Mercury 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:
Mercury Binding Sites:
The binding sites of Mercury 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 Mercury atom.
In total 6 binding sites of Mercury where determined in the
Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution, PDB code: 1u19:
Jump to Mercury binding site number:
1;
2;
3;
4;
5;
6;
Mercury binding site 1 out
of 6 in 1u19
Go back to
Mercury Binding Sites List in 1u19
Mercury binding site 1 out
of 6 in the Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg 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:Hg901
b:77.5
occ:0.89
|
SG
|
A:CYS264
|
2.8
|
48.6
|
1.0
|
CB
|
A:CYS264
|
3.0
|
43.8
|
1.0
|
OG1
|
A:THR297
|
3.1
|
39.2
|
1.0
|
CD2
|
A:TYR301
|
3.6
|
41.3
|
1.0
|
CA
|
A:CYS264
|
3.7
|
42.5
|
1.0
|
CZ
|
A:PHE294
|
3.9
|
34.7
|
1.0
|
CE2
|
A:TYR301
|
3.9
|
42.5
|
1.0
|
O
|
A:ALA260
|
4.0
|
45.9
|
1.0
|
N
|
A:CYS264
|
4.1
|
42.4
|
1.0
|
CB
|
A:THR297
|
4.2
|
39.2
|
1.0
|
CE1
|
A:PHE294
|
4.4
|
34.1
|
1.0
|
CG
|
A:TYR301
|
4.4
|
41.4
|
1.0
|
CE2
|
A:PHE294
|
4.4
|
34.8
|
1.0
|
C
|
A:THR297
|
4.7
|
39.5
|
1.0
|
N
|
A:SER298
|
4.7
|
39.9
|
1.0
|
O
|
A:PHE294
|
4.8
|
38.2
|
1.0
|
CB
|
A:TYR301
|
4.8
|
41.7
|
1.0
|
O
|
A:THR297
|
4.8
|
39.2
|
1.0
|
CG2
|
A:ILE263
|
5.0
|
37.5
|
1.0
|
C
|
A:ILE263
|
5.0
|
42.0
|
1.0
|
CZ
|
A:TYR301
|
5.0
|
42.8
|
1.0
|
|
Mercury binding site 2 out
of 6 in 1u19
Go back to
Mercury Binding Sites List in 1u19
Mercury binding site 2 out
of 6 in the Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg 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:Hg903
b:82.6
occ:0.75
|
SG
|
A:CYS222
|
2.3
|
69.1
|
1.0
|
O
|
A:CYS222
|
3.4
|
70.6
|
1.0
|
O
|
A:ALA132
|
3.4
|
54.8
|
1.0
|
C
|
A:CYS222
|
3.5
|
70.1
|
1.0
|
CB
|
A:CYS222
|
3.5
|
68.2
|
1.0
|
N
|
A:TYR223
|
3.7
|
71.6
|
1.0
|
CD2
|
A:LEU226
|
3.8
|
92.0
|
1.0
|
CA
|
A:ALA132
|
3.9
|
54.9
|
1.0
|
CA
|
A:TYR223
|
4.0
|
73.2
|
1.0
|
C
|
A:ALA132
|
4.1
|
55.1
|
1.0
|
CD1
|
A:LEU226
|
4.1
|
91.9
|
1.0
|
CA
|
A:CYS222
|
4.1
|
68.8
|
1.0
|
CB
|
A:ALA132
|
4.2
|
54.9
|
1.0
|
CB
|
A:ARG135
|
4.2
|
59.0
|
1.0
|
CG
|
A:ARG135
|
4.3
|
58.4
|
1.0
|
CG
|
A:LEU226
|
4.4
|
92.2
|
1.0
|
O
|
A:ILE219
|
4.6
|
59.9
|
1.0
|
CB
|
A:LEU226
|
4.6
|
92.2
|
1.0
|
N
|
A:TYR136
|
4.6
|
65.0
|
1.0
|
CB
|
A:TYR223
|
4.8
|
73.1
|
1.0
|
CB
|
A:TYR136
|
4.9
|
66.8
|
1.0
|
CA
|
A:TYR136
|
5.0
|
66.7
|
1.0
|
|
Mercury binding site 3 out
of 6 in 1u19
Go back to
Mercury Binding Sites List in 1u19
Mercury binding site 3 out
of 6 in the Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg 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:Hg905
b:74.9
occ:0.58
|
SG
|
A:CYS316
|
2.5
|
55.8
|
1.0
|
O
|
A:HOH2061
|
2.6
|
47.2
|
1.0
|
O
|
A:GLN312
|
3.2
|
50.5
|
1.0
|
N
|
A:VAL337
|
3.3
|
84.8
|
1.0
|
N
|
A:CYS316
|
3.5
|
55.5
|
1.0
|
CB
|
A:CYS316
|
3.6
|
56.6
|
1.0
|
CG1
|
A:VAL337
|
3.7
|
82.2
|
1.0
|
O
|
A:VAL337
|
3.7
|
77.6
|
1.0
|
CA
|
A:THR336
|
3.7
|
89.7
|
1.0
|
CA
|
A:CYS316
|
3.7
|
57.0
|
1.0
|
C
|
A:THR336
|
3.8
|
87.3
|
1.0
|
CG
|
A:GLN312
|
3.8
|
54.4
|
1.0
|
CG2
|
A:THR336
|
4.1
|
90.4
|
1.0
|
CB
|
A:ASN315
|
4.1
|
52.2
|
1.0
|
CB
|
A:THR336
|
4.1
|
90.0
|
1.0
|
C
|
A:GLN312
|
4.2
|
50.1
|
1.0
|
C
|
A:ASN315
|
4.2
|
53.6
|
1.0
|
CA
|
A:VAL337
|
4.3
|
81.9
|
1.0
|
C
|
A:VAL337
|
4.4
|
79.7
|
1.0
|
CA
|
A:GLN312
|
4.5
|
51.0
|
1.0
|
CB
|
A:VAL337
|
4.6
|
82.0
|
1.0
|
NE2
|
A:GLN312
|
4.7
|
56.4
|
1.0
|
CA
|
A:ASN315
|
4.8
|
51.8
|
1.0
|
CD
|
A:GLN312
|
4.8
|
55.8
|
1.0
|
CB
|
A:GLN312
|
4.8
|
51.9
|
1.0
|
O
|
A:THR336
|
4.8
|
86.9
|
1.0
|
O
|
A:ASN315
|
4.8
|
54.3
|
1.0
|
ND1
|
A:HIS65
|
4.9
|
61.0
|
1.0
|
N
|
A:THR336
|
5.0
|
92.5
|
1.0
|
|
Mercury binding site 4 out
of 6 in 1u19
Go back to
Mercury Binding Sites List in 1u19
Mercury binding site 4 out
of 6 in the Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg 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
|
B:Hg902
b:79.3
occ:0.83
|
SG
|
B:CYS264
|
2.7
|
54.7
|
1.0
|
CB
|
B:CYS264
|
3.3
|
50.9
|
1.0
|
OG1
|
B:THR297
|
3.5
|
44.6
|
1.0
|
O
|
B:ALA260
|
3.6
|
51.8
|
1.0
|
CD2
|
B:TYR301
|
3.7
|
46.2
|
1.0
|
CA
|
B:CYS264
|
3.8
|
50.0
|
1.0
|
CE2
|
B:TYR301
|
3.9
|
47.8
|
1.0
|
N
|
B:CYS264
|
4.1
|
50.4
|
1.0
|
CZ
|
B:PHE294
|
4.2
|
40.1
|
1.0
|
CG
|
B:TYR301
|
4.3
|
46.3
|
1.0
|
C
|
B:ALA260
|
4.5
|
50.9
|
1.0
|
CE2
|
B:PHE294
|
4.6
|
40.3
|
1.0
|
C
|
B:ILE263
|
4.6
|
50.7
|
1.0
|
CB
|
B:THR297
|
4.7
|
43.3
|
1.0
|
CZ
|
B:TYR301
|
4.8
|
47.8
|
1.0
|
CB
|
B:TYR301
|
4.8
|
45.7
|
1.0
|
CE1
|
B:PHE294
|
4.9
|
40.6
|
1.0
|
CG2
|
B:ILE263
|
4.9
|
48.2
|
1.0
|
CA
|
B:ALA260
|
4.9
|
51.3
|
1.0
|
O
|
B:ILE263
|
5.0
|
51.3
|
1.0
|
CB
|
B:ILE263
|
5.0
|
48.5
|
1.0
|
|
Mercury binding site 5 out
of 6 in 1u19
Go back to
Mercury Binding Sites List in 1u19
Mercury binding site 5 out
of 6 in the Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg 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:Hg904
b:96.2
occ:0.66
|
SG
|
B:CYS222
|
2.3
|
79.0
|
1.0
|
O
|
B:CYS222
|
3.3
|
76.8
|
1.0
|
O
|
B:ALA132
|
3.3
|
68.2
|
1.0
|
C
|
B:CYS222
|
3.4
|
76.9
|
1.0
|
CB
|
B:CYS222
|
3.6
|
77.8
|
1.0
|
N
|
B:TYR223
|
3.6
|
77.3
|
1.0
|
CA
|
B:ALA132
|
3.8
|
67.0
|
1.0
|
CA
|
B:TYR223
|
3.8
|
78.1
|
1.0
|
CB
|
B:ARG135
|
4.0
|
75.5
|
1.0
|
C
|
B:ALA132
|
4.0
|
68.2
|
1.0
|
CA
|
B:CYS222
|
4.1
|
76.8
|
1.0
|
CD2
|
B:LEU226
|
4.1
|
93.2
|
1.0
|
CB
|
B:ALA132
|
4.2
|
66.0
|
1.0
|
CD1
|
B:LEU226
|
4.2
|
93.5
|
1.0
|
CG
|
B:ARG135
|
4.3
|
75.1
|
1.0
|
O
|
B:ILE219
|
4.5
|
66.2
|
1.0
|
CB
|
B:TYR223
|
4.6
|
77.1
|
1.0
|
CG
|
B:LEU226
|
4.6
|
93.9
|
1.0
|
N
|
B:TYR136
|
4.7
|
78.4
|
1.0
|
CB
|
B:LEU226
|
4.9
|
93.8
|
1.0
|
C
|
B:TYR223
|
5.0
|
79.7
|
1.0
|
|
Mercury binding site 6 out
of 6 in 1u19
Go back to
Mercury Binding Sites List in 1u19
Mercury binding site 6 out
of 6 in the Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Mercury with other atoms in the Hg 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:Hg906
b:0.3
occ:0.36
|
O
|
B:VAL337
|
2.0
|
0.1
|
1.0
|
O
|
B:THR336
|
2.0
|
0.2
|
1.0
|
CB
|
B:CYS316
|
2.3
|
62.5
|
1.0
|
SG
|
B:CYS316
|
2.4
|
63.0
|
1.0
|
ND1
|
B:HIS65
|
2.7
|
69.0
|
1.0
|
CA
|
B:CYS316
|
2.9
|
62.9
|
1.0
|
C
|
B:THR336
|
3.1
|
0.4
|
1.0
|
C
|
B:VAL337
|
3.2
|
0.6
|
1.0
|
CE1
|
B:HIS65
|
3.5
|
68.9
|
1.0
|
OG
|
B:SER338
|
3.6
|
0.6
|
1.0
|
CG
|
B:HIS65
|
3.8
|
68.8
|
1.0
|
N
|
B:VAL337
|
3.9
|
0.1
|
1.0
|
C
|
B:CYS316
|
3.9
|
62.7
|
1.0
|
O
|
B:CYS316
|
4.0
|
62.6
|
1.0
|
N
|
B:CYS316
|
4.0
|
62.9
|
1.0
|
CA
|
B:VAL337
|
4.0
|
0.4
|
1.0
|
N
|
B:SER338
|
4.1
|
0.1
|
1.0
|
CA
|
B:THR336
|
4.2
|
0.8
|
1.0
|
CB
|
B:HIS65
|
4.2
|
68.5
|
1.0
|
CE
|
B:LYS67
|
4.2
|
75.9
|
1.0
|
CA
|
B:SER338
|
4.4
|
1.0
|
1.0
|
CB
|
B:SER338
|
4.6
|
0.0
|
1.0
|
NZ
|
B:LYS67
|
4.7
|
77.1
|
1.0
|
NE2
|
B:HIS65
|
4.7
|
68.8
|
1.0
|
CB
|
B:THR336
|
4.7
|
0.6
|
1.0
|
OG1
|
B:THR319
|
4.8
|
70.1
|
1.0
|
CG2
|
B:THR342
|
4.8
|
0.2
|
1.0
|
CG2
|
B:VAL337
|
4.8
|
0.3
|
1.0
|
CD1
|
B:LEU68
|
4.9
|
62.5
|
1.0
|
CD2
|
B:HIS65
|
4.9
|
68.7
|
1.0
|
CD
|
B:LYS67
|
4.9
|
74.0
|
1.0
|
C
|
B:ASN315
|
4.9
|
63.0
|
1.0
|
O
|
B:GLN312
|
5.0
|
62.6
|
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: Sun Aug 11 01:39:34 2024
|