Zinc in PDB 5w8f: Crystal Structure of Human Mcl-1 in Complex with Modified Bim BH3 Peptide Sah-MS1-14

The structure of Crystal Structure of Human Mcl-1 in Complex with Modified Bim BH3 Peptide Sah-MS1-14, PDB code: 5w8f was solved by R.Rezaei Araghi, J.M.Jenson, R.A.Grant, A.E.Keating, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.62 / 1.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	46.850, 46.850, 167.440, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 28.9

The binding sites of Zinc atom in the Crystal Structure of Human Mcl-1 in Complex with Modified Bim BH3 Peptide Sah-MS1-14 (pdb code 5w8f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Mcl-1 in Complex with Modified Bim BH3 Peptide Sah-MS1-14, PDB code: 5w8f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Mcl-1 in Complex with Modified Bim BH3 Peptide Sah-MS1-14


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 Human Mcl-1 in Complex with Modified Bim BH3 Peptide Sah-MS1-14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:40.2 occ:1.00 OE2 A:GLU240 2.1 50.5 1.0 SG A:CYS286 2.2 40.1 1.0 OE1 A:GLU240 2.7 45.4 1.0 CD A:GLU240 2.7 50.2 1.0 HA A:CYS286 3.1 43.5 1.0 CB A:CYS286 3.3 36.9 1.0 HB3 A:CYS286 3.3 44.4 1.0 HG21 A:VAL243 3.6 72.4 1.0 CA A:CYS286 3.7 36.1 1.0 HG11 A:VAL243 3.8 85.3 1.0 HB2 A:CYS286 4.1 44.4 1.0 HA A:GLU240 4.2 75.5 1.0 CG A:GLU240 4.2 57.6 1.0 N A:CYS286 4.3 38.1 1.0 HE21 A:GLN283 4.3 63.2 1.0 HG2 A:PRO289 4.3 48.8 1.0 O A:HOH549 4.5 46.2 1.0 HB A:VAL243 4.5 79.8 1.0 HB3 A:GLU240 4.5 71.6 1.0 CG2 A:VAL243 4.5 60.2 1.0 H A:CYS286 4.6 45.9 1.0 HG3 A:GLU240 4.6 69.3 1.0 HG2 A:GLU240 4.7 69.3 1.0 CG1 A:VAL243 4.7 71.0 1.0 CB A:GLU240 4.8 59.5 1.0 CB A:VAL243 4.8 66.3 1.0 C A:SER285 4.9 38.4 1.0 NE2 A:GLN283 4.9 52.5 1.0 CA A:GLU240 4.9 62.8 1.0 HG23 A:VAL243 4.9 72.4 1.0 C A:CYS286 4.9 38.2 1.0 HB2 A:PRO289 5.0 48.4 1.0 O A:SER285 5.0 37.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Mcl-1 in Complex with Modified Bim BH3 Peptide Sah-MS1-14


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 Human Mcl-1 in Complex with Modified Bim BH3 Peptide Sah-MS1-14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:79.1 occ:1.00 O A:HOH552 2.1 46.8 1.0 NE2 A:HIS224 2.3 51.0 1.0 CD2 A:HIS224 3.2 45.2 1.0 CE1 A:HIS224 3.3 52.9 1.0 HD2 A:HIS224 3.4 54.5 1.0 HE1 A:HIS224 3.4 63.7 1.0 HG12 B:ILE14 3.5 49.8 1.0 HB2 A:ASN223 3.8 55.3 1.0 HD11 B:ILE14 3.9 56.6 1.0 HB3 A:ASN223 4.0 55.3 1.0 HD21 A:ASN223 4.0 59.5 1.0 HG13 B:ILE14 4.1 49.8 1.0 HD11 B:LEU10 4.2 67.4 1.0 CG1 B:ILE14 4.2 41.3 1.0 CB A:ASN223 4.4 46.0 1.0 ND1 A:HIS224 4.4 52.5 1.0 CG A:HIS224 4.4 49.1 1.0 CD1 B:ILE14 4.5 47.0 1.0 HD12 B:LEU10 4.6 67.4 1.0 HA A:VAL220 4.6 42.9 1.0 ND2 A:ASN223 4.7 49.4 1.0 CD1 B:LEU10 4.8 56.0 1.0 HG22 A:VAL220 4.8 41.5 1.0 HD13 B:ILE14 4.9 56.6 1.0

R.Rezaei Araghi, G.H.Bird, J.A.Ryan, J.M.Jenson, M.Godes, J.R.Pritz, R.A.Grant, A.Letai, L.D.Walensky, A.E.Keating. Iterative Optimization Yields Mcl-1-Targeting Stapled Peptides with Selective Cytotoxicity to Mcl-1-Dependent Cancer Cells. Proc. Natl. Acad. Sci. V. 115 E886 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29339518
DOI: 10.1073/PNAS.1712952115