Zinc in PDB 2hpy: Crystallographic Model of Lumirhodopsin

The structure of Crystallographic Model of Lumirhodopsin, PDB code: 2hpy 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 / 2.80
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	96.720, 96.720, 150.400, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 23.8

The structure of Crystallographic Model of Lumirhodopsin also contains other interesting chemical elements:

Mercury

(Hg)

6 atoms

The binding sites of Zinc atom in the Crystallographic Model of Lumirhodopsin (pdb code 2hpy). 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 Lumirhodopsin, PDB code: 2hpy:
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 Lumirhodopsin


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 Lumirhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn957 b:53.2 occ:0.66 NE2 A:GLN279 1.7 63.3 0.4 OE1 A:GLN279 2.2 64.0 0.4 CD A:GLN279 2.2 63.1 0.4 OE1 A:GLU201 2.2 61.0 0.4 CD A:GLU201 3.0 62.0 0.4 OE2 A:GLU201 3.0 61.9 0.4 CG A:GLN279 3.7 60.1 0.4 O A:PHE276 4.2 63.0 0.4 CE1 A:PHE276 4.2 55.1 0.4 CZ A:PHE276 4.3 52.4 0.4 CG A:PRO194 4.4 63.4 0.4 CG A:GLU201 4.4 62.5 0.4 CB A:GLN279 4.5 55.8 0.4 O A:HOH2057 4.6 65.3 1.0 CD1 A:PHE276 4.7 56.7 0.4 CE2 A:PHE276 4.8 53.4 0.4

Zinc binding site 2 out of 7 in the Crystallographic Model of Lumirhodopsin


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 Lumirhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn959 b:92.0 occ:0.85 NZ A:LYS311 2.0 79.0 0.4 CE1 B:HIS100 2.5 65.2 0.4 N A:ASP330 2.6 0.7 1.0 CG A:ASP330 2.8 0.4 1.0 OD2 A:ASP330 2.8 0.1 1.0 CB A:ASP330 3.0 0.0 1.0 C A:GLY329 3.3 0.4 1.0 CA A:ASP330 3.3 0.6 1.0 ND1 B:HIS100 3.3 64.4 0.4 CE A:LYS311 3.4 78.3 0.4 NE2 B:HIS100 3.4 65.5 0.4 OD1 A:ASP330 3.5 0.8 1.0 CA A:GLY329 3.5 0.7 1.0 C A:ASP330 4.1 0.7 1.0 O A:GLY329 4.2 0.6 1.0 N A:ASP331 4.3 0.3 1.0 CG B:HIS100 4.6 62.8 0.4 O A:ASP331 4.6 0.6 1.0 CD2 B:HIS100 4.6 63.0 0.4 CD A:LYS311 4.6 75.7 0.4 CG A:LYS311 4.9 71.2 0.4 N A:GLY329 5.0 0.3 1.0

Zinc binding site 3 out of 7 in the Crystallographic Model of Lumirhodopsin


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 Lumirhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn962 b:80.1 occ:0.62 OE1 A:GLU122 2.2 56.2 0.4 CD A:GLU122 2.6 56.7 0.4 CG A:GLU122 3.0 56.1 0.4 ND1 A:HIS211 3.1 68.0 0.4 NE1 A:TRP126 3.1 71.7 0.4 CG A:HIS211 3.1 66.4 0.4 SG A:CYS167 3.2 73.3 0.4 O A:MET163 3.4 67.9 0.4 CB A:HIS211 3.5 64.8 0.4 OE2 A:GLU122 3.5 57.6 0.4 CE1 A:HIS211 3.6 68.8 0.4 CB A:CYS167 3.6 66.1 0.4 CD2 A:HIS211 3.7 68.4 0.4 CA A:ALA164 3.8 66.5 0.4 CB A:GLU122 3.8 56.3 0.4 CD1 A:TRP126 3.9 71.5 0.4 NE2 A:HIS211 3.9 69.9 0.4 C A:MET163 4.0 67.5 0.4 N A:ALA164 4.1 67.1 0.4 CE2 A:TRP126 4.2 71.4 0.4 O A:ALA164 4.3 67.1 0.4 C A:ALA164 4.4 66.4 0.4 CA A:HIS211 4.5 65.0 0.4 CZ2 A:TRP126 4.6 71.8 0.4 CE A:MET207 4.8 69.9 0.4 CB A:ALA164 4.8 66.4 0.4 O A:HIS211 4.9 64.1 0.4 CA A:CYS167 5.0 65.0 0.4

Zinc binding site 4 out of 7 in the Crystallographic Model of Lumirhodopsin


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 Lumirhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2011 b:53.4 occ:0.68 NE2 A:HIS195 2.2 59.3 0.4 CE1 A:HIS195 3.1 60.4 0.4 CD2 A:HIS195 3.3 59.7 0.4 ND1 A:HIS195 4.2 60.5 0.4 CG A:HIS195 4.4 60.0 0.4 O A:PRO7 4.4 58.7 1.0 OE1 A:GLU197 4.4 89.8 0.4 O A:HOH2062 4.6 46.2 1.0 CB A:GLU197 4.9 74.3 0.4 NH1 A:ARG177 4.9 56.6 0.4

Zinc binding site 5 out of 7 in the Crystallographic Model of Lumirhodopsin


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 Lumirhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn956 b:60.2 occ:0.68 OE1 B:GLU197 2.3 91.3 0.4 NE2 B:HIS195 2.3 60.9 0.4 CD2 B:HIS195 3.2 62.2 0.4 CE1 B:HIS195 3.4 60.8 0.4 CD B:GLU197 3.5 89.2 0.4 O B:PRO7 3.9 64.7 1.0 OE2 B:GLU197 4.3 89.9 0.4 CG B:HIS195 4.4 62.2 0.4 ND1 B:HIS195 4.5 61.6 0.4 CB B:GLU197 4.5 75.3 0.4 CG B:GLU197 4.5 83.3 0.4 NH1 B:ARG177 4.5 52.9 0.4 C B:PRO7 4.9 61.3 1.0 CB B:PRO7 4.9 59.0 1.0 CA B:PRO7 5.0 60.0 1.0

Zinc binding site 6 out of 7 in the Crystallographic Model of Lumirhodopsin


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 Lumirhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn958 b:43.0 occ:0.51 NE2 B:GLN279 1.7 59.8 0.4 OE2 B:GLU201 2.6 62.1 0.4 CD B:GLN279 2.9 61.1 0.4 CD B:GLU201 3.2 62.1 0.4 OE1 B:GLU201 3.3 61.2 0.4 OE1 B:GLN279 3.3 62.2 0.4 CG B:GLN279 4.1 59.4 0.4 O B:PHE276 4.3 64.5 0.4 CZ B:PHE276 4.4 53.9 0.4 CE1 B:PHE276 4.4 56.5 0.4 CG B:GLU201 4.7 63.3 0.4 CE2 B:PHE276 4.7 54.7 0.4 CG B:PRO194 4.8 63.4 0.4 CD1 B:PHE276 4.9 56.8 0.4 CB B:GLN279 4.9 57.0 0.4 O B:HOH2069 5.0 62.0 1.0

Zinc binding site 7 out of 7 in the Crystallographic Model of Lumirhodopsin


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 Lumirhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn963 b:94.0 occ:0.68 CB B:CYS167 2.9 68.1 0.4 CA B:ALA164 3.0 67.5 0.4 CB B:GLU122 3.0 59.0 0.4 ND1 B:HIS211 3.0 70.4 0.4 O B:MET163 3.1 68.5 0.4 CE1 B:HIS211 3.1 70.8 0.4 CG B:GLU122 3.2 60.7 0.4 CD B:GLU122 3.3 62.5 0.4 NE1 B:TRP126 3.3 75.0 0.4 CG B:HIS211 3.4 69.3 0.4 SG B:CYS167 3.4 78.7 0.4 NE2 B:HIS211 3.4 69.5 0.4 N B:ALA164 3.6 68.3 0.4 C B:MET163 3.6 68.8 0.4 CD2 B:HIS211 3.6 70.0 0.4 OE2 B:GLU122 3.6 61.2 0.4 CD1 B:TRP126 3.7 74.7 0.4 C B:ALA164 3.7 67.1 0.4 OE1 B:GLU122 3.7 64.7 0.4 O B:ALA164 3.8 67.7 0.4 CB B:ALA164 3.9 67.3 0.4 CB B:HIS211 4.1 66.5 0.4 CA B:GLU122 4.2 59.3 0.4 CA B:CYS167 4.3 66.6 0.4 CE2 B:TRP126 4.5 74.5 0.4 C B:GLU122 4.6 60.5 0.4 N B:CYS167 4.7 66.3 0.4 N B:LEU165 4.8 65.9 0.4 O B:GLU122 4.9 62.6 0.4 CA B:MET163 4.9 69.1 0.4 CG B:TRP126 4.9 73.5 0.4

H.Nakamichi, T.Okada. Local Peptide Movement in the Photoreaction Intermediate of Rhodopsin Proc.Natl.Acad.Sci.Usa V. 103 12729 2006.
ISSN: ISSN 0027-8424
PubMed: 16908857
DOI: 10.1073/PNAS.0601765103