Zinc in PDB 1u19: Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution
Protein crystallography data
The structure of Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution, PDB code: 1u19
was solved by
T.Okada,
M.Sugihara,
A.N.Bondar,
M.Elstner,
P.Entel,
V.Buss,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.20
|
Space group
|
P 41
|
Cell size a, b, c (Å), α, β, γ (°)
|
96.680,
96.680,
150.200,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20 /
22.2
|
Other elements in 1u19:
The structure of Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution
(pdb code 1u19). 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 2.2 Angstroms Resolution, PDB code: 1u19:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
Zinc binding site 1 out
of 7 in 1u19
Go back to
Zinc Binding Sites List in 1u19
Zinc binding site 1 out
of 7 in the Crystal Structure of Bovine Rhodopsin at 2.2 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 2.2 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn957
b:35.1
occ:0.66
|
NE2
|
A:GLN279
|
1.7
|
46.5
|
1.0
|
OE2
|
A:GLU201
|
2.0
|
46.0
|
1.0
|
OE1
|
A:GLU201
|
2.3
|
46.1
|
1.0
|
CD
|
A:GLU201
|
2.4
|
45.6
|
1.0
|
CD
|
A:GLN279
|
2.6
|
47.5
|
1.0
|
OE1
|
A:GLN279
|
3.0
|
49.1
|
1.0
|
CG
|
A:GLU201
|
4.0
|
45.7
|
1.0
|
CG
|
A:GLN279
|
4.0
|
46.4
|
1.0
|
O
|
A:PHE276
|
4.1
|
42.7
|
1.0
|
CE1
|
A:PHE276
|
4.3
|
36.4
|
1.0
|
CG
|
A:PRO194
|
4.5
|
50.9
|
1.0
|
CZ
|
A:PHE276
|
4.6
|
34.9
|
1.0
|
O
|
A:HOH2057
|
4.7
|
71.5
|
1.0
|
CD1
|
A:PHE276
|
4.7
|
38.0
|
1.0
|
CB
|
A:PRO194
|
4.9
|
50.5
|
1.0
|
CB
|
A:GLU201
|
4.9
|
46.3
|
1.0
|
CB
|
A:GLN279
|
4.9
|
44.9
|
1.0
|
|
Zinc binding site 2 out
of 7 in 1u19
Go back to
Zinc Binding Sites List in 1u19
Zinc binding site 2 out
of 7 in the Crystal Structure of Bovine Rhodopsin at 2.2 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 2.2 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn959
b:66.8
occ:0.85
|
NZ
|
A:LYS311
|
1.8
|
59.0
|
1.0
|
CE1
|
B:HIS100
|
2.4
|
50.9
|
1.0
|
N
|
A:ASP330
|
2.4
|
0.2
|
1.0
|
NE2
|
B:HIS100
|
3.0
|
51.2
|
1.0
|
CB
|
A:ASP330
|
3.0
|
0.7
|
1.0
|
C
|
A:GLY329
|
3.1
|
0.1
|
1.0
|
CG
|
A:ASP330
|
3.2
|
0.1
|
1.0
|
OD2
|
A:ASP330
|
3.2
|
0.1
|
1.0
|
CE
|
A:LYS311
|
3.2
|
59.3
|
1.0
|
CA
|
A:ASP330
|
3.2
|
0.5
|
1.0
|
CA
|
A:GLY329
|
3.3
|
0.6
|
1.0
|
ND1
|
B:HIS100
|
3.5
|
50.1
|
1.0
|
OD1
|
A:ASP330
|
3.9
|
0.1
|
1.0
|
C
|
A:ASP330
|
4.0
|
0.4
|
1.0
|
N
|
A:ASP331
|
4.1
|
0.9
|
1.0
|
O
|
A:GLY329
|
4.2
|
0.4
|
1.0
|
CD
|
A:LYS311
|
4.3
|
58.8
|
1.0
|
CD2
|
B:HIS100
|
4.3
|
49.7
|
1.0
|
O
|
A:ASP331
|
4.4
|
0.3
|
1.0
|
CG
|
B:HIS100
|
4.6
|
48.8
|
1.0
|
CE1
|
B:TYR96
|
4.6
|
53.7
|
1.0
|
OH
|
B:TYR96
|
4.6
|
55.2
|
1.0
|
NH2
|
A:ARG314
|
4.7
|
44.7
|
1.0
|
CG
|
A:LYS311
|
4.8
|
56.5
|
1.0
|
N
|
A:GLY329
|
4.8
|
0.3
|
1.0
|
ND2
|
A:ASN315
|
4.8
|
55.1
|
1.0
|
CZ
|
B:TYR96
|
4.9
|
54.7
|
1.0
|
O
|
A:ASP330
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 3 out
of 7 in 1u19
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Zinc Binding Sites List in 1u19
Zinc binding site 3 out
of 7 in the Crystal Structure of Bovine Rhodopsin at 2.2 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 2.2 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn962
b:56.7
occ:0.62
|
ND1
|
A:HIS211
|
2.4
|
48.3
|
1.0
|
OE1
|
A:GLU122
|
2.6
|
45.1
|
1.0
|
NE1
|
A:TRP126
|
2.7
|
48.8
|
1.0
|
O
|
A:MET163
|
2.7
|
51.3
|
1.0
|
CE1
|
A:HIS211
|
3.0
|
49.3
|
1.0
|
CG
|
A:HIS211
|
3.1
|
47.8
|
1.0
|
CB
|
A:CYS167
|
3.1
|
50.4
|
1.0
|
CD
|
A:GLU122
|
3.3
|
44.5
|
1.0
|
C
|
A:MET163
|
3.3
|
50.7
|
1.0
|
CD1
|
A:TRP126
|
3.4
|
48.6
|
1.0
|
CG
|
A:GLU122
|
3.6
|
43.3
|
1.0
|
CA
|
A:ALA164
|
3.6
|
49.7
|
1.0
|
CB
|
A:HIS211
|
3.6
|
47.4
|
1.0
|
N
|
A:ALA164
|
3.7
|
50.1
|
1.0
|
CB
|
A:GLU122
|
3.8
|
42.4
|
1.0
|
CE2
|
A:TRP126
|
3.8
|
48.9
|
1.0
|
NE2
|
A:HIS211
|
3.8
|
49.6
|
1.0
|
CD2
|
A:HIS211
|
3.9
|
48.8
|
1.0
|
SG
|
A:CYS167
|
4.1
|
57.5
|
1.0
|
O
|
A:ALA164
|
4.2
|
49.8
|
1.0
|
C
|
A:ALA164
|
4.2
|
49.7
|
1.0
|
OE2
|
A:GLU122
|
4.3
|
44.1
|
1.0
|
N
|
A:CYS167
|
4.3
|
48.6
|
1.0
|
CZ2
|
A:TRP126
|
4.4
|
49.0
|
1.0
|
CA
|
A:CYS167
|
4.4
|
48.7
|
1.0
|
CA
|
A:MET163
|
4.4
|
50.7
|
1.0
|
CB
|
A:MET163
|
4.4
|
51.1
|
1.0
|
CA
|
A:HIS211
|
4.7
|
47.7
|
1.0
|
CG
|
A:TRP126
|
4.7
|
47.5
|
1.0
|
CB
|
A:ALA164
|
4.7
|
49.8
|
1.0
|
O
|
A:GLU122
|
4.9
|
42.8
|
1.0
|
CA
|
A:GLU122
|
4.9
|
42.7
|
1.0
|
CD2
|
A:TRP126
|
4.9
|
48.5
|
1.0
|
|
Zinc binding site 4 out
of 7 in 1u19
Go back to
Zinc Binding Sites List in 1u19
Zinc binding site 4 out
of 7 in the Crystal Structure of Bovine Rhodopsin at 2.2 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 2.2 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2011
b:44.0
occ:0.68
|
NE2
|
A:HIS195
|
2.2
|
48.1
|
1.0
|
OE1
|
A:GLU197
|
2.4
|
67.4
|
1.0
|
CE1
|
A:HIS195
|
3.2
|
48.5
|
1.0
|
CD2
|
A:HIS195
|
3.2
|
47.6
|
1.0
|
CD
|
A:GLU197
|
3.3
|
64.7
|
1.0
|
OE2
|
A:GLU197
|
3.7
|
66.4
|
1.0
|
O
|
A:PRO7
|
4.0
|
42.5
|
1.0
|
ND1
|
A:HIS195
|
4.3
|
48.6
|
1.0
|
CG
|
A:HIS195
|
4.3
|
47.8
|
1.0
|
O
|
A:HOH2062
|
4.4
|
40.5
|
1.0
|
CG
|
A:GLU197
|
4.5
|
60.2
|
1.0
|
CB
|
A:GLU197
|
4.5
|
54.1
|
1.0
|
NH1
|
A:ARG177
|
4.5
|
43.2
|
1.0
|
C
|
A:PRO7
|
4.9
|
42.5
|
1.0
|
|
Zinc binding site 5 out
of 7 in 1u19
Go back to
Zinc Binding Sites List in 1u19
Zinc binding site 5 out
of 7 in the Crystal Structure of Bovine Rhodopsin at 2.2 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 2.2 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn956
b:49.4
occ:0.68
|
NE2
|
B:HIS195
|
2.1
|
53.3
|
1.0
|
OE1
|
B:GLU197
|
2.1
|
71.9
|
1.0
|
CD
|
B:GLU197
|
2.7
|
70.4
|
1.0
|
OE2
|
B:GLU197
|
2.8
|
72.0
|
1.0
|
CE1
|
B:HIS195
|
3.0
|
53.7
|
1.0
|
CD2
|
B:HIS195
|
3.1
|
54.3
|
1.0
|
O
|
B:PRO7
|
3.8
|
49.1
|
1.0
|
CG
|
B:GLU197
|
4.1
|
66.2
|
1.0
|
ND1
|
B:HIS195
|
4.1
|
54.3
|
1.0
|
CG
|
B:HIS195
|
4.2
|
53.6
|
1.0
|
CB
|
B:GLU197
|
4.4
|
61.0
|
1.0
|
NH1
|
B:ARG177
|
4.4
|
42.2
|
1.0
|
CB
|
B:PRO7
|
4.7
|
47.6
|
1.0
|
C
|
B:PRO7
|
4.7
|
48.4
|
1.0
|
CA
|
B:PRO7
|
4.8
|
47.5
|
1.0
|
|
Zinc binding site 6 out
of 7 in 1u19
Go back to
Zinc Binding Sites List in 1u19
Zinc binding site 6 out
of 7 in the Crystal Structure of Bovine Rhodopsin at 2.2 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 2.2 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn958
b:29.8
occ:0.51
|
NE2
|
B:GLN279
|
1.8
|
46.1
|
1.0
|
OE2
|
B:GLU201
|
2.2
|
51.8
|
1.0
|
OE1
|
B:GLU201
|
2.4
|
50.6
|
1.0
|
CD
|
B:GLU201
|
2.6
|
51.7
|
1.0
|
CD
|
B:GLN279
|
2.9
|
46.2
|
1.0
|
OE1
|
B:GLN279
|
3.5
|
47.3
|
1.0
|
O
|
B:PHE276
|
3.8
|
47.7
|
1.0
|
CG
|
B:GLN279
|
3.9
|
45.8
|
1.0
|
CG
|
B:GLU201
|
4.1
|
52.4
|
1.0
|
CE1
|
B:PHE276
|
4.5
|
41.7
|
1.0
|
CZ
|
B:PHE276
|
4.7
|
40.8
|
1.0
|
CG
|
B:PRO194
|
4.8
|
52.5
|
1.0
|
CD1
|
B:PHE276
|
4.8
|
43.2
|
1.0
|
|
Zinc binding site 7 out
of 7 in 1u19
Go back to
Zinc Binding Sites List in 1u19
Zinc binding site 7 out
of 7 in the Crystal Structure of Bovine Rhodopsin at 2.2 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 2.2 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn963
b:65.7
occ:0.68
|
ND1
|
B:HIS211
|
2.4
|
61.7
|
1.0
|
NE1
|
B:TRP126
|
2.5
|
62.0
|
1.0
|
OE1
|
B:GLU122
|
2.7
|
56.6
|
1.0
|
O
|
B:MET163
|
2.7
|
57.5
|
1.0
|
CE1
|
B:HIS211
|
2.8
|
62.2
|
1.0
|
C
|
B:MET163
|
3.1
|
58.1
|
1.0
|
CG
|
B:HIS211
|
3.2
|
60.8
|
1.0
|
CD1
|
B:TRP126
|
3.3
|
62.0
|
1.0
|
N
|
B:ALA164
|
3.4
|
57.8
|
1.0
|
CA
|
B:ALA164
|
3.5
|
57.1
|
1.0
|
CD
|
B:GLU122
|
3.5
|
54.9
|
1.0
|
CB
|
B:CYS167
|
3.5
|
57.6
|
1.0
|
CE2
|
B:TRP126
|
3.6
|
62.4
|
1.0
|
CG
|
B:GLU122
|
3.6
|
53.0
|
1.0
|
NE2
|
B:HIS211
|
3.6
|
62.2
|
1.0
|
CB
|
B:GLU122
|
3.7
|
51.2
|
1.0
|
CD2
|
B:HIS211
|
3.8
|
62.3
|
1.0
|
CB
|
B:HIS211
|
3.9
|
58.0
|
1.0
|
CB
|
B:MET163
|
3.9
|
59.4
|
1.0
|
CA
|
B:MET163
|
4.0
|
58.3
|
1.0
|
O
|
B:ALA164
|
4.0
|
57.7
|
1.0
|
CZ2
|
B:TRP126
|
4.1
|
63.3
|
1.0
|
C
|
B:ALA164
|
4.1
|
57.1
|
1.0
|
N
|
B:CYS167
|
4.3
|
57.2
|
1.0
|
SG
|
B:CYS167
|
4.5
|
65.9
|
1.0
|
CG
|
B:TRP126
|
4.5
|
61.2
|
1.0
|
OE2
|
B:GLU122
|
4.5
|
54.6
|
1.0
|
CA
|
B:CYS167
|
4.6
|
56.5
|
1.0
|
CD2
|
B:TRP126
|
4.7
|
62.2
|
1.0
|
CB
|
B:ALA164
|
4.7
|
56.9
|
1.0
|
CA
|
B:GLU122
|
4.8
|
51.2
|
1.0
|
CA
|
B:HIS211
|
4.8
|
56.0
|
1.0
|
O
|
B:GLU122
|
5.0
|
52.5
|
1.0
|
|
Reference:
T.Okada,
M.Sugihara,
A.N.Bondar,
M.Elstner,
P.Entel,
V.Buss.
The Retinal Conformation and Its Environment in Rhodopsin in Light of A New 2.2 A Crystal Structure J.Mol.Biol. V. 342 571 2004.
ISSN: ISSN 0022-2836
PubMed: 15327956
DOI: 10.1016/J.JMB.2004.07.044
Page generated: Wed Oct 16 19:23:19 2024
|