Zinc in PDB 3io9: BIML12Y in Complex with Mcl-1

The structure of BIML12Y in Complex with Mcl-1, PDB code: 3io9 was solved by P.E.Czabotar, E.F.Lee, H.Yang, B.E.Sleebs, G.Lessene, P.M.Colman, B.J.Smith, W.D.Fairlie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.39 / 2.40
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	52.537, 74.119, 117.541, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.1

The binding sites of Zinc atom in the BIML12Y in Complex with Mcl-1 (pdb code 3io9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the BIML12Y in Complex with Mcl-1, PDB code: 3io9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the BIML12Y in Complex with Mcl-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of BIML12Y in Complex with Mcl-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:57.4 occ:0.80 OE2 A:GLU292 2.2 41.2 1.0 CD A:GLU292 2.9 40.8 1.0 OE1 A:GLU292 3.0 42.8 1.0 CG A:GLU288 3.4 46.6 1.0 CB A:GLU288 4.3 46.8 1.0 CG A:GLU292 4.4 40.1 1.0 CD A:GLU288 4.4 46.7 0.0 OE1 A:GLU288 4.6 46.7 0.0 C A:GLU288 5.0 45.9 1.0

Zinc binding site 2 out of 4 in the BIML12Y in Complex with Mcl-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of BIML12Y in Complex with Mcl-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:33.9 occ:1.00 OD1 A:ASP313 2.2 39.4 1.0 OE2 A:GLU317 2.4 33.0 1.0 CG A:ASP313 3.0 37.9 1.0 CD A:GLU317 3.1 32.8 1.0 OD2 A:ASP313 3.1 36.7 1.0 CG A:GLU317 3.3 32.4 1.0 OE1 A:GLU317 4.1 34.5 1.0 O A:ASP313 4.4 35.0 1.0 CB A:ASP313 4.4 35.1 1.0 NH2 A:ARG310 4.6 50.5 1.0 CB A:GLU317 4.7 31.1 1.0 CA A:ASP313 4.9 35.8 1.0

Zinc binding site 3 out of 4 in the BIML12Y in Complex with Mcl-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of BIML12Y in Complex with Mcl-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:36.3 occ:1.00 NE2 A:HIS252 2.1 33.2 1.0 O A:HOH328 2.2 26.0 1.0 CE1 A:HIS252 3.1 35.6 1.0 CD2 A:HIS252 3.2 34.6 1.0 ND1 A:HIS252 4.2 34.2 1.0 CG A:HIS252 4.3 34.6 1.0 CG1 B:ILE56 4.5 42.6 1.0 NH1 B:ARG63 4.7 35.6 1.0 CD1 B:ILE56 4.8 42.3 1.0

Zinc binding site 4 out of 4 in the BIML12Y in Complex with Mcl-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of BIML12Y in Complex with Mcl-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4 b:46.1 occ:1.00 OE1 B:GLU61 2.1 39.0 1.0 CD B:GLU61 2.8 37.8 1.0 OE2 B:GLU61 2.9 40.0 1.0 O B:HOH80 2.9 42.4 1.0 NE B:ARG64 3.9 28.9 1.0 NE1 B:TRP57 4.1 43.2 1.0 CG B:GLU61 4.3 37.5 1.0 CZ2 B:TRP57 4.4 42.1 1.0 CE2 B:TRP57 4.5 42.3 1.0 NH2 B:ARG64 4.6 29.4 1.0 CZ B:ARG64 4.6 30.4 1.0 CD B:ARG64 4.7 31.4 1.0 CB B:GLU61 4.9 34.7 1.0

E.F.Lee, P.E.Czabotar, H.Yang, B.E.Sleebs, G.Lessene, P.M.Colman, B.J.Smith, W.D.Fairlie. Conformational Changes in Bcl-2 Pro-Survival Proteins Determine Their Capacity to Bind Ligands. J.Biol.Chem. V. 284 30508 2009.
ISSN: ISSN 0021-9258
PubMed: 19726685
DOI: 10.1074/JBC.M109.040725