Zinc in PDB 3kj1: Mcl-1 in Complex with Bim BH3 Mutant I2DA

The structure of Mcl-1 in Complex with Bim BH3 Mutant I2DA, PDB code: 3kj1 was solved by E.Fire, 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)	28.89 / 1.95
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	53.066, 72.007, 117.845, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.3

The structure of Mcl-1 in Complex with Bim BH3 Mutant I2DA also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Mcl-1 in Complex with Bim BH3 Mutant I2DA (pdb code 3kj1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Mcl-1 in Complex with Bim BH3 Mutant I2DA, PDB code: 3kj1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Mcl-1 in Complex with Bim BH3 Mutant I2DA


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mcl-1 in Complex with Bim BH3 Mutant I2DA within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:40.9 occ:1.00 OXT A:ACT1428 1.8 30.0 1.0 CE1 A:HIS252 2.1 28.2 1.0 NE2 A:HIS252 2.8 39.4 1.0 C A:ACT1428 3.0 42.8 1.0 ND1 A:HIS252 3.3 38.5 1.0 O A:ACT1428 3.5 51.4 1.0 CD2 A:HIS252 4.1 39.0 1.0 CH3 A:ACT1428 4.2 27.9 1.0 CG A:HIS252 4.3 33.9 1.0 OG A:SER255 4.7 23.5 1.0 CG2 B:ILE4 4.8 42.2 1.0

Zinc binding site 2 out of 5 in the Mcl-1 in Complex with Bim BH3 Mutant I2DA


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mcl-1 in Complex with Bim BH3 Mutant I2DA within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:58.1 occ:1.00 OE2 A:GLU292 2.3 50.5 1.0 OE1 A:GLU292 2.8 47.8 1.0 CD A:GLU292 2.9 46.5 1.0 OE1 A:GLU288 4.4 79.5 1.0 CB A:GLU288 4.4 43.9 1.0 CG A:GLU292 4.4 40.8 1.0

Zinc binding site 3 out of 5 in the Mcl-1 in Complex with Bim BH3 Mutant I2DA


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mcl-1 in Complex with Bim BH3 Mutant I2DA within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:28.2 occ:1.00 OE2 A:GLU317 2.0 26.3 1.0 OD1 A:ASP313 2.0 24.1 1.0 CG A:ASP313 2.8 26.3 1.0 CD A:GLU317 2.8 28.9 1.0 OD2 A:ASP313 2.9 24.6 1.0 CG A:GLU317 3.1 27.8 1.0 OE1 A:GLU317 4.0 27.0 1.0 O A:HOH40 4.0 36.0 1.0 O A:HOH63 4.1 37.6 1.0 CB A:ASP313 4.2 24.9 1.0 O A:ASP313 4.5 23.6 1.0 CB A:GLU317 4.6 27.5 1.0 NH2 A:ARG310 4.8 49.2 1.0 CA A:ASP313 4.8 28.0 1.0 O A:HOH47 4.9 37.8 1.0

Zinc binding site 4 out of 5 in the Mcl-1 in Complex with Bim BH3 Mutant I2DA


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mcl-1 in Complex with Bim BH3 Mutant I2DA within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5 b:79.2 occ:1.00 ND1 A:HIS277 2.4 59.5 1.0 CG A:HIS277 3.3 54.0 1.0 O A:HOH72 3.4 48.8 1.0 OE1 A:GLN229 3.4 64.0 1.0 CB A:HIS277 3.4 44.9 1.0 CE1 A:HIS277 3.4 57.5 1.0 CA A:HIS277 3.9 44.1 1.0 CD2 A:LEU232 4.3 49.0 1.0 CD2 A:HIS277 4.4 55.2 1.0 NE2 A:HIS277 4.5 55.8 1.0 CD A:GLN229 4.5 61.6 1.0 OG1 A:THR280 4.7 73.0 1.0 N A:HIS277 4.8 39.0 1.0 C A:HIS277 5.0 46.6 1.0

Zinc binding site 5 out of 5 in the Mcl-1 in Complex with Bim BH3 Mutant I2DA


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Mcl-1 in Complex with Bim BH3 Mutant I2DA within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn23 b:42.5 occ:1.00 OE1 B:GLU9 2.0 43.9 1.0 O B:HOH24 2.4 48.9 1.0 CD B:GLU9 2.9 39.8 1.0 OE2 B:GLU9 3.0 40.9 1.0 NE1 B:TRP5 4.0 41.5 1.0 NE B:ARG12 4.3 27.0 1.0 CG B:GLU9 4.3 36.2 1.0 CZ2 B:TRP5 4.5 45.3 1.0 CE2 B:TRP5 4.5 40.2 1.0 NH2 B:ARG12 4.6 24.0 1.0 CB B:GLU9 4.8 31.8 1.0 CZ B:ARG12 4.8 27.6 1.0 CD1 B:TRP5 5.0 43.1 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