Zinc in PDB 5uum: Human Mcl-1 in Complex with A Bfl-1-Specific Selected Peptide

The structure of Human Mcl-1 in Complex with A Bfl-1-Specific Selected Peptide, PDB code: 5uum was solved by 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)	27.33 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.617, 62.760, 48.788, 90.00, 98.14, 90.00
R / Rfree (%)	21.6 / 25.1

The binding sites of Zinc atom in the Human Mcl-1 in Complex with A Bfl-1-Specific Selected Peptide (pdb code 5uum). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Human Mcl-1 in Complex with A Bfl-1-Specific Selected Peptide, PDB code: 5uum:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Human Mcl-1 in Complex with A Bfl-1-Specific Selected Peptide


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 A Bfl-1-Specific Selected Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:0.6 occ:1.00 NE2 A:HIS252 2.0 41.8 1.0 CE1 A:HIS252 2.9 38.9 1.0 HE1 A:HIS252 3.0 46.7 1.0 HG2 C:ARG4 3.0 74.8 1.0 CD2 A:HIS252 3.1 32.0 1.0 HD2 A:HIS252 3.4 38.4 1.0 CG C:ARG4 4.0 62.3 1.0 ND1 A:HIS252 4.0 38.4 1.0 HB3 C:ARG4 4.1 64.6 1.0 CG A:HIS252 4.2 33.2 1.0 HH12 C:ARG11 4.3 41.2 1.0 HD2 C:ARG4 4.3 85.1 1.0 HE C:ARG4 4.4 89.0 1.0 HA C:ARG4 4.4 57.9 1.0 HG3 C:ARG4 4.5 74.8 1.0 CB C:ARG4 4.5 53.9 1.0 CD C:ARG4 4.6 71.0 1.0 OG A:SER255 4.7 34.2 1.0 HG A:SER255 4.7 41.0 1.0 HH22 C:ARG11 4.7 38.5 1.0 NE C:ARG4 4.8 74.2 1.0 HD1 A:HIS252 4.8 46.1 1.0 NH1 C:ARG11 4.9 34.4 1.0

Zinc binding site 2 out of 8 in the Human Mcl-1 in Complex with A Bfl-1-Specific Selected Peptide


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 A Bfl-1-Specific Selected Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:55.4 occ:1.00 OE2 A:GLU322 1.8 32.5 1.0 ND1 A:HIS320 2.0 34.3 1.0 OE1 A:GLU317 2.2 50.1 1.0 CD A:GLU322 2.8 38.4 1.0 CE1 A:HIS320 2.9 37.2 1.0 HE1 A:HIS320 2.9 44.6 1.0 CD A:GLU317 3.1 46.8 1.0 HB3 A:HIS320 3.2 40.9 1.0 CG A:HIS320 3.2 33.2 1.0 OE2 A:GLU317 3.3 43.1 1.0 OE1 A:GLU322 3.4 35.2 1.0 CB A:HIS320 3.7 34.1 1.0 HA A:GLU317 3.9 34.7 1.0 HB2 A:HIS320 4.0 40.9 1.0 NE2 A:HIS320 4.0 39.1 1.0 CG A:GLU322 4.1 33.6 1.0 HG2 A:GLU322 4.1 40.3 1.0 CD2 A:HIS320 4.2 43.6 1.0 O A:HOH517 4.2 42.6 1.0 HG3 A:GLU322 4.4 40.3 1.0 CG A:GLU317 4.5 45.2 1.0 HB3 A:GLU317 4.5 45.6 1.0 CA A:GLU317 4.7 28.9 1.0 HE2 A:HIS320 4.8 46.9 1.0 CB A:GLU317 4.8 38.0 1.0 O A:HIS320 4.9 28.4 1.0 HG3 A:GLU317 4.9 54.2 1.0 HA A:GLU322 5.0 43.9 1.0

Zinc binding site 3 out of 8 in the Human Mcl-1 in Complex with A Bfl-1-Specific Selected Peptide


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 A Bfl-1-Specific Selected Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:0.9 occ:1.00 OD1 A:ASP236 2.0 60.0 1.0 OD2 A:ASP242 2.0 68.5 1.0 NE2 A:HIS277 2.1 62.2 1.0 CG A:ASP236 2.8 64.2 1.0 CG A:ASP242 2.9 60.6 1.0 O A:HOH553 2.9 62.0 1.0 CE1 A:HIS277 3.1 59.3 1.0 CD2 A:HIS277 3.1 54.1 1.0 OD1 A:ASP242 3.2 53.3 1.0 OD2 A:ASP236 3.2 62.7 1.0 HE1 A:HIS277 3.2 71.1 1.0 HD2 A:HIS277 3.3 65.0 1.0 HA A:ASP236 3.8 82.1 1.0 HD23 A:LEU278 3.8 68.4 1.0 HD13 A:ILE281 3.8 63.9 1.0 HD21 A:LEU278 3.8 68.4 1.0 CB A:ASP236 4.0 61.8 1.0 HD11 A:LEU232 4.1 65.2 1.0 HB3 A:ASP236 4.1 74.1 1.0 ND1 A:HIS277 4.2 51.9 1.0 CG A:HIS277 4.2 51.8 1.0 CD2 A:LEU278 4.2 57.0 1.0 CB A:ASP242 4.3 61.0 1.0 CA A:ASP236 4.4 68.4 1.0 HB2 A:ASP242 4.5 73.1 1.0 HD22 A:LEU278 4.5 68.4 1.0 HD12 A:LEU232 4.6 65.2 1.0 HB3 A:ASP242 4.6 73.1 1.0 CD1 A:ILE281 4.6 53.3 1.0 HD11 A:ILE281 4.6 63.9 1.0 HG21 A:ILE281 4.7 72.0 1.0 HB2 A:ASP236 4.7 74.1 1.0 CD1 A:LEU232 4.8 54.4 1.0 HD1 A:HIS277 4.9 62.3 1.0 HD12 A:ILE281 4.9 63.9 1.0 N A:ASP236 5.0 63.4 1.0

Zinc binding site 4 out of 8 in the Human Mcl-1 in Complex with A Bfl-1-Specific Selected Peptide


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 A Bfl-1-Specific Selected Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:0.9 occ:1.00 NE2 A:HIS224 2.1 44.2 1.0 HB3 C:ASP16 2.6 51.3 1.0 CE1 A:HIS224 2.6 44.9 1.0 HE1 A:HIS224 2.7 53.9 1.0 O A:HOH551 2.7 35.6 1.0 CD2 A:HIS224 3.2 44.7 1.0 HB2 C:ASP16 3.2 51.3 1.0 CB C:ASP16 3.3 42.8 1.0 HB3 A:ASN223 3.4 57.6 1.0 HB2 A:ASN223 3.5 57.6 1.0 HD22 A:ASN223 3.6 54.2 1.0 HD2 A:HIS224 3.6 53.6 1.0 OE1 C:GLN20 3.7 53.6 1.0 ND1 A:HIS224 3.8 37.4 1.0 CB A:ASN223 3.9 48.0 1.0 OD2 C:ASP16 3.9 56.3 1.0 CG C:ASP16 4.0 54.3 1.0 CG A:HIS224 4.1 39.3 1.0 ND2 A:ASN223 4.2 45.2 1.0 HG22 C:VAL17 4.4 39.2 1.0 HG23 C:VAL17 4.4 39.2 1.0 HA C:ALA13 4.5 44.3 1.0 O C:ALA13 4.5 29.3 1.0 HD1 A:HIS224 4.5 44.9 1.0 CG A:ASN223 4.5 46.9 1.0 CA C:ASP16 4.6 52.1 1.0 C C:ASP16 4.6 38.3 1.0 O C:HOH104 4.6 51.6 1.0 HA A:VAL220 4.6 50.4 1.0 N C:VAL17 4.7 39.2 1.0 H C:VAL17 4.7 47.0 1.0 CD C:GLN20 4.7 64.0 1.0 HE22 C:GLN20 4.7 85.6 1.0 HA C:VAL17 4.9 42.8 1.0 CG2 C:VAL17 4.9 32.6 1.0 HD21 A:ASN223 4.9 54.2 1.0 OD1 C:ASP16 5.0 68.6 1.0 HG13 A:VAL220 5.0 45.8 1.0

Zinc binding site 5 out of 8 in the Human Mcl-1 in Complex with A Bfl-1-Specific Selected Peptide


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 A Bfl-1-Specific Selected Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:48.0 occ:1.00 OE2 B:GLU322 1.9 35.3 1.0 ND1 B:HIS320 2.2 44.8 1.0 OE1 B:GLU317 2.5 43.6 1.0 CD B:GLU322 2.9 39.5 1.0 CE1 B:HIS320 2.9 34.3 1.0 HE1 B:HIS320 3.0 41.2 1.0 OE1 B:GLU322 3.2 44.1 1.0 HB3 B:HIS320 3.2 41.9 1.0 CG B:HIS320 3.3 44.3 1.0 CD B:GLU317 3.6 52.8 1.0 CB B:HIS320 3.7 34.9 1.0 OE2 B:GLU317 3.9 56.8 1.0 NE2 B:HIS320 4.1 41.9 1.0 HA B:GLU317 4.1 40.4 1.0 HB2 B:HIS320 4.2 41.9 1.0 CD2 B:HIS320 4.3 39.8 1.0 CG B:GLU322 4.3 39.1 1.0 HG2 B:GLU322 4.4 46.9 1.0 O B:HIS320 4.5 39.5 1.0 HG3 B:GLU322 4.7 46.9 1.0 HA B:GLU322 4.8 43.9 1.0 HE2 B:HIS320 4.8 50.3 1.0 HB3 B:GLU317 4.8 39.3 1.0 CG B:GLU317 4.9 44.7 1.0 CA B:GLU317 5.0 33.7 1.0 CA B:HIS320 5.0 38.4 1.0

Zinc binding site 6 out of 8 in the Human Mcl-1 in Complex with A Bfl-1-Specific Selected Peptide


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 A Bfl-1-Specific Selected Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:94.5 occ:1.00 NE2 B:HIS252 2.0 61.7 1.0 CE1 B:HIS252 2.7 78.3 1.0 HE1 B:HIS252 2.7 93.9 1.0 HG3 D:ARG4 2.9 64.2 1.0 CD2 B:HIS252 3.2 44.8 1.0 HD2 B:HIS252 3.6 53.7 1.0 CG D:ARG4 3.8 53.5 1.0 ND1 B:HIS252 3.9 76.2 1.0 HD3 D:ARG4 4.0 70.2 1.0 HH12 D:ARG11 4.1 44.3 1.0 HD2 D:ARG4 4.1 70.2 1.0 CG B:HIS252 4.2 42.6 1.0 CD D:ARG4 4.2 58.5 1.0 HG2 D:ARG4 4.3 64.2 1.0 HA D:ARG4 4.4 54.4 1.0 HH22 D:ARG11 4.4 38.0 1.0 HB2 D:ARG4 4.5 62.5 1.0 HD1 B:HIS252 4.6 91.4 1.0 CB D:ARG4 4.7 52.1 1.0 OG B:SER255 4.7 33.4 1.0 NH1 D:ARG11 4.8 36.9 1.0 HG B:SER255 4.9 40.0 1.0

Zinc binding site 7 out of 8 in the Human Mcl-1 in Complex with A Bfl-1-Specific Selected Peptide


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 A Bfl-1-Specific Selected Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:99.4 occ:1.00 OD2 B:ASP242 2.0 68.6 1.0 NE2 B:HIS277 2.1 77.4 1.0 OD2 B:ASP236 2.4 76.7 1.0 CG B:ASP236 2.4 85.5 1.0 HB2 B:ASP236 2.5 83.8 1.0 CE1 B:HIS277 2.7 77.6 1.0 HE1 B:HIS277 2.8 93.1 1.0 CG B:ASP242 2.8 72.6 1.0 OD1 B:ASP236 2.9 93.5 1.0 CB B:ASP236 3.0 69.9 1.0 OD1 B:ASP242 3.0 74.4 1.0 CD2 B:HIS277 3.2 71.7 1.0 HD11 B:LEU232 3.4 76.4 1.0 HD2 B:HIS277 3.6 86.0 1.0 HA B:ASP236 3.6 87.2 1.0 HB3 B:ASP236 3.7 83.8 1.0 ND1 B:HIS277 3.9 64.6 1.0 CA B:ASP236 3.9 72.6 1.0 HD12 B:LEU232 4.1 76.4 1.0 HD13 B:ILE281 4.1 89.7 1.0 HD11 B:ILE281 4.1 89.7 1.0 CG B:HIS277 4.1 66.3 1.0 HD23 B:LEU278 4.1 72.8 1.0 CD1 B:LEU232 4.2 63.7 1.0 CB B:ASP242 4.2 61.2 1.0 HD21 B:LEU278 4.3 72.8 1.0 HD22 B:LEU235 4.4 84.9 1.0 HB3 B:ASP242 4.4 73.4 1.0 CD1 B:ILE281 4.5 74.8 1.0 HD1 B:HIS277 4.6 77.5 1.0 HD23 B:LEU235 4.6 84.9 1.0 HB2 B:ASP242 4.6 73.4 1.0 CD2 B:LEU278 4.7 60.7 1.0 OE1 B:GLN283 4.7 83.8 1.0 HD12 B:ILE281 4.7 89.7 1.0 HD13 B:LEU232 4.7 76.4 1.0 N B:ASP236 4.7 68.2 1.0 HE22 B:GLN283 4.8 85.6 1.0 H B:ASP236 4.9 81.8 1.0 CD2 B:LEU235 4.9 70.7 1.0 HG B:LEU232 5.0 63.6 1.0

Zinc binding site 8 out of 8 in the Human Mcl-1 in Complex with A Bfl-1-Specific Selected Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human Mcl-1 in Complex with A Bfl-1-Specific Selected Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:0.0 occ:1.00 NE2 B:HIS224 2.1 38.5 1.0 O B:HOH531 2.3 42.8 1.0 HE22 D:GLN20 2.3 72.9 1.0 HB3 D:ASP16 2.7 47.0 1.0 CE1 B:HIS224 2.8 37.3 1.0 HE1 B:HIS224 2.8 44.7 1.0 HB2 D:ASP16 3.0 47.0 1.0 NE2 D:GLN20 3.2 60.7 1.0 CD2 B:HIS224 3.2 39.0 1.0 CB D:ASP16 3.2 39.2 1.0 HD22 B:ASN223 3.4 63.5 1.0 HB2 B:ASN223 3.5 54.9 1.0 HD2 B:HIS224 3.5 46.8 1.0 HE21 D:GLN20 3.7 72.9 1.0 HB3 B:ASN223 3.7 54.9 1.0 HG23 D:VAL17 3.9 39.5 1.0 ND1 B:HIS224 4.0 29.5 1.0 OD2 D:ASP16 4.0 48.3 1.0 CB B:ASN223 4.0 45.7 1.0 OE1 D:GLN20 4.0 65.2 1.0 CD D:GLN20 4.0 66.5 1.0 CG D:ASP16 4.1 48.8 1.0 ND2 B:ASN223 4.2 52.9 1.0 HG22 D:VAL17 4.2 39.5 1.0 CG B:HIS224 4.2 35.9 1.0 O D:ALA13 4.4 29.1 1.0 C D:ASP16 4.4 38.1 1.0 N D:VAL17 4.4 36.5 1.0 CA D:ASP16 4.4 38.7 1.0 H D:VAL17 4.4 43.8 1.0 CG2 D:VAL17 4.5 32.9 1.0 HA D:ALA13 4.6 35.8 1.0 HA B:VAL220 4.6 52.3 1.0 HA D:VAL17 4.6 45.4 1.0 CG B:ASN223 4.6 46.2 1.0 HD1 B:HIS224 4.7 35.4 1.0 HD21 B:ASN223 4.8 63.5 1.0 O D:ASP16 4.9 43.2 1.0 HB1 D:ALA13 4.9 36.0 1.0 HG13 B:VAL220 5.0 33.8 1.0 HA D:ASP16 5.0 46.4 1.0

J.M.Jenson, J.A.Ryan, R.A.Grant, A.Letai, A.E.Keating. Epistatic Mutations in Puma BH3 Drive An Alternate Binding Mode to Potently and Selectively Inhibit Anti-Apoptotic Bfl-1. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28594323
DOI: 10.7554/ELIFE.25541