Zinc in PDB 1ec5: Crystal Structure of Four-Helix Bundle Model

The structure of Crystal Structure of Four-Helix Bundle Model, PDB code: 1ec5 was solved by S.Geremia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	36.070, 89.160, 79.890, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 30.4

The binding sites of Zinc atom in the Crystal Structure of Four-Helix Bundle Model (pdb code 1ec5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Four-Helix Bundle Model, PDB code: 1ec5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Four-Helix Bundle Model


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 Four-Helix Bundle Model within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn50 b:29.6 occ:1.00 OE2 A:GLU10 1.9 34.7 1.0 OE1 A:GLU10 2.0 34.7 1.0 ND1 A:HIS39 2.0 32.4 1.0 OE1 A:GLU36 2.1 34.6 1.0 CD A:GLU10 2.3 35.4 1.0 CE1 A:HIS39 2.8 31.9 1.0 CG A:HIS39 3.2 32.3 1.0 CD A:GLU36 3.4 35.4 1.0 CB A:HIS39 3.6 32.8 1.0 CG A:GLU10 3.8 35.2 1.0 NE2 A:HIS39 4.0 32.7 1.0 CA A:GLU36 4.1 32.9 1.0 OE2 A:GLU36 4.1 36.0 1.0 CD2 A:HIS39 4.2 32.6 1.0 CG A:GLU36 4.5 34.3 1.0 CB A:GLU36 4.5 34.2 1.0 CB A:GLU10 4.7 37.0 1.0 O A:GLU36 4.7 30.4 1.0 N A:GLU36 4.8 33.4 1.0 O A:ASP35 4.8 32.9 1.0 C A:GLU36 4.9 32.3 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Four-Helix Bundle Model


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 Four-Helix Bundle Model within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn50 b:35.1 occ:1.00 OE1 B:GLU10 2.0 32.5 1.0 OE2 C:GLU36 2.1 34.1 1.0 ND1 B:HIS39 2.1 36.0 1.0 OE1 B:GLU36 2.1 40.3 1.0 OE2 B:GLU10 2.2 36.6 1.0 CD B:GLU10 2.5 34.7 1.0 CD C:GLU36 2.9 33.9 1.0 CE1 B:HIS39 3.0 37.5 1.0 CG B:HIS39 3.2 36.7 1.0 OE1 C:GLU36 3.3 34.2 1.0 CD B:GLU36 3.3 40.9 1.0 CB B:HIS39 3.7 37.5 1.0 ZN C:ZN50 3.9 34.8 1.0 OE2 B:GLU36 3.9 42.8 1.0 CD2 C:LEU13 4.0 40.7 1.0 CG B:GLU10 4.0 34.7 1.0 CG2 C:ILE32 4.1 38.2 1.0 NE2 B:HIS39 4.1 37.0 1.0 CG C:GLU36 4.2 34.0 1.0 CD2 B:HIS39 4.3 36.5 1.0 CA B:GLU36 4.3 37.3 1.0 CG B:GLU36 4.5 40.0 1.0 CB B:GLU10 4.6 35.7 1.0 OH C:TYR17 4.6 44.1 1.0 CE1 C:HIS39 4.7 33.1 1.0 OE1 C:GLU10 4.7 38.3 1.0 CB B:GLU36 4.7 38.8 1.0 O B:ASP35 4.8 36.8 1.0 CE1 C:TYR17 4.8 45.3 1.0 CG C:LEU13 4.8 40.5 1.0 N B:GLU36 4.9 36.2 1.0 O B:GLU36 5.0 36.1 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Four-Helix Bundle Model


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 Four-Helix Bundle Model within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn50 b:34.8 occ:1.00 OE1 C:GLU36 1.8 34.2 1.0 ND1 C:HIS39 1.9 32.7 1.0 OE2 C:GLU10 2.1 38.7 1.0 OE2 B:GLU36 2.1 42.8 1.0 OE1 C:GLU10 2.1 38.3 1.0 CD C:GLU10 2.4 39.9 1.0 CE1 C:HIS39 2.7 33.1 1.0 CD B:GLU36 2.9 40.9 1.0 CD C:GLU36 2.9 33.9 1.0 CG C:HIS39 3.1 33.0 1.0 OE1 B:GLU36 3.2 40.3 1.0 OE2 C:GLU36 3.7 34.1 1.0 CG C:GLU10 3.7 39.2 1.0 CB C:HIS39 3.7 32.8 1.0 CD2 B:LEU13 3.8 38.6 1.0 NE2 C:HIS39 3.9 31.8 1.0 ZN B:ZN50 3.9 35.1 1.0 CG C:GLU36 4.0 34.0 1.0 CD2 C:HIS39 4.1 33.0 1.0 CG2 B:ILE32 4.1 34.3 1.0 CA C:GLU36 4.2 34.1 1.0 CG B:GLU36 4.3 40.0 1.0 CB C:GLU36 4.7 35.2 1.0 O C:GLU36 4.7 33.1 1.0 OE1 B:GLU10 4.8 32.5 1.0 CG B:LEU13 4.8 37.3 1.0 CD2 C:LEU13 4.9 40.7 1.0 OH B:TYR17 4.9 29.7 1.0 CB C:GLU10 4.9 38.5 1.0 N C:GLU36 5.0 35.9 1.0

A.Lombardi, C.M.Summa, S.Geremia, L.Randaccio, V.Pavone, W.F.Degrado. Inaugural Article: Retrostructural Analysis of Metalloproteins: Application to the Design of A Minimal Model For Diiron Proteins. Proc.Natl.Acad.Sci.Usa V. 97 6298 2000.
ISSN: ISSN 0027-8424
PubMed: 10841536
DOI: 10.1073/PNAS.97.12.6298