Zinc in PDB 4bpj: Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3

The structure of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3, PDB code: 4bpj 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)	19.693 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.458, 60.260, 44.804, 90.00, 118.47, 90.00
R / Rfree (%)	19.93 / 23.01

The structure of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3 (pdb code 4bpj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3, PDB code: 4bpj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1323 b:33.6 occ:1.00 SG A:CYS286 2.1 29.7 1.0 O A:HOH2002 2.4 43.1 1.0 CB A:CYS286 3.0 30.6 1.0 CB A:GLU288 4.0 27.5 1.0 CD A:PRO289 4.0 29.8 1.0 CA A:CYS286 4.5 29.2 1.0 CG A:PRO289 4.6 30.1 1.0 N A:GLU288 4.7 23.8 1.0 CA A:GLU288 4.9 23.9 1.0 C A:CYS286 4.9 30.2 1.0 CG A:GLU288 5.0 36.8 1.0

Zinc binding site 2 out of 7 in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1324 b:28.2 occ:0.63 ZN A:ZN1324 0.0 28.2 0.6 ZN A:ZN1324 1.6 35.9 0.4 NE2 A:HIS252 1.9 43.5 1.0 O A:HOH2167 2.0 36.5 1.0 O A:HOH2074 2.3 30.8 1.0 CE1 A:HIS252 2.6 37.0 1.0 CD2 A:HIS252 2.9 40.0 1.0 ND1 A:HIS252 3.6 34.3 1.0 NH2 D:ARG95 3.8 17.2 1.0 CG A:HIS252 3.8 32.2 1.0 NH1 D:ARG95 3.9 18.1 1.0 O D:HOH2032 4.0 37.1 1.0 CZ D:ARG95 4.2 16.0 1.0 OG A:SER255 4.5 17.9 1.0 O A:HIS252 4.5 18.1 1.0 N D:ALA92 5.0 24.6 1.0

Zinc binding site 3 out of 7 in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1324 b:35.9 occ:0.37 ZN A:ZN1324 0.0 35.9 0.4 ZN A:ZN1324 1.6 28.2 0.6 NE2 A:HIS252 2.1 43.5 1.0 CE1 A:HIS252 2.1 37.0 1.0 O A:HOH2167 2.2 36.5 1.0 CD2 A:HIS252 3.4 40.0 1.0 ND1 A:HIS252 3.4 34.3 1.0 O A:HOH2074 3.8 30.8 1.0 CG A:HIS252 4.1 32.2 1.0 OG A:SER255 4.6 17.9 1.0 O D:HOH2032 4.7 37.1 1.0

Zinc binding site 4 out of 7 in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1325 b:29.3 occ:0.56 ZN A:ZN1325 0.0 29.3 0.6 O A:HOH2176 1.9 30.8 1.0 NE2 A:HIS224 2.1 23.6 0.6 O A:HOH2021 2.2 40.6 1.0 O A:HOH2083 2.2 16.5 0.5 CE1 A:HIS224 2.2 23.9 0.5 ND1 A:HIS224 3.0 22.7 0.5 CD2 A:HIS224 3.1 21.4 0.6 CE1 A:HIS224 3.1 25.7 0.6 NE2 A:HIS224 3.3 24.7 0.5 O A:HOH2083 3.6 18.4 0.5 O A:HOH2099 3.9 23.2 1.0 ND1 A:HIS224 4.2 25.6 0.6 CG A:HIS224 4.2 22.8 0.6 CG A:HIS224 4.3 23.5 0.5 O D:MET97 4.4 17.0 0.5 NE2 D:GLN104 4.4 47.3 1.0 CB A:ASN223 4.4 24.4 1.0 CD2 A:HIS224 4.4 26.0 0.5 CB D:MET97 4.4 19.2 0.5 O D:MET97 4.5 16.1 0.5 ZN A:ZN1325 4.5 26.3 0.4 ND2 A:ASN223 4.6 28.7 1.0 O A:HOH2132 4.6 45.8 1.0 CA D:MET97 4.8 17.3 0.5 CA D:MET97 4.9 14.9 0.5 CB D:MET97 5.0 17.1 0.5 CG A:ASN223 5.0 29.6 1.0

Zinc binding site 5 out of 7 in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1325 b:26.3 occ:0.44 ZN A:ZN1325 0.0 26.3 0.4 NE2 A:HIS224 2.1 24.7 0.5 O A:HOH2132 2.4 45.8 1.0 CE1 A:HIS224 2.4 25.7 0.6 O A:HOH2141 2.7 39.1 1.0 CD2 A:HIS224 2.8 26.0 0.5 O A:HOH2076 2.9 39.1 1.0 ND1 A:HIS224 3.1 25.6 0.6 CE1 A:HIS224 3.2 23.9 0.5 NE2 A:HIS224 3.6 23.6 0.6 CG A:HIS224 4.1 23.5 0.5 ND1 A:HIS224 4.2 22.7 0.5 CG A:HIS224 4.4 22.8 0.6 ZN A:ZN1325 4.5 29.3 0.6 O A:HOH2021 4.5 40.6 1.0 CD2 A:HIS224 4.6 21.4 0.6 O A:HOH2176 4.8 30.8 1.0 CG D:MET97 4.9 18.8 0.5

Zinc binding site 6 out of 7 in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1326 b:40.0 occ:1.00 OE2 A:GLU180 2.0 31.5 1.0 CD A:GLU180 2.7 33.6 1.0 OE1 A:GLU180 2.7 35.9 1.0 O A:HOH2165 2.7 53.6 1.0 O A:HOH2210 2.9 58.2 1.0 CG A:GLU180 4.2 26.6 1.0 O A:HOH2114 4.8 35.8 0.4

Zinc binding site 7 out of 7 in the Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Mcl-1 Bound to Alpha Beta Puma BH3 Peptide 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1327 b:38.6 occ:1.00 NE2 A:HIS277 2.0 28.9 1.0 O A:HOH2215 2.5 39.6 1.0 OD2 A:ASP236 2.9 55.7 1.0 CD2 A:HIS277 3.0 32.1 1.0 CE1 A:HIS277 3.0 29.7 1.0 OE1 A:GLU240 3.2 50.9 1.0 OE2 A:GLU240 3.6 26.8 1.0 CD A:GLU240 3.8 39.7 1.0 CG A:ASP236 4.1 56.5 1.0 ND1 A:HIS277 4.1 29.9 1.0 CG A:HIS277 4.1 26.3 1.0 CG1 A:ILE281 4.4 34.8 1.0 CD1 A:ILE281 4.6 36.7 1.0 OD1 A:ASP236 4.7 63.1 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