Zinc in PDB 6zie: Crystal Structure of Mcl-1 in Complex with A Neutralizing Alphabody Cmpx-383B

The structure of Crystal Structure of Mcl-1 in Complex with A Neutralizing Alphabody Cmpx-383B, PDB code: 6zie was solved by E.Pannecoucke, S.N.Savvides, J.Desmet, I.Lasters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.33 / 2.30
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	69.699, 69.699, 261.289, 90, 90, 120
R / Rfree (%)	24 / 25.9

The binding sites of Zinc atom in the Crystal Structure of Mcl-1 in Complex with A Neutralizing Alphabody Cmpx-383B (pdb code 6zie). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Mcl-1 in Complex with A Neutralizing Alphabody Cmpx-383B, PDB code: 6zie:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Mcl-1 in Complex with A Neutralizing Alphabody Cmpx-383B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Mcl-1 in Complex with A Neutralizing Alphabody Cmpx-383B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:54.6 occ:1.00 NE2 A:HIS143 1.9 71.0 1.0 CE1 A:HIS138 2.0 69.2 1.0 CE1 A:HIS143 2.7 73.7 1.0 ND1 A:HIS138 2.9 66.7 1.0 NE2 A:HIS138 3.1 70.0 1.0 CD2 A:HIS143 3.1 69.4 1.0 ND1 A:HIS143 4.0 74.5 1.0 CG A:HIS138 4.1 64.2 1.0 CG A:HIS143 4.1 71.0 1.0 CD2 A:HIS138 4.2 67.4 1.0 CB A:ALA142 4.6 70.9 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Mcl-1 in Complex with A Neutralizing Alphabody Cmpx-383B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Mcl-1 in Complex with A Neutralizing Alphabody Cmpx-383B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:84.5 occ:1.00 OE2 A:GLU133 2.0 87.5 1.0 OE2 A:GLU137 2.2 74.3 1.0 CD A:GLU137 3.0 70.8 1.0 CD A:GLU133 3.1 82.6 1.0 OE1 A:GLU137 3.1 72.8 1.0 O A:HOH318 3.2 67.5 1.0 CG A:GLU133 3.9 68.9 1.0 O A:HOH308 4.0 61.7 1.0 O A:HOH309 4.1 76.3 1.0 OE1 A:GLU133 4.1 84.5 1.0 CG A:GLU137 4.5 62.7 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Mcl-1 in Complex with A Neutralizing Alphabody Cmpx-383B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Mcl-1 in Complex with A Neutralizing Alphabody Cmpx-383B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:79.8 occ:1.00 NE2 B:HIS252 2.3 77.1 1.0 OE2 A:GLU49 2.3 96.5 1.0 OE1 A:GLU49 2.8 90.5 1.0 CD A:GLU49 2.9 92.3 1.0 CE1 B:HIS252 3.1 78.0 1.0 CD2 B:HIS252 3.4 73.0 1.0 ND1 B:HIS252 4.3 75.2 1.0 CG A:GLU49 4.4 86.7 1.0 CG B:HIS252 4.5 70.8 1.0 O B:ARG248 4.6 70.3 1.0 NH2 B:ARG248 5.0 110.4 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Mcl-1 in Complex with A Neutralizing Alphabody Cmpx-383B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Mcl-1 in Complex with A Neutralizing Alphabody Cmpx-383B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:118.7 occ:1.00 OE1 A:GLU108 2.5 79.0 1.0 CD A:GLU108 3.0 77.0 1.0 OE2 A:GLU108 3.1 78.0 1.0 NZ A:LYS136 3.8 71.2 1.0 CG A:GLU108 4.2 71.8 1.0 OE2 A:GLU104 4.5 86.9 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Mcl-1 in Complex with A Neutralizing Alphabody Cmpx-383B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Mcl-1 in Complex with A Neutralizing Alphabody Cmpx-383B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:80.8 occ:1.00 OD2 B:ASP242 1.9 98.5 1.0 NE2 B:HIS277 2.0 77.8 1.0 OD1 B:ASP236 2.0 110.5 1.0 CG B:ASP242 2.8 96.3 1.0 CG B:ASP236 3.0 110.8 1.0 CD2 B:HIS277 3.0 73.8 1.0 CE1 B:HIS277 3.0 79.5 1.0 OD1 B:ASP242 3.0 99.6 1.0 OD2 B:ASP236 3.3 113.4 1.0 CD1 B:ILE281 4.0 86.8 1.0 CG B:HIS277 4.1 72.8 1.0 ND1 B:HIS277 4.1 77.3 1.0 CB B:ASP242 4.2 89.3 1.0 CB B:ASP236 4.3 107.4 1.0 CD1 B:LEU232 4.6 77.9 1.0 CA B:ASP236 4.7 104.9 1.0

E.Pannecoucke, M.Van Trimpont, J.Desmet, T.Pieters, L.Reunes, L.Demoen, M.Vuylsteke, S.Loverix, K.Vandenbroucke, P.Alard, P.Henderikx, S.Deroo, F.Baatz, E.Lorent, S.Thiolloy, K.Somers, Y.Mcgrath, P.Van Vlierberghe, I.Lasters, S.N.Savvides. Cell-Penetrating Alphabody Protein Scaffolds For Intracellular Drug Targeting. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 33771865
DOI: 10.1126/SCIADV.ABE1682