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

Protein crystallography data

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

Zinc Binding Sites:

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 3oax

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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 3oax

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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 3oax

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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 3oax

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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 3oax

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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 3oax

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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 3oax

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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

Reference:

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
Page generated: Sat Sep 26 12:11:55 2020
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