Zinc in PDB 6qfm: Structure of Human Mcl-1 in Complex with Puma BH3 Peptide

The structure of Structure of Human Mcl-1 in Complex with Puma BH3 Peptide, PDB code: 6qfm was solved by P.Dokurno, J.Murray, J.Davidson, I.Chen, B.Davis, C.J.Graham, R.Harris, A.M.Jordan, N.Matassova, C.Pedder, S.Ray, S.Roughley, J.Smith, C.Walmsley, Y.Wang, N.Whitehead, D.S.Williamson, P.Casara, T.Le Diguarher, J.Hickman, J.Stark, A.Kotschy, O.Geneste, R.E.Hubbard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.98 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.042, 58.345, 76.922, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 26.1

The structure of Structure of Human Mcl-1 in Complex with Puma BH3 Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the Structure of Human Mcl-1 in Complex with Puma BH3 Peptide (pdb code 6qfm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Human Mcl-1 in Complex with Puma BH3 Peptide, PDB code: 6qfm:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of Human Mcl-1 in Complex with Puma BH3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Mcl-1 in Complex with Puma BH3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:25.8 occ:1.00 O B:HOH302 2.1 23.6 1.0 ND1 A:HIS252 2.1 19.9 1.0 CL A:CL405 2.2 30.6 1.0 O B:HOH306 2.6 36.3 1.0 CG A:HIS252 3.1 20.7 1.0 CE1 A:HIS252 3.1 21.1 1.0 CB A:HIS252 3.4 19.2 1.0 CA A:HIS252 3.9 20.5 1.0 CG A:LYS255 4.0 30.9 1.0 NZ A:LYS255 4.1 33.0 1.0 NE2 A:HIS252 4.2 21.4 1.0 CD2 A:HIS252 4.2 21.9 1.0 CG B:ARG135 4.4 30.0 1.0 OE1 B:GLU131 4.5 53.7 1.0 N A:HIS252 4.7 18.1 1.0 CB A:LYS255 4.8 25.8 1.0

Zinc binding site 2 out of 3 in the Structure of Human Mcl-1 in Complex with Puma BH3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Mcl-1 in Complex with Puma BH3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:26.0 occ:1.00 NE2 A:HIS224 2.1 24.6 1.0 CL B:CL201 2.2 31.2 1.0 CL A:CL404 2.3 21.3 1.0 CE1 A:HIS224 3.0 24.5 1.0 CD2 A:HIS224 3.2 21.9 1.0 ND1 A:HIS224 4.2 23.0 1.0 O A:HOH564 4.2 32.5 1.0 CG A:HIS224 4.2 20.4 1.0 O A:HOH535 4.5 43.1 1.0 O B:MET144 4.5 20.5 1.0 CB B:MET144 4.6 21.8 1.0 O A:HOH558 4.8 28.6 1.0 OD1 B:ASP147 5.0 23.0 1.0

Zinc binding site 3 out of 3 in the Structure of Human Mcl-1 in Complex with Puma BH3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Mcl-1 in Complex with Puma BH3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:43.4 occ:1.00 OD2 A:ASP242 2.1 43.7 1.0 OD1 A:ASP236 2.2 36.6 1.0 NE2 A:HIS277 2.5 32.9 1.0 OD2 A:ASP236 2.6 45.9 1.0 CG A:ASP236 2.7 44.0 1.0 CG A:ASP242 2.9 40.8 1.0 OD1 A:ASP242 3.0 35.1 1.0 CD2 A:HIS277 3.1 34.1 1.0 O A:HOH526 3.1 22.6 1.0 O A:HOH561 3.2 54.7 1.0 CE1 A:HIS277 3.6 33.6 1.0 CB A:ASP236 4.1 45.3 1.0 CD1 A:LEU232 4.3 36.9 1.0 CB A:ASP242 4.3 40.8 1.0 CG A:HIS277 4.4 32.2 1.0 ND1 A:HIS277 4.6 34.9 1.0 CA A:ASP236 4.8 46.5 1.0

J.B.Murray, J.Davidson, I.Chen, B.Davis, P.Dokurno, C.J.Graham, R.Harris, A.Jordan, N.Matassova, C.Pedder, S.Ray, S.D.Roughley, J.Smith, C.Walmsley, Y.Wang, N.Whitehead, D.S.Williamson, P.Casara, T.Le Diguarher, J.Hickman, J.Stark, A.Kotschy, O.Geneste, R.E.Hubbard. Establishing Drug Discovery and Identification of Hit Series For the Anti-Apoptotic Proteins, Bcl-2 and Mcl-1. Acs Omega V. 4 8892 2019.
ISSN: ESSN 2470-1343
PubMed: 31459977
DOI: 10.1021/ACSOMEGA.9B00611