Zinc in PDB 1f88: Crystal Structure of Bovine Rhodopsin

The structure of Crystal Structure of Bovine Rhodopsin, PDB code: 1f88 was solved by T.Okada, K.Palczewski, R.E.Stenkamp, M.Miyano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	97.246, 97.246, 149.544, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.8

The structure of Crystal Structure of Bovine Rhodopsin also contains other interesting chemical elements:

Mercury

(Hg)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of Bovine Rhodopsin (pdb code 1f88). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Bovine Rhodopsin, PDB code: 1f88:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Bovine Rhodopsin


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 Bovine Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn907 b:0.8 occ:1.00 NE2 A:GLN279 2.2 54.0 1.0 OE1 A:GLU201 2.6 69.8 1.0 OE1 A:GLN279 2.9 53.6 1.0 CD A:GLN279 2.9 53.9 1.0 CD A:GLU201 3.6 70.2 1.0 CA A:PRO194 4.2 60.3 1.0 OE2 A:GLU201 4.3 68.5 1.0 CG A:PRO194 4.3 60.8 1.0 CB A:PRO194 4.3 59.9 1.0 CB A:GLU201 4.4 69.1 1.0 CG A:GLN279 4.4 51.5 1.0 CG A:GLU201 4.5 70.3 1.0 N A:PRO194 4.7 59.0 1.0 O A:PHE276 4.8 54.2 1.0 CE1 A:PHE276 5.0 50.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Bovine Rhodopsin


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 Bovine Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn910 b:64.4 occ:0.96 NZ A:LYS311 3.3 46.1 1.0 NH2 A:ARG314 3.5 38.4 1.0 NE2 B:HIS100 3.7 53.5 1.0 NE A:ARG314 3.8 37.7 1.0 ND2 A:ASN315 3.9 56.8 1.0 OD1 A:ASN315 3.9 56.0 1.0 CE1 B:TYR96 4.0 56.8 1.0 CE A:LYS311 4.1 47.1 1.0 CZ A:ARG314 4.1 37.8 1.0 CE1 B:HIS100 4.2 53.8 1.0 CG A:ASN315 4.3 54.5 1.0 CG A:LYS311 4.4 45.0 1.0 CD1 B:TYR96 4.6 54.5 1.0 CZ B:TYR96 4.8 56.8 1.0 CD2 B:HIS100 4.8 50.7 1.0 OH B:TYR96 4.9 56.7 1.0 CD A:LYS311 4.9 45.7 1.0 O A:HOH962 5.0 27.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Bovine Rhodopsin


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 Bovine Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn908 b:0.3 occ:0.89 O B:PHE276 3.5 48.4 1.0 NE2 B:GLN279 3.6 50.8 1.0 CD B:GLN279 3.7 49.9 1.0 CE1 B:PHE276 3.7 45.0 1.0 CG B:GLU201 3.7 68.9 1.0 OE1 B:GLN279 4.0 51.5 1.0 OE1 B:GLU201 4.0 70.5 1.0 O B:HOH961 4.0 32.0 1.0 CD B:GLU201 4.1 70.7 1.0 CZ B:PHE276 4.1 45.1 1.0 CG B:GLN279 4.2 49.8 1.0 CD1 B:PHE276 4.3 44.2 1.0 C B:PHE276 4.7 47.2 1.0 O B:THR277 4.8 53.5 1.0 OE2 B:GLU201 4.9 70.5 1.0 CB B:GLN279 4.9 51.7 1.0 CE2 B:PHE276 4.9 44.8 1.0 CB B:GLU201 5.0 68.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Bovine Rhodopsin


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 Bovine Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn909 b:77.2 occ:0.54 NE2 B:HIS195 2.5 58.4 1.0 O B:PRO7 3.0 46.0 1.0 CE1 B:HIS195 3.5 58.2 1.0 CD2 B:HIS195 3.5 59.8 1.0 OE2 B:GLU197 3.7 75.1 1.0 C B:PRO7 3.9 45.1 1.0 CA B:PRO7 4.0 44.9 1.0 NH1 B:ARG177 4.1 46.6 1.0 OE1 B:GLU197 4.2 75.9 1.0 CD B:GLU197 4.2 74.9 1.0 CB B:PRO7 4.3 45.1 1.0 ND1 B:HIS195 4.6 59.5 1.0 CG B:HIS195 4.6 60.1 1.0

K.Palczewski, T.Kumasaka, T.Hori, C.A.Behnke, H.Motoshima, B.A.Fox, I.Le Trong, D.C.Teller, T.Okada, R.E.Stenkamp, M.Yamamoto, M.Miyano. Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor. Science V. 289 739 2000.
ISSN: ISSN 0036-8075
PubMed: 10926528
DOI: 10.1126/SCIENCE.289.5480.739