Zinc in PDB 1cy5: Crystal Structure of the Apaf-1 Card

The structure of Crystal Structure of the Apaf-1 Card, PDB code: 1cy5 was solved by D.E.Vaughn, L.Joshua-Tor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.350, 46.910, 54.350, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 19.9

The binding sites of Zinc atom in the Crystal Structure of the Apaf-1 Card (pdb code 1cy5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Apaf-1 Card, PDB code: 1cy5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Apaf-1 Card


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 the Apaf-1 Card within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:19.4 occ:0.50 ZN A:ZN101 0.0 19.4 0.5 ZN A:ZN101 1.3 18.5 0.5 OE1 A:GLU17 1.6 32.5 1.0 O A:HOH290 1.9 31.7 1.0 CD A:GLU17 2.4 28.4 1.0 OE2 A:GLU17 2.7 31.3 1.0 O A:HOH201 3.2 21.1 1.0 NE2 A:GLN50 3.4 30.6 1.0 CG A:GLU17 3.8 29.4 1.0 CB A:GLU17 4.2 27.8 1.0 O A:HOH247 4.4 34.6 0.9 CB A:ALA54 4.5 29.1 1.0 NE A:ARG13 4.6 23.4 1.0 CG A:ARG13 4.6 24.7 1.0 CD A:GLN50 4.7 32.0 1.0 CD A:ARG13 4.8 25.5 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Apaf-1 Card


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 the Apaf-1 Card within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:18.5 occ:0.50 ZN A:ZN101 0.0 18.5 0.5 ZN A:ZN101 1.3 19.4 0.5 O A:HOH201 2.0 21.1 1.0 OE1 A:GLU17 2.4 32.5 1.0 O A:HOH290 2.8 31.7 1.0 CD A:GLU17 3.2 28.4 1.0 OE2 A:GLU17 3.3 31.3 1.0 CD A:ARG13 4.2 25.5 1.0 CG A:ARG13 4.2 24.7 1.0 NE A:ARG13 4.3 23.4 1.0 NE2 A:GLN50 4.5 30.6 1.0 CG A:GLU17 4.6 29.4 1.0 CA A:GLU14 5.0 26.8 1.0 CB A:GLU17 5.0 27.8 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Apaf-1 Card


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 the Apaf-1 Card within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:21.4 occ:1.00 O A:HOH282 1.9 23.5 1.0 OE2 A:GLU40 1.9 21.4 1.0 OD1 A:ASP27 2.0 20.2 1.0 CD A:GLU40 2.6 20.2 1.0 OE1 A:GLU40 2.6 21.6 1.0 CG A:ASP27 3.0 21.2 1.0 O A:HOH221 3.3 33.8 1.0 OD2 A:ASP27 3.5 28.7 1.0 CD1 A:ILE30 3.6 24.2 1.0 O A:HOH205 3.7 22.0 1.0 O A:HOH223 3.9 31.0 1.0 CG A:GLU40 4.0 21.0 1.0 CB A:ASP27 4.3 17.9 1.0 CA A:ASP27 4.5 17.2 1.0 N A:ASP27 4.9 17.3 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Apaf-1 Card


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 the Apaf-1 Card within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:57.6 occ:0.50 NE2 A:HIS28 2.2 26.1 1.0 OD1 A:ASP32 2.4 34.1 1.0 O A:HOH299 2.8 43.9 1.0 OD2 A:ASP32 3.0 45.2 1.0 CG A:ASP32 3.0 33.1 1.0 CE1 A:HIS28 3.0 27.5 1.0 CD2 A:HIS28 3.2 25.1 1.0 O A:HOH283 3.8 35.1 0.6 O A:HOH236 3.9 36.4 1.0 ND1 A:HIS28 4.1 27.6 1.0 CB A:ASN73 4.1 18.1 1.0 CD2 A:HIS77 4.2 37.7 1.0 CG A:HIS28 4.3 22.8 1.0 O A:HOH246 4.3 38.8 1.0 CB A:ASP32 4.5 24.6 1.0 NE2 A:HIS77 4.7 39.8 1.0 ND2 A:ASN73 4.7 22.4 1.0 CG A:ASN73 4.9 17.8 1.0 O A:HIS28 5.0 18.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Apaf-1 Card


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 the Apaf-1 Card within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:28.7 occ:0.29 OE2 A:GLU41 1.6 38.5 1.0 CD A:GLU41 2.4 32.5 1.0 OE1 A:GLU41 2.6 33.2 1.0 CG A:GLU41 3.7 29.8 1.0 CB A:GLU41 4.9 23.6 1.0 OD1 A:ASN45 5.0 40.6 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Apaf-1 Card


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Apaf-1 Card within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn105 b:28.3 occ:0.50 ND1 A:HIS28 1.8 27.6 1.0 OE2 A:GLU78 1.9 43.0 1.0 O A:HOH305 2.6 55.2 1.0 CE1 A:HIS28 2.8 27.5 1.0 CG A:HIS28 2.8 22.8 1.0 O A:HOH306 2.9 52.8 1.0 CD A:GLU78 3.0 32.2 1.0 CB A:HIS28 3.3 20.0 1.0 CG A:GLU78 3.4 27.9 1.0 O A:HOH236 3.8 36.4 1.0 CB A:HIS77 3.9 21.4 1.0 NE2 A:HIS28 3.9 26.1 1.0 CD2 A:HIS28 3.9 25.1 1.0 OE1 A:GLU78 4.1 32.7 1.0 CA A:HIS28 4.2 17.3 1.0 O A:HOH230 4.2 30.4 1.0 O A:HOH283 4.6 35.1 0.6 CG A:HIS77 4.7 29.4 1.0 C A:HIS77 4.8 20.3 1.0 O A:HIS77 4.8 24.5 1.0 CB A:GLU78 4.9 26.1 1.0 CA A:HIS77 5.0 21.0 1.0 N A:HIS28 5.0 17.4 1.0

D.E.Vaughn, J.Rodriguez, Y.Lazebnik, L.Joshua-Tor. Crystal Structure of Apaf-1 Caspase Recruitment Domain: An Alpha-Helical Greek Key Fold For Apoptotic Signaling. J.Mol.Biol. V. 293 439 1999.
ISSN: ISSN 0022-2836
PubMed: 10543941
DOI: 10.1006/JMBI.1999.3177