Zinc in PDB 2ped: Crystallographic Model of 9-Cis-Rhodopsin

The structure of Crystallographic Model of 9-Cis-Rhodopsin, PDB code: 2ped was solved by H.Nakamichi, T.Okada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.95
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	95.960, 95.960, 150.840, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 28.9

The structure of Crystallographic Model of 9-Cis-Rhodopsin also contains other interesting chemical elements:

Mercury

(Hg)

6 atoms

The binding sites of Zinc atom in the Crystallographic Model of 9-Cis-Rhodopsin (pdb code 2ped). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystallographic Model of 9-Cis-Rhodopsin, PDB code: 2ped:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystallographic Model of 9-Cis-Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystallographic Model of 9-Cis-Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn956 b:68.2 occ:0.73 NE2 B:HIS195 2.3 65.8 1.0 OE1 B:GLU197 2.7 79.2 1.0 CD2 B:HIS195 3.0 66.2 1.0 CD B:GLU197 3.3 76.8 1.0 OE2 B:GLU197 3.3 75.3 1.0 CE1 B:HIS195 3.4 66.0 1.0 O B:PRO7 3.8 56.8 1.0 CG B:HIS195 4.3 65.5 1.0 ND1 B:HIS195 4.4 66.4 1.0 NH1 B:ARG177 4.6 49.6 1.0 CG B:GLU197 4.6 73.4 1.0 O B:HOH2103 4.7 45.9 1.0 C B:PRO7 4.8 56.2 1.0 CB B:GLU197 4.8 69.6 1.0 CB B:PRO7 4.9 55.1 1.0 CA B:PRO7 4.9 55.5 1.0

Zinc binding site 2 out of 7 in the Crystallographic Model of 9-Cis-Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystallographic Model of 9-Cis-Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn957 b:53.2 occ:0.69 NE2 A:GLN279 1.9 61.0 1.0 OE2 A:GLU201 2.0 58.3 1.0 OE1 A:GLU201 2.4 60.4 1.0 CD A:GLU201 2.5 59.4 1.0 CD A:GLN279 2.8 60.7 1.0 OE1 A:GLN279 3.2 62.0 1.0 CG A:GLU201 4.0 59.6 1.0 O A:PHE276 4.0 54.8 1.0 CG A:GLN279 4.1 58.2 1.0 CE1 A:PHE276 4.4 51.2 1.0 CZ A:PHE276 4.6 50.4 1.0 CG A:PRO194 4.8 61.5 1.0 CD1 A:PHE276 4.9 50.3 1.0 CB A:GLU201 5.0 58.5 1.0 CB A:GLN279 5.0 54.2 1.0

Zinc binding site 3 out of 7 in the Crystallographic Model of 9-Cis-Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystallographic Model of 9-Cis-Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn958 b:41.7 occ:0.55 OE2 B:GLU201 2.0 64.0 1.0 NE2 B:GLN279 2.4 51.9 1.0 OE1 B:GLU201 2.5 65.0 1.0 CD B:GLU201 2.6 65.9 1.0 CD B:GLN279 2.9 53.4 1.0 OE1 B:GLN279 3.0 53.8 1.0 O B:PHE276 3.8 59.2 1.0 CG B:GLN279 4.1 53.1 1.0 CG B:GLU201 4.1 66.1 1.0 CE1 B:PHE276 4.3 57.7 1.0 CZ B:PHE276 4.5 56.9 1.0 CD1 B:PHE276 4.7 57.9 1.0 CB B:GLN279 4.9 53.5 1.0 C B:PHE276 5.0 58.3 1.0

Zinc binding site 4 out of 7 in the Crystallographic Model of 9-Cis-Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystallographic Model of 9-Cis-Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn959 b:85.3 occ:0.86 NZ A:LYS311 2.1 71.5 1.0 N A:ASP330 2.2 0.4 1.0 CE1 B:HIS100 2.3 57.5 1.0 C A:GLY329 2.6 1.0 1.0 CB A:ASP330 2.6 0.3 1.0 CA A:ASP330 2.9 0.9 1.0 CA A:GLY329 3.0 0.9 1.0 NE2 B:HIS100 3.0 58.8 1.0 CG A:ASP330 3.1 0.9 1.0 CE A:LYS311 3.3 71.6 1.0 OD2 A:ASP330 3.3 0.5 1.0 O A:GLY329 3.4 0.5 1.0 ND1 B:HIS100 3.5 56.1 1.0 C A:ASP330 3.8 0.9 1.0 OD1 A:ASP330 3.9 0.7 1.0 N A:ASP331 4.2 0.6 1.0 CD2 B:HIS100 4.3 56.9 1.0 N A:GLY329 4.5 0.8 1.0 CG B:HIS100 4.5 55.3 1.0 O A:ASP330 4.6 0.5 1.0 CD A:LYS311 4.6 70.0 1.0 O A:ASP331 4.7 0.2 1.0 NH2 A:ARG314 4.8 52.4 1.0 OH B:TYR96 4.9 62.7 1.0 CE1 B:TYR96 4.9 61.3 1.0 O A:LEU328 4.9 0.2 1.0

Zinc binding site 5 out of 7 in the Crystallographic Model of 9-Cis-Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystallographic Model of 9-Cis-Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn962 b:0.7 occ:0.60 ND1 A:HIS211 2.5 62.0 1.0 NE1 A:TRP126 2.7 64.1 1.0 OE1 A:GLU122 2.7 52.6 1.0 O A:MET163 2.8 60.5 1.0 CE1 A:HIS211 2.8 62.6 1.0 CG A:HIS211 3.0 60.5 1.0 C A:MET163 3.3 60.1 1.0 CD A:GLU122 3.4 52.5 1.0 CD1 A:TRP126 3.4 63.6 1.0 NE2 A:HIS211 3.5 63.1 1.0 CG A:GLU122 3.5 52.0 1.0 CD2 A:HIS211 3.6 62.4 1.0 CB A:HIS211 3.7 58.1 1.0 CA A:ALA164 3.7 59.1 1.0 N A:ALA164 3.7 59.8 1.0 CB A:GLU122 3.8 52.3 1.0 CE2 A:TRP126 3.9 62.5 1.0 CB A:CYS167 4.0 59.3 1.0 CB A:MET163 4.2 60.5 1.0 CA A:MET163 4.3 60.3 1.0 N A:CYS167 4.3 59.9 1.0 CZ2 A:TRP126 4.4 61.8 1.0 OE2 A:GLU122 4.5 53.3 1.0 C A:ALA164 4.5 58.4 1.0 O A:ALA164 4.5 59.2 1.0 CG A:TRP126 4.7 62.0 1.0 CA A:HIS211 4.7 57.6 1.0 CA A:CYS167 4.7 60.2 1.0 CB A:ALA164 4.9 60.4 1.0 CA A:GLU122 4.9 52.6 1.0 CD2 A:TRP126 4.9 62.1 1.0

Zinc binding site 6 out of 7 in the Crystallographic Model of 9-Cis-Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystallographic Model of 9-Cis-Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn963 b:0.2 occ:0.64 ND1 B:HIS211 2.5 75.2 1.0 O B:MET163 2.8 69.6 1.0 CE1 B:HIS211 2.8 75.7 1.0 CG B:HIS211 2.8 73.3 1.0 NE1 B:TRP126 3.3 76.8 1.0 OE1 B:GLU122 3.3 63.1 1.0 NE2 B:HIS211 3.3 75.1 1.0 CD2 B:HIS211 3.3 74.8 1.0 C B:MET163 3.4 69.5 1.0 CB B:HIS211 3.5 70.7 1.0 CB B:CYS167 3.5 59.0 1.0 CD B:GLU122 3.7 61.7 1.0 N B:CYS167 3.7 61.1 1.0 CG B:GLU122 3.7 60.6 1.0 CA B:ALA164 3.9 65.6 1.0 N B:ALA164 3.9 67.8 1.0 O B:ALA164 4.0 64.9 1.0 CB B:GLU122 4.1 59.9 1.0 CD1 B:TRP126 4.1 76.8 1.0 CA B:CYS167 4.2 60.0 1.0 CE2 B:TRP126 4.3 77.3 1.0 C B:ALA164 4.3 64.4 1.0 CA B:MET163 4.4 70.4 1.0 CB B:MET163 4.4 71.8 1.0 CB B:ALA166 4.6 62.0 1.0 OE2 B:GLU122 4.6 62.0 1.0 CZ2 B:TRP126 4.6 77.9 1.0 CA B:HIS211 4.6 68.9 1.0 C B:ALA166 4.7 62.0 1.0 SG B:CYS167 4.9 55.2 1.0

Zinc binding site 7 out of 7 in the Crystallographic Model of 9-Cis-Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystallographic Model of 9-Cis-Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2011 b:53.0 occ:0.71 NE2 A:HIS195 2.3 60.9 1.0 OE1 A:GLU197 2.6 79.6 1.0 OE2 A:GLU197 3.0 77.7 1.0 CD A:GLU197 3.0 78.1 1.0 CD2 A:HIS195 3.2 60.7 1.0 CE1 A:HIS195 3.3 60.9 1.0 O A:PRO7 4.1 48.5 1.0 O A:HOH2062 4.3 55.0 1.0 ND1 A:HIS195 4.4 60.7 1.0 CG A:GLU197 4.4 74.3 1.0 CG A:HIS195 4.4 61.3 1.0 NH1 A:ARG177 4.5 51.2 1.0 CB A:GLU197 4.6 68.9 1.0 C A:PRO7 5.0 48.8 1.0

H.Nakamichi, V.Buss, T.Okada. Photoisomerization Mechanism of Rhodopsin and 9-Cis-Rhodopsin Revealed By X-Ray Crystallography Biophys.J. V. 92 L106 2007.
ISSN: ISSN 0006-3495
PubMed: 17449675
DOI: 10.1529/BIOPHYSJ.107.108225