Zinc in PDB 6mbd: Human Mcl-1 in Complex with the Designed Peptide DM1

The structure of Human Mcl-1 in Complex with the Designed Peptide DM1, PDB code: 6mbd was solved by J.M.Jenson, A.E.Keating, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.30 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.792, 69.733, 84.853, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24

The binding sites of Zinc atom in the Human Mcl-1 in Complex with the Designed Peptide DM1 (pdb code 6mbd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Human Mcl-1 in Complex with the Designed Peptide DM1, PDB code: 6mbd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Human Mcl-1 in Complex with the Designed Peptide DM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Mcl-1 in Complex with the Designed Peptide DM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:63.6 occ:1.00 NE2 B:HIS252 2.1 40.3 1.0 OD1 A:ASP304 2.2 26.6 1.0 HZ3 D:LYS2 2.2 73.1 1.0 O A:HOH501 2.2 34.0 1.0 OD2 A:ASP304 2.8 24.3 1.0 CG A:ASP304 2.9 25.8 1.0 CE1 B:HIS252 2.9 49.4 1.0 O A:HOH574 2.9 49.2 1.0 HE1 B:HIS252 2.9 59.2 1.0 NZ D:LYS2 3.0 60.9 1.0 HZ2 D:LYS2 3.2 73.1 1.0 CD2 B:HIS252 3.3 35.3 1.0 HG2 A:ARG303 3.3 37.6 1.0 HZ1 D:LYS2 3.4 73.1 1.0 HD2 B:HIS252 3.6 42.4 1.0 HG3 D:LYS2 3.7 58.6 1.0 HG3 A:ARG303 3.9 37.6 1.0 HD2 D:LYS2 3.9 76.0 1.0 CG A:ARG303 4.0 31.3 1.0 ND1 B:HIS252 4.1 48.4 1.0 CE D:LYS2 4.2 64.6 1.0 HD2 A:ARG303 4.2 51.2 1.0 CG B:HIS252 4.3 33.2 1.0 CB A:ASP304 4.3 22.5 1.0 CD D:LYS2 4.4 63.3 1.0 HE2 D:LYS2 4.4 77.6 1.0 CG D:LYS2 4.5 48.8 1.0 HA A:ASP304 4.5 29.0 1.0 HH22 D:ARG9 4.6 31.9 1.0 CD A:ARG303 4.7 42.7 1.0 OG B:SER255 4.8 26.2 1.0 HG B:SER255 4.8 31.5 1.0 HB2 A:ASP304 4.8 27.0 1.0 HH12 D:ARG9 4.8 36.3 1.0 HD1 B:HIS252 4.8 58.1 1.0 HB3 A:ASP304 4.9 27.0 1.0 CA A:ASP304 4.9 24.1 1.0 H A:ASP304 4.9 27.4 1.0 HE3 D:LYS2 5.0 77.6 1.0 HB2 D:LYS2 5.0 48.1 1.0

Zinc binding site 2 out of 7 in the Human Mcl-1 in Complex with the Designed Peptide DM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Mcl-1 in Complex with the Designed Peptide DM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:28.5 occ:0.53 ZN A:ZN402 0.0 28.5 0.5 ZN A:ZN402 1.7 39.8 0.5 OE2 C:GLU13 2.0 65.9 1.0 OE1 C:GLU13 2.0 36.3 1.0 CD C:GLU13 2.0 45.5 1.0 NE2 A:HIS224 2.1 30.2 1.0 HE1 A:HIS224 2.8 38.1 1.0 CE1 A:HIS224 2.8 31.7 1.0 HG2 C:GLU13 3.2 56.1 1.0 CG C:GLU13 3.3 46.7 1.0 CD2 A:HIS224 3.3 25.8 1.0 HD2 A:HIS224 3.7 30.9 1.0 HG3 C:GLU13 3.8 56.1 1.0 HG23 C:ILE10 3.9 29.7 1.0 ND1 A:HIS224 4.0 25.5 1.0 HB3 C:GLU13 4.1 48.6 1.0 CB C:GLU13 4.3 40.5 1.0 CG A:HIS224 4.3 26.4 1.0 HA C:ILE10 4.5 26.2 1.0 HG13 C:ILE14 4.5 32.7 1.0 HB2 C:GLU13 4.6 48.6 1.0 HG12 C:ILE10 4.7 29.5 1.0 HD1 A:HIS224 4.7 30.6 1.0 CG2 C:ILE10 4.8 24.7 1.0 HB3 A:ASN223 4.8 35.4 1.0

Zinc binding site 3 out of 7 in the Human Mcl-1 in Complex with the Designed Peptide DM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Mcl-1 in Complex with the Designed Peptide DM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:39.8 occ:0.47 ZN A:ZN402 0.0 39.8 0.5 ZN A:ZN402 1.7 28.5 0.5 HE1 A:HIS224 1.9 38.1 1.0 CE1 A:HIS224 2.3 31.7 1.0 NE2 A:HIS224 2.4 30.2 1.0 OE2 C:GLU13 3.1 65.9 1.0 CD C:GLU13 3.4 45.5 1.0 O A:HOH565 3.5 41.1 1.0 ND1 A:HIS224 3.5 25.5 1.0 HB3 A:ASN223 3.6 35.4 1.0 OE1 C:GLU13 3.6 36.3 1.0 CD2 A:HIS224 3.7 25.8 1.0 HB2 A:ASN223 3.9 35.4 1.0 HG2 C:GLU13 3.9 56.1 1.0 HD1 A:HIS224 4.0 30.6 1.0 HD22 A:ASN223 4.2 35.4 1.0 CB A:ASN223 4.2 29.5 1.0 CG A:HIS224 4.2 26.4 1.0 HD2 A:HIS224 4.3 30.9 1.0 CG C:GLU13 4.3 46.7 1.0 HG23 C:ILE10 4.4 29.7 1.0 HG13 C:ILE14 4.4 32.7 1.0 HD11 C:ILE14 4.7 40.6 1.0 ND2 A:ASN223 4.8 29.5 1.0 HG3 C:GLU13 4.8 56.1 1.0 HG12 C:ILE14 4.8 32.7 1.0 O A:ASN223 4.8 20.6 1.0 HA A:VAL220 5.0 26.2 1.0 CG A:ASN223 5.0 31.7 1.0

Zinc binding site 4 out of 7 in the Human Mcl-1 in Complex with the Designed Peptide DM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Mcl-1 in Complex with the Designed Peptide DM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:55.5 occ:1.00 HZ3 C:LYS1 1.7 65.6 1.0 OD1 B:ASP304 2.1 25.9 1.0 NE2 A:HIS252 2.1 33.3 1.0 NZ C:LYS1 2.4 54.6 1.0 O B:HOH558 2.4 37.8 1.0 HZ2 C:LYS1 2.6 65.6 1.0 OD2 B:ASP304 2.6 27.3 1.0 CG B:ASP304 2.6 25.1 1.0 HZ1 C:LYS1 2.7 65.6 1.0 CD2 A:HIS252 3.1 32.9 1.0 CE1 A:HIS252 3.2 42.6 1.0 HD2 A:HIS252 3.2 39.5 1.0 HE1 A:HIS252 3.4 51.2 1.0 OE2 C:GLU5 3.5 56.8 1.0 HG3 C:LYS1 3.5 57.1 1.0 CE C:LYS1 3.6 58.2 1.0 HD2 C:LYS1 3.6 63.9 1.0 HD2 B:ARG303 3.6 50.7 1.0 HE2 C:LYS1 3.9 69.9 1.0 CD C:LYS1 4.0 53.3 1.0 CB B:ASP304 4.1 24.4 1.0 HH22 C:ARG8 4.2 29.7 1.0 CG A:HIS252 4.2 29.1 1.0 CG C:LYS1 4.2 47.6 1.0 ND1 A:HIS252 4.2 49.3 1.0 HG2 B:ARG303 4.3 38.6 1.0 HH12 C:ARG8 4.3 29.6 1.0 O A:HOH581 4.4 43.0 1.0 HE3 C:LYS1 4.4 69.9 1.0 HA B:ASP304 4.4 28.9 1.0 CD B:ARG303 4.5 42.2 1.0 HB3 B:ASP304 4.6 29.3 1.0 HD3 B:ARG303 4.6 50.7 1.0 HB2 B:ASP304 4.6 29.3 1.0 CD C:GLU5 4.6 47.6 1.0 HG A:SER255 4.6 24.4 1.0 CA B:ASP304 4.8 24.1 1.0 OG A:SER255 4.8 20.4 1.0 H B:ASP304 4.8 30.2 1.0 NH2 C:ARG8 4.8 24.8 1.0 HB3 B:ARG303 4.9 33.8 1.0 CG B:ARG303 4.9 32.2 1.0 HG2 C:LYS1 4.9 57.1 1.0 HD3 C:LYS1 4.9 63.9 1.0 HB2 C:LYS1 5.0 49.8 1.0 N B:ASP304 5.0 25.1 1.0 NH1 C:ARG8 5.0 24.7 1.0

Zinc binding site 5 out of 7 in the Human Mcl-1 in Complex with the Designed Peptide DM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Mcl-1 in Complex with the Designed Peptide DM1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:32.3 occ:1.00 ND1 A:HIS320 1.9 26.7 1.0 O A:HIS320 2.2 25.2 1.0 HB2 A:HIS320 2.8 32.0 1.0 CE1 A:HIS320 2.9 34.1 1.0 CG A:HIS320 2.9 31.6 1.0 HE1 A:HIS320 3.1 40.9 1.0 C A:HIS320 3.3 28.9 1.0 CB A:HIS320 3.3 26.7 1.0 CA A:HIS320 3.9 27.5 1.0 O A:PHE319 3.9 24.8 1.0 NE2 A:HIS320 4.0 30.7 1.0 CD2 A:HIS320 4.1 37.1 1.0 HB3 A:HIS320 4.2 32.0 1.0 HA A:VAL321 4.3 31.4 1.0 N A:VAL321 4.4 28.3 1.0 HB2 A:GLU322 4.5 63.1 1.0 HA A:HIS320 4.6 33.0 1.0 CA A:VAL321 4.7 26.2 1.0 O A:HOH525 4.7 45.3 1.0 C A:PHE319 4.7 27.0 1.0 N A:HIS320 4.7 29.7 1.0 C A:VAL321 4.8 36.2 1.0 HE2 A:HIS320 4.8 36.8 1.0 N A:GLU322 4.9 45.2 1.0 H A:GLU322 4.9 54.2 1.0 HD2 A:HIS320 4.9 44.5 1.0

Zinc binding site 6 out of 7 in the Human Mcl-1 in Complex with the Designed Peptide DM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Mcl-1 in Complex with the Designed Peptide DM1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:44.9 occ:1.00 NE2 B:HIS277 2.0 50.1 1.0 O B:HOH565 2.1 43.3 1.0 O B:HOH546 2.6 35.0 1.0 CE1 B:HIS277 2.9 45.9 1.0 CD2 B:HIS277 3.0 40.4 1.0 HE1 B:HIS277 3.1 55.0 1.0 HD2 B:HIS277 3.2 48.5 1.0 HG13 B:ILE281 3.7 66.2 1.0 O B:ILE237 4.0 36.9 1.0 O B:HOH537 4.0 33.9 1.0 ND1 B:HIS277 4.0 47.5 1.0 CG B:HIS277 4.1 42.8 1.0 CG1 B:ILE281 4.6 55.1 1.0 HA B:LYS238 4.7 50.3 1.0 HD21 B:LEU232 4.7 44.3 1.0 HG12 B:ILE281 4.7 66.2 1.0 HD1 B:HIS277 4.8 57.0 1.0 HG21 B:ILE281 4.8 72.0 1.0 HD11 B:LEU232 4.9 32.5 1.0 HD11 B:ILE281 5.0 62.4 1.0 HD23 B:LEU278 5.0 58.3 1.0

Zinc binding site 7 out of 7 in the Human Mcl-1 in Complex with the Designed Peptide DM1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Mcl-1 in Complex with the Designed Peptide DM1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:32.6 occ:1.00 OD1 B:ASP236 2.1 27.2 1.0 HE2 B:LYS238 2.4 54.9 1.0 CG B:ASP236 2.8 32.6 1.0 OD2 B:ASP236 2.8 34.6 1.0 HE3 B:LYS238 3.1 54.9 1.0 CE B:LYS238 3.2 45.7 1.0 HG2 B:LYS238 3.3 53.4 1.0 HG3 B:LYS238 3.9 53.4 1.0 CG B:LYS238 3.9 44.5 1.0 CD B:LYS238 4.1 45.2 1.0 HZ3 B:LYS238 4.1 80.3 1.0 NZ B:LYS238 4.2 66.9 1.0 CB B:ASP236 4.3 31.6 1.0 HD3 B:LYS238 4.4 54.3 1.0 HZ2 B:LYS238 4.5 80.3 1.0 O B:HOH524 4.5 31.9 1.0 O B:ASP236 4.6 28.3 1.0 HA B:ASP236 4.6 35.5 1.0 HB2 B:ASP236 4.6 37.9 1.0 HB3 B:ASP236 4.8 37.9 1.0 CA B:ASP236 4.9 29.6 1.0 HD2 B:LYS238 4.9 54.3 1.0 HZ1 B:LYS238 4.9 80.3 1.0 C B:ASP236 5.0 30.8 1.0

V.Frappier, J.M.Jenson, J.Zhou, G.Grigoryan, A.E.Keating. Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides That Bind Anti-Apoptotic Bfl-1 and Mcl-1. Structure V. 27 606 2019.
ISSN: ISSN 1878-4186
PubMed: 30773399
DOI: 10.1016/J.STR.2019.01.008