Cadmium in PDB 4bpi: Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2

The structure of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2, PDB code: 4bpi was solved by B.J.Smith, E.F.Lee, J.W.Checco, S.H.Gellman, W.D.Fairlie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.688 / 1.98
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	53.780, 53.780, 93.965, 90.00, 90.00, 120.00
R / Rfree (%)	21.69 / 24.3

The binding sites of Cadmium atom in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2 (pdb code 4bpi). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2, PDB code: 4bpi:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1323 b:51.8 occ:1.00 O A:HOH2006 2.3 45.5 1.0 ND1 A:HIS277 2.3 45.4 1.0 CE1 A:HIS277 3.3 55.2 1.0 CG A:HIS277 3.4 47.5 1.0 CB A:HIS277 3.7 43.3 1.0 CA A:HIS277 4.0 43.7 1.0 CD2 A:LEU232 4.3 61.2 1.0 NE2 A:HIS277 4.4 54.8 1.0 OE1 A:GLN229 4.4 73.7 1.0 CD2 A:HIS277 4.5 48.0 1.0 NE2 A:GLN229 4.6 80.3 1.0 O A:HIS277 4.7 39.4 1.0 O A:HOH2011 4.7 46.0 1.0 C A:HIS277 4.8 36.7 1.0 CD A:GLN229 5.0 76.6 1.0

Cadmium binding site 2 out of 6 in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1324 b:59.8 occ:0.71 CD A:CD1324 0.0 59.8 0.7 O A:HOH2016 2.2 48.2 1.0 O A:HOH2015 2.4 67.5 1.0 SG A:CYS286 3.0 89.0 1.0 OE1 A:GLU288 3.4 73.7 1.0 CD A:CD1324 3.6 43.6 0.3 CB A:CYS286 3.8 55.0 1.0 CD A:GLU288 4.2 62.7 1.0 OE2 A:GLU288 4.4 37.9 1.0

Cadmium binding site 3 out of 6 in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1324 b:43.6 occ:0.29 CD A:CD1324 0.0 43.6 0.3 OE1 A:GLU240 2.4 93.5 1.0 O A:HOH2016 2.8 48.2 1.0 SG A:CYS286 3.0 89.0 1.0 CD A:GLU240 3.3 93.9 1.0 CB A:CYS286 3.4 55.0 1.0 OE2 A:GLU240 3.5 96.7 1.0 CD A:CD1324 3.6 59.8 0.7 N A:CYS286 3.7 52.5 1.0 CA A:CYS286 4.2 51.5 1.0 O A:HOH2015 4.4 67.5 1.0 C A:SER285 4.6 58.6 1.0 CG A:GLU240 4.7 90.1 1.0 O A:GLU284 4.7 81.7 1.0 CA A:SER285 4.8 66.2 1.0

Cadmium binding site 4 out of 6 in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1325 b:37.8 occ:1.00 NE2 A:HIS252 2.2 45.6 1.0 OF2 B:B3E89 2.4 68.8 1.0 OF1 B:B3E89 2.5 66.0 1.0 CE B:B3E89 2.8 63.8 1.0 CE1 A:HIS252 3.0 45.3 1.0 CD2 A:HIS252 3.4 44.3 1.0 NH2 B:ARG95 4.2 28.0 1.0 ND1 A:HIS252 4.2 41.5 1.0 CD B:B3E89 4.3 61.7 0.0 CG A:HIS252 4.4 43.9 1.0 CB B:ALA92 4.5 43.5 1.0 NH1 B:ARG95 4.7 31.3 1.0 OG A:SER255 4.9 24.6 1.0 CZ B:ARG95 4.9 37.5 1.0 O B:GLU88 4.9 56.9 1.0

Cadmium binding site 5 out of 6 in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1326 b:78.6 occ:1.00 O A:ILE237 2.5 89.2 1.0 NE2 A:HIS277 2.5 54.8 1.0 O A:ASP236 2.5 94.9 1.0 CD2 A:HIS277 2.9 48.0 1.0 C A:ILE237 3.6 85.2 1.0 CE1 A:HIS277 3.7 55.2 1.0 C A:ASP236 3.7 88.4 1.0 CB A:ILE237 4.0 79.0 1.0 CG A:HIS277 4.2 47.5 1.0 CA A:ILE237 4.2 83.7 1.0 CD1 A:LEU232 4.4 50.4 1.0 N A:ILE237 4.4 86.6 1.0 ND1 A:HIS277 4.6 45.4 1.0 CG A:LEU232 4.6 54.5 1.0 N A:LYS238 4.7 79.3 1.0 CG2 A:ILE237 4.8 77.4 1.0 CA A:ASP236 4.8 83.1 1.0 O A:LEU232 4.9 60.0 1.0 CD2 A:LEU278 4.9 49.5 1.0 CG1 A:ILE237 4.9 76.1 1.0

Cadmium binding site 6 out of 6 in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1327 b:79.0 occ:1.00 O A:HOH2017 2.9 56.6 1.0 O A:HOH2012 3.9 38.0 1.0

B.J.Smith, E.F.Lee, J.W.Checco, M.Evangelista, S.H.Gellman, W.D.Fairlie. Structure-Guided Rational Design of Alpha/Beta-Peptide Foldamers with High Affinity For Bcl-2 Family Prosurvival Proteins. Chembiochem V. 14 1564 2013.
ISSN: ISSN 1439-4227
PubMed: 23929624
DOI: 10.1002/CBIC.201300351