Zinc in PDB 1l9h: Crystal Structure of Bovine Rhodopsin at 2.6 Angstroms Resolution

The structure of Crystal Structure of Bovine Rhodopsin at 2.6 Angstroms Resolution, PDB code: 1l9h was solved by T.Okada, Y.Fujiyoshi, M.Silow, J.Navarro, E.M.Landau, Y.Shichida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.60
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	96.745, 96.745, 149.300, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.5

The structure of Crystal Structure of Bovine Rhodopsin at 2.6 Angstroms Resolution also contains other interesting chemical elements:

Mercury

(Hg)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of Bovine Rhodopsin at 2.6 Angstroms Resolution (pdb code 1l9h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Bovine Rhodopsin at 2.6 Angstroms Resolution, PDB code: 1l9h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of Bovine Rhodopsin at 2.6 Angstroms Resolution


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 at 2.6 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn957 b:36.6 occ:0.50 NE2 A:GLN279 1.9 56.1 1.0 OE2 A:GLU201 1.9 61.9 1.0 OE1 A:GLN279 2.2 56.9 1.0 CD A:GLN279 2.3 57.0 1.0 CD A:GLU201 2.7 62.2 1.0 OE1 A:GLU201 2.8 60.6 1.0 CG A:GLN279 3.8 57.1 1.0 O A:PHE276 3.9 62.7 1.0 CG A:GLU201 4.1 62.6 1.0 CE1 A:PHE276 4.2 57.5 1.0 CZ A:PHE276 4.5 56.2 1.0 CD1 A:PHE276 4.6 57.5 1.0 CG A:PRO194 4.6 60.3 1.0 CB A:GLN279 4.7 57.2 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of Bovine Rhodopsin at 2.6 Angstroms Resolution


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 at 2.6 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn959 b:72.0 occ:0.70 NZ A:LYS311 2.5 64.9 1.0 CA A:GLY329 2.8 0.3 1.0 CE1 B:HIS100 3.1 67.0 1.0 CE A:LYS311 3.2 65.8 1.0 NH2 A:ARG314 3.5 54.0 1.0 N A:ASP330 3.6 0.7 1.0 CE2 B:TYR96 3.7 87.0 1.0 C A:GLY329 3.7 0.8 1.0 ND2 A:ASN315 3.7 63.5 1.0 N A:GLY329 3.8 0.9 1.0 NE2 B:HIS100 3.8 68.9 1.0 OH B:TYR96 3.8 89.0 1.0 NE A:ARG314 3.9 52.4 1.0 O A:PRO327 4.0 0.9 1.0 CZ B:TYR96 4.2 87.9 1.0 CZ A:ARG314 4.2 52.4 1.0 ND1 B:HIS100 4.2 65.8 1.0 CG A:LYS311 4.3 64.5 1.0 CD A:LYS311 4.4 65.4 1.0 O A:LEU328 4.4 0.7 1.0 C A:LEU328 4.4 0.1 1.0 OD1 A:ASN315 4.4 61.8 1.0 CG A:ASN315 4.5 61.9 1.0 CD2 B:TYR96 4.7 84.2 1.0 O A:GLY329 4.8 0.3 1.0 CA A:ASP330 4.9 1.0 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of Bovine Rhodopsin at 2.6 Angstroms Resolution


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 at 2.6 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn962 b:64.8 occ:0.50 ND1 A:HIS211 2.5 46.0 1.0 NE1 A:TRP126 2.6 54.8 1.0 O A:MET163 2.7 62.4 1.0 CB A:CYS167 2.8 54.1 1.0 OE1 A:GLU122 2.9 46.7 1.0 CG A:HIS211 3.0 45.0 1.0 CE1 A:HIS211 3.1 46.2 1.0 C A:MET163 3.3 62.3 1.0 CD A:GLU122 3.3 46.7 1.0 CG A:GLU122 3.4 46.8 1.0 CD1 A:TRP126 3.4 55.1 1.0 CB A:HIS211 3.5 46.5 1.0 CA A:ALA164 3.6 60.4 1.0 CB A:GLU122 3.6 47.1 1.0 N A:ALA164 3.7 61.9 1.0 CE2 A:TRP126 3.8 54.7 1.0 CD2 A:HIS211 3.8 46.8 1.0 SG A:CYS167 3.8 64.4 1.0 NE2 A:HIS211 3.9 48.2 1.0 O A:ALA164 4.1 58.7 1.0 CA A:CYS167 4.1 52.9 1.0 N A:CYS167 4.1 54.7 1.0 C A:ALA164 4.1 59.1 1.0 CZ2 A:TRP126 4.3 53.8 1.0 OE2 A:GLU122 4.3 45.0 1.0 CA A:MET163 4.4 61.9 1.0 CB A:MET163 4.5 61.5 1.0 CA A:HIS211 4.6 47.4 1.0 CG A:TRP126 4.7 54.0 1.0 CA A:GLU122 4.8 47.0 1.0 CB A:ALA164 4.8 60.1 1.0 CD2 A:TRP126 4.9 54.0 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of Bovine Rhodopsin at 2.6 Angstroms Resolution


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 at 2.6 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2011 b:43.7 occ:0.70 NE2 A:HIS195 2.3 63.7 1.0 OE1 A:GLU197 2.4 78.5 1.0 CD A:GLU197 3.0 78.1 1.0 OE2 A:GLU197 3.0 77.8 1.0 CE1 A:HIS195 3.1 62.3 1.0 CD2 A:HIS195 3.3 64.6 1.0 O A:PRO7 3.7 51.8 1.0 ND1 A:HIS195 4.3 62.0 1.0 CB A:PRO7 4.3 51.7 1.0 CG A:GLU197 4.4 75.1 1.0 CA A:PRO7 4.4 51.7 1.0 CG A:HIS195 4.4 63.4 1.0 C A:PRO7 4.5 52.0 1.0 CB A:GLU197 4.7 71.0 1.0 NH1 A:ARG177 4.8 49.8 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of Bovine Rhodopsin at 2.6 Angstroms Resolution


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 Bovine Rhodopsin at 2.6 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn956 b:40.9 occ:0.50 OE1 B:GLU197 1.9 83.3 1.0 NE2 B:HIS195 2.1 62.7 1.0 CD B:GLU197 2.5 84.6 1.0 OE2 B:GLU197 2.5 83.7 1.0 CE1 B:HIS195 2.7 61.6 1.0 CD2 B:HIS195 3.4 65.2 1.0 O B:PRO7 3.5 57.2 1.0 CB B:PRO7 3.9 55.4 1.0 CG B:GLU197 3.9 84.0 1.0 ND1 B:HIS195 4.0 62.7 1.0 CA B:PRO7 4.1 55.5 1.0 C B:PRO7 4.2 56.6 1.0 CG B:HIS195 4.3 65.2 1.0 CB B:GLU197 4.4 82.7 1.0 NH1 B:ARG177 4.4 52.7 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of Bovine Rhodopsin at 2.6 Angstroms Resolution


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 Bovine Rhodopsin at 2.6 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn958 b:27.0 occ:0.40 OE2 B:GLU201 2.2 76.7 1.0 NE2 B:GLN279 2.2 63.0 1.0 OE1 B:GLU201 2.4 77.6 1.0 CD B:GLU201 2.6 77.1 1.0 OE1 B:GLN279 2.7 60.6 1.0 CD B:GLN279 2.8 61.5 1.0 O B:PHE276 3.9 57.0 1.0 CG B:GLU201 4.1 77.0 1.0 CE1 B:PHE276 4.1 54.8 1.0 CG B:GLN279 4.3 60.5 1.0 CD1 B:PHE276 4.5 55.0 1.0 CZ B:PHE276 4.6 54.2 1.0 CG B:PRO194 4.9 65.8 1.0 CB B:PRO194 5.0 65.6 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of Bovine Rhodopsin at 2.6 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Bovine Rhodopsin at 2.6 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn963 b:85.0 occ:0.50 ND1 B:HIS211 2.3 60.4 1.0 O B:MET163 2.4 69.7 1.0 CE1 B:HIS211 2.6 60.6 1.0 CB B:CYS167 2.8 62.1 1.0 CG B:HIS211 2.9 60.0 1.0 NE1 B:TRP126 2.9 71.5 1.0 C B:MET163 3.2 69.0 1.0 NE2 B:HIS211 3.2 61.6 1.0 CD2 B:HIS211 3.4 60.9 1.0 N B:CYS167 3.6 64.2 1.0 CG B:GLU122 3.6 61.3 1.0 CB B:HIS211 3.7 59.4 1.0 CA B:ALA164 3.7 66.3 1.0 OE1 B:GLU122 3.7 61.6 1.0 CD1 B:TRP126 3.7 71.6 1.0 CD B:GLU122 3.7 62.3 1.0 N B:ALA164 3.7 68.0 1.0 CA B:CYS167 3.8 61.9 1.0 CB B:GLU122 3.8 60.2 1.0 CE2 B:TRP126 4.0 72.3 1.0 SG B:CYS167 4.0 66.5 1.0 C B:ALA164 4.1 65.3 1.0 O B:ALA164 4.1 65.9 1.0 CA B:MET163 4.2 69.0 1.0 CB B:MET163 4.4 70.1 1.0 CZ2 B:TRP126 4.4 73.2 1.0 C B:ALA166 4.4 65.5 1.0 OE2 B:GLU122 4.4 62.0 1.0 CA B:HIS211 4.7 60.1 1.0 N B:ALA166 4.8 64.9 1.0 CB B:ALA166 4.8 64.0 1.0 N B:LEU165 4.9 64.2 1.0 CA B:ALA166 4.9 65.1 1.0 C B:CYS167 4.9 59.6 1.0 CG B:TRP126 5.0 71.1 1.0

T.Okada, Y.Fujiyoshi, M.Silow, J.Navarro, E.M.Landau, Y.Shichida. Functional Role of Internal Water Molecules in Rhodopsin Revealed By X-Ray Crystallography. Proc.Natl.Acad.Sci.Usa V. 99 5982 2002.
ISSN: ISSN 0027-8424
PubMed: 11972040
DOI: 10.1073/PNAS.082666399