Zinc in PDB 3oax: Crystal Structure of Bovine Rhodopsin with Beta-Ionone

The structure of Crystal Structure of Bovine Rhodopsin with Beta-Ionone, PDB code: 3oax was solved by C.L.Makino, C.K.Riley, J.Looney, R.K.Crouch, T.Okada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.60
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	96.990, 96.990, 149.800, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 26.2

The structure of Crystal Structure of Bovine Rhodopsin with Beta-Ionone also contains other interesting chemical elements:

Mercury

(Hg)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of Bovine Rhodopsin with Beta-Ionone (pdb code 3oax). 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 with Beta-Ionone, PDB code: 3oax:
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 with Beta-Ionone


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 with Beta-Ionone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn957 b:53.8 occ:0.69 NE2 A:GLN279 1.8 63.0 1.0 OE2 A:GLU201 2.1 58.4 1.0 OE1 A:GLU201 2.6 62.4 1.0 CD A:GLU201 2.7 61.0 1.0 CD A:GLN279 2.9 61.2 1.0 OE1 A:GLN279 3.6 62.1 1.0 CG A:GLN279 3.9 59.3 1.0 O A:PHE276 4.1 53.6 1.0 CG A:GLU201 4.2 61.5 1.0 CE1 A:PHE276 4.3 46.0 1.0 CZ A:PHE276 4.6 46.0 1.0 CD1 A:PHE276 4.7 48.2 1.0 CG A:PRO194 4.8 60.5 1.0 O A:HOH2057 4.9 50.5 0.9

Zinc binding site 2 out of 7 in the Crystal Structure of Bovine Rhodopsin with Beta-Ionone


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 with Beta-Ionone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn959 b:96.2 occ:0.86 NZ A:LYS311 1.9 72.0 1.0 OD1 A:ASP330 2.2 0.3 1.0 CE1 B:HIS100 2.4 62.0 1.0 CG A:ASP330 2.5 1.0 1.0 NE2 B:HIS100 2.8 60.9 1.0 CB A:ASP330 2.9 1.0 1.0 CE A:LYS311 3.3 73.0 1.0 OD2 A:ASP330 3.3 0.2 1.0 ND1 B:HIS100 3.6 60.2 1.0 OH B:TYR96 4.1 69.5 1.0 CD2 B:HIS100 4.2 59.5 1.0 CA A:ASP330 4.2 0.8 1.0 CE1 B:TYR96 4.3 66.7 1.0 CD A:LYS311 4.3 72.4 1.0 N A:ASP330 4.4 0.5 1.0 CZ B:TYR96 4.5 68.3 1.0 CG B:HIS100 4.5 58.6 1.0 OD1 A:ASN315 5.0 73.3 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of Bovine Rhodopsin with Beta-Ionone


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 with Beta-Ionone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn962 b:0.9 occ:0.60 ND1 A:HIS211 2.4 57.1 1.0 O A:MET163 2.7 61.8 1.0 CE1 A:HIS211 2.9 57.4 1.0 CB A:CYS167 3.0 57.2 1.0 NE1 A:TRP126 3.0 55.5 1.0 OE1 A:GLU122 3.0 48.9 1.0 CG A:HIS211 3.1 56.8 1.0 C A:MET163 3.3 60.7 1.0 CA A:ALA164 3.5 59.3 1.0 CD1 A:TRP126 3.5 55.2 1.0 CD A:GLU122 3.5 50.8 1.0 CG A:GLU122 3.6 48.4 1.0 N A:ALA164 3.7 60.5 1.0 NE2 A:HIS211 3.7 58.5 1.0 CB A:GLU122 3.7 48.6 1.0 CB A:HIS211 3.8 56.9 1.0 CD2 A:HIS211 3.9 57.4 1.0 O A:ALA164 4.0 60.4 1.0 SG A:CYS167 4.0 61.0 1.0 C A:ALA164 4.1 58.8 1.0 N A:CYS167 4.2 57.4 1.0 CA A:CYS167 4.2 57.2 1.0 CE2 A:TRP126 4.2 56.5 1.0 CA A:MET163 4.4 60.4 1.0 CB A:MET163 4.4 59.9 1.0 OE2 A:GLU122 4.5 53.1 1.0 CB A:ALA164 4.6 59.0 1.0 CA A:HIS211 4.8 57.1 1.0 CG A:TRP126 4.8 55.1 1.0 CZ2 A:TRP126 4.9 57.1 1.0 CA A:GLU122 4.9 48.7 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of Bovine Rhodopsin with Beta-Ionone


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 with Beta-Ionone within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2011 b:59.9 occ:0.71 NE2 A:HIS195 2.2 54.2 1.0 OE1 A:GLU197 2.8 92.1 1.0 CD2 A:HIS195 3.1 53.7 1.0 CE1 A:HIS195 3.2 53.5 1.0 CD A:GLU197 3.3 88.6 1.0 OE2 A:GLU197 3.3 90.9 1.0 O A:PRO7 4.2 53.2 1.0 CG A:HIS195 4.3 54.7 1.0 ND1 A:HIS195 4.3 55.4 1.0 CG A:GLU197 4.5 81.4 1.0 CB A:GLU197 4.5 72.1 1.0 NH1 A:ARG177 4.6 49.0 1.0 O A:HOH2062 4.8 58.1 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of Bovine Rhodopsin with Beta-Ionone


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 with Beta-Ionone within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn956 b:70.8 occ:0.73 NE2 B:HIS195 2.2 56.4 1.0 OE1 B:GLU197 2.9 85.0 1.0 CD2 B:HIS195 3.1 57.2 1.0 CE1 B:HIS195 3.2 56.9 1.0 CD B:GLU197 3.3 82.3 1.0 OE2 B:GLU197 3.3 82.6 1.0 O B:PRO7 4.2 60.4 1.0 ND1 B:HIS195 4.3 57.5 1.0 CG B:HIS195 4.3 56.9 1.0 NH1 B:ARG177 4.5 48.1 1.0 CG B:GLU197 4.5 77.7 1.0 CB B:GLU197 4.6 70.6 1.0 O B:HOH2103 4.8 70.0 1.0 CB B:PRO7 4.9 59.7 1.0 CA B:PRO7 5.0 59.1 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of Bovine Rhodopsin with Beta-Ionone


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 with Beta-Ionone within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn958 b:42.0 occ:0.55 OE2 B:GLU201 2.3 64.4 1.0 OE1 B:GLU201 2.5 65.8 1.0 NE2 B:GLN279 2.6 52.5 1.0 CD B:GLU201 2.7 65.4 1.0 OE1 B:GLN279 2.9 53.3 1.0 CD B:GLN279 2.9 51.7 1.0 O B:PHE276 4.0 61.6 1.0 CG B:GLU201 4.2 66.2 1.0 CG B:GLN279 4.2 51.1 1.0 CE1 B:PHE276 4.4 49.9 1.0 CZ B:PHE276 4.7 48.8 1.0 CG B:PRO194 4.8 60.9 1.0 CD1 B:PHE276 4.8 50.6 1.0 CB B:GLN279 4.9 49.5 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of Bovine Rhodopsin with Beta-Ionone


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 with Beta-Ionone within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn963 b:0.8 occ:0.64 ND1 B:HIS211 2.4 66.1 1.0 O B:MET163 2.6 67.5 1.0 NE1 B:TRP126 2.8 76.0 1.0 CE1 B:HIS211 2.9 65.7 1.0 OE1 B:GLU122 3.0 65.8 1.0 C B:MET163 3.0 67.8 1.0 CG B:HIS211 3.2 65.3 1.0 CB B:CYS167 3.3 66.9 1.0 CD1 B:TRP126 3.3 75.4 1.0 N B:ALA164 3.3 66.6 1.0 CA B:ALA164 3.4 65.5 1.0 NE2 B:HIS211 3.7 65.2 1.0 CD B:GLU122 3.7 63.6 1.0 CB B:HIS211 3.9 63.9 1.0 CG B:GLU122 3.9 61.2 1.0 CD2 B:HIS211 3.9 65.7 1.0 CB B:GLU122 3.9 58.9 1.0 CB B:MET163 3.9 68.2 1.0 CE2 B:TRP126 4.0 75.4 1.0 CA B:MET163 4.0 68.3 1.0 C B:ALA164 4.0 65.8 1.0 O B:ALA164 4.1 65.7 1.0 N B:CYS167 4.3 68.3 1.0 SG B:CYS167 4.3 69.7 1.0 CA B:CYS167 4.4 66.6 1.0 CB B:ALA164 4.6 64.8 1.0 CZ2 B:TRP126 4.6 76.9 1.0 CG B:TRP126 4.6 74.3 1.0 CA B:HIS211 4.7 63.1 1.0 OE2 B:GLU122 4.8 64.2 1.0 CD2 B:TRP126 4.9 75.3 1.0

C.L.Makino, C.K.Riley, J.Looney, R.K.Crouch, T.Okada. Binding of More Than One Retinoid to Visual Opsins Biophys.J. V. 99 2366 2010.
ISSN: ISSN 0006-3495
PubMed: 20923672
DOI: 10.1016/J.BPJ.2010.08.003