Atomistry » Zinc » PDB 3o57-3oj7 » 3oax
Atomistry »
  Zinc »
    PDB 3o57-3oj7 »
      3oax »

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

Other elements in 3oax:

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

Mercury (Hg) 6 atoms

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

Go back to Zinc Binding Sites List in 3oax
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

Go back to Zinc Binding Sites List in 3oax
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

Go back to Zinc Binding Sites List in 3oax
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

Go back to Zinc Binding Sites List in 3oax
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

Go back to Zinc Binding Sites List in 3oax
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

Go back to Zinc Binding Sites List in 3oax
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

Go back to Zinc Binding Sites List in 3oax
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: Wed Dec 16 04:40:11 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy