.0 O A:HOH514 4.0 34.8 1.0 OE1 A:GLU33 4.0 18.9 1.0 O A:HOH368 4.0 20.1 1.0 OE2 A:GLU33 4.2 20.6 1.0 O A:HOH337 4.2 21.0 1.0 NE2 A:GLN66 4.2 15.0 1.0 O A:HOH431 4.2 18.5 1.0 O A:HOH323 4.2 22.2 1.0 O C:HOH410 4.3 44.5 1.0 CD A:GLU33 4.5 16.0 1.0 O A:HOH455 4.6 48.7 1.0 CB C:ALA104 4.7 27.0 1.0 O A:HOH467 4.7 37.7 1.0 O A:HOH383 4.9 31.7 1.0 CB A:SER69 5.0 18.9 1.0

Magnesium binding site 6 out of 6 in the Bak in Complex with Bim-H3GLG


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Bak in Complex with Bim-H3GLG within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:18.4 occ:1.00 O C:HOH452 2.0 20.9 1.0 O A:HOH439 2.0 20.5 1.0 O C:HOH346 2.0 19.9 1.0 O C:HOH342 2.0 19.9 1.0 O C:HOH335 2.1 21.1 1.0 O A:HOH494 2.2 27.6 1.0 O C:HOH364 4.0 23.4 1.0 OE1 C:GLU33 4.0 21.1 1.0 O C:HOH394 4.1 21.5 1.0 NE2 C:GLN66 4.1 17.2 1.0 O C:HOH325 4.2 24.9 1.0 OE2 C:GLU33 4.2 20.3 1.0 O C:HOH320 4.3 26.1 1.0 OE2 A:GLU105 4.4 85.4 1.0 O C:HOH432 4.5 27.6 1.0 O A:HOH344 4.5 42.8 1.0 CB A:ALA104 4.6 24.0 1.0 CD C:GLU33 4.6 20.9 1.0 CB C:SER69 4.9 20.3 1.0 O C:HOH371 5.0 24.5 1.0

J.M.Brouwer, P.Lan, A.D.Cowan, J.P.Bernardini, R.W.Birkinshaw, M.F.Van Delft, B.E.Sleebs, A.Y.Robin, A.Wardak, I.K.Tan, B.Reljic, E.F.Lee, W.D.Fairlie, M.J.Call, B.J.Smith, G.Dewson, G.Lessene, P.M.Colman, P.E.Czabotar. Conversion of Bim-BH3 From Activator to Inhibitor of Bak Through Structure-Based Design. Mol. Cell V. 68 659 2017.
ISSN: ISSN 1097-4164
PubMed: 29149594
DOI: 10.1016/J.MOLCEL.2017.11.001