Zinc in PDB 3d7v: Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand

The structure of Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand, PDB code: 3d7v was solved by E.F.Lee, P.E.Czabotar, P.M.Colman, W.D.Fairlie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.03
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	51.171, 69.635, 120.654, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 24.1

The binding sites of Zinc atom in the Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand (pdb code 3d7v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand, PDB code: 3d7v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:33.1 occ:1.00 NE2 A:HIS252 2.1 22.1 1.0 O B:HOH77 2.3 13.4 1.0 CD2 A:HIS252 2.9 20.0 1.0 CE1 A:HIS252 3.2 23.2 1.0 NH2 B:ARG63 4.0 14.2 1.0 NH1 B:ARG63 4.0 16.0 1.0 CG A:HIS252 4.2 21.2 1.0 ND1 A:HIS252 4.3 24.2 1.0 CZ B:ARG63 4.3 17.9 1.0 CG2 B:ILE56 4.4 28.4 1.0 O A:HOH399 4.4 42.6 1.0 O A:HIS252 4.8 15.9 1.0 OG A:SER255 5.0 18.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:29.8 occ:1.00 OE1 B:GLU68 1.9 22.8 1.0 NE2 A:HIS224 2.0 17.1 1.0 O B:HOH102 2.1 35.1 1.0 O A:HOH347 2.3 14.7 1.0 CD B:GLU68 2.8 22.1 1.0 CE1 A:HIS224 2.9 16.6 1.0 CD2 A:HIS224 3.0 17.9 1.0 OE2 B:GLU68 3.0 25.0 1.0 O B:HOH103 3.5 31.7 1.0 O B:HOH82 3.5 26.9 1.0 ND1 A:HIS224 4.1 18.2 1.0 CG A:HIS224 4.1 19.6 1.0 CG B:GLU68 4.2 20.2 1.0 CB A:ASN223 4.5 24.1 1.0 N B:ALA69 4.8 17.4 1.0 CB B:GLU68 4.8 17.7 1.0 CG2 B:ILE65 4.8 16.8 1.0 CB B:ALA69 4.9 17.2 1.0 CA B:ALA69 4.9 18.1 1.0 O B:ILE65 4.9 17.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:49.3 occ:0.50 SG A:CYS286 2.3 40.6 1.0 CB A:CYS286 3.1 37.0 1.0 O A:HOH384 3.3 30.6 0.5 OE1 A:GLU288 3.3 44.6 1.0 CD A:GLU288 3.6 39.5 1.0 OE2 A:GLU288 3.6 41.4 1.0 CB A:GLU288 4.5 29.9 1.0 CA A:CYS286 4.5 37.2 1.0 CG A:GLU288 4.6 33.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Mcl-1 in Complex with An Mcl-1 Selective BH3 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4 b:34.1 occ:1.00 NE2 A:HIS320 2.1 21.7 1.0 OE1 A:GLU322 2.2 40.4 1.0 O A:HOH362 2.3 41.6 1.0 CG A:GLU322 2.7 36.9 1.0 CD A:GLU322 2.9 39.3 1.0 CD2 A:HIS320 3.0 20.6 1.0 CE1 A:HIS320 3.1 22.1 1.0 OE2 A:GLU322 4.1 43.9 1.0 O A:HOH389 4.2 39.3 1.0 CG A:HIS320 4.2 20.6 1.0 ND1 A:HIS320 4.2 22.4 1.0 CB A:GLU322 4.2 36.8 1.0 O A:VAL321 4.6 32.3 1.0 CA A:GLU322 4.8 36.4 1.0 N A:GLU322 5.0 34.2 1.0

E.F.Lee, P.E.Czabotar, M.F.Van Delft, E.M.Michalak, M.J.Boyle, S.N.Willis, H.Puthalakath, P.Bouillet, P.M.Colman, D.C.S.Huang, W.D.Fairlie. A Novel BH3 Ligand That Selectively Targets Mcl-1 Reveals That Apoptosis Can Proceed Without Mcl-1 Degradation. J.Cell Biol. V. 180 341 2008.
ISSN: ISSN 0021-9525
PubMed: 18209102
DOI: 10.1083/JCB.200708096