Zinc in PDB 2pqk: X-Ray Crystal Structure of Human Mcl-1 in Complex with Bim BH3

The structure of X-Ray Crystal Structure of Human Mcl-1 in Complex with Bim BH3, PDB code: 2pqk was solved by E.Bare, 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)	34.60 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	53.087, 71.846, 118.145, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.9

The structure of X-Ray Crystal Structure of Human Mcl-1 in Complex with Bim BH3 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

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

Zinc binding site 1 out of 3 in the X-Ray Crystal Structure of Human Mcl-1 in Complex with Bim BH3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of Human Mcl-1 in Complex with Bim BH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:37.1 occ:1.00 O A:HOH93 1.9 21.3 1.0 OD1 A:ASP304 2.0 26.0 1.0 O A:HOH53 2.2 37.3 1.0 CG A:ASP304 2.8 25.3 1.0 OD2 A:ASP304 2.8 26.5 1.0 CG A:ARG303 4.1 29.2 1.0 CB A:ASP304 4.2 24.6 1.0 CA A:ASP304 4.7 25.3 1.0 N A:ASP304 4.7 25.0 1.0

Zinc binding site 2 out of 3 in the X-Ray Crystal Structure of Human Mcl-1 in Complex with Bim BH3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of Human Mcl-1 in Complex with Bim BH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:27.3 occ:1.00 OE2 A:GLU317 1.8 22.2 1.0 OD1 A:ASP313 2.0 27.9 1.0 CD A:GLU317 2.7 24.4 1.0 CG A:ASP313 2.8 29.6 1.0 OD2 A:ASP313 3.0 30.6 1.0 CG A:GLU317 3.0 24.3 1.0 OE1 A:GLU317 3.9 25.1 1.0 O A:HOH15 4.0 30.8 1.0 CB A:ASP313 4.2 27.6 1.0 O A:ASP313 4.6 26.8 1.0 O A:HOH8 4.6 37.8 1.0 CB A:GLU317 4.6 24.9 1.0 NH2 A:ARG310 4.8 38.1 1.0 CA A:ASP313 4.8 27.9 1.0

Zinc binding site 3 out of 3 in the X-Ray Crystal Structure of Human Mcl-1 in Complex with Bim BH3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of Human Mcl-1 in Complex with Bim BH3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:42.7 occ:1.00 O B:HOH421 1.4 30.5 1.0 OE1 B:GLU9 2.1 37.9 1.0 O B:HOH416 2.3 39.3 1.0 CD B:GLU9 2.8 35.5 1.0 OE2 B:GLU9 2.9 37.5 1.0 O B:HOH418 3.8 56.1 1.0 NE1 B:TRP5 4.2 39.9 1.0 NE B:ARG12 4.2 25.7 1.0 CG B:GLU9 4.3 33.9 1.0 CZ2 B:TRP5 4.4 38.8 1.0 CE2 B:TRP5 4.6 39.0 1.0 NH2 B:ARG12 4.6 26.6 1.0 CZ B:ARG12 4.8 25.5 1.0 CB B:GLU9 4.9 30.6 1.0

E.Fire, S.V.Gulla, R.A.Grant, A.E.Keating. Mcl-1-Bim Complexes Accommodate Surprising Point Mutations Via Minor Structural Changes. Protein Sci. V. 19 507 2010.
ISSN: ISSN 0961-8368
PubMed: 20066663
DOI: 10.1002/PRO.329