Terbium in PDB 2ojr: Structure of Ubiquitin Solved By Sad Using the Lanthanide-Binding Tag
Protein crystallography data
The structure of Structure of Ubiquitin Solved By Sad Using the Lanthanide-Binding Tag, PDB code: 2ojr
was solved by
N.R.Silvaggi,
K.N.Allen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.49 /
2.60
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.870,
57.870,
115.260,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
21.6 /
25.4
|
Terbium Binding Sites:
The binding sites of Terbium atom in the Structure of Ubiquitin Solved By Sad Using the Lanthanide-Binding Tag
(pdb code 2ojr). This binding sites where shown within
5.0 Angstroms radius around Terbium atom.
In total 2 binding sites of Terbium where determined in the
Structure of Ubiquitin Solved By Sad Using the Lanthanide-Binding Tag, PDB code: 2ojr:
Jump to Terbium binding site number:
1;
2;
Terbium binding site 1 out
of 2 in 2ojr
Go back to
Terbium Binding Sites List in 2ojr
Terbium binding site 1 out
of 2 in the Structure of Ubiquitin Solved By Sad Using the Lanthanide-Binding Tag
Mono view
Stereo pair view
|
A full contact list of Terbium with other atoms in the Tb binding
site number 1 of Structure of Ubiquitin Solved By Sad Using the Lanthanide-Binding Tag within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tb500
b:57.7
occ:1.00
|
OD1
|
A:ASN73
|
2.2
|
59.1
|
1.0
|
OD1
|
A:ASP71
|
2.2
|
54.9
|
1.0
|
OE1
|
A:GLU79
|
2.2
|
63.3
|
1.0
|
O
|
A:TRP77
|
2.3
|
59.8
|
1.0
|
OE2
|
A:GLU79
|
2.4
|
62.2
|
1.0
|
OE2
|
A:GLU82
|
2.5
|
55.7
|
1.0
|
CD
|
A:GLU79
|
2.6
|
62.4
|
1.0
|
OD1
|
A:ASP75
|
2.7
|
58.0
|
1.0
|
OE1
|
A:GLU82
|
2.7
|
56.5
|
1.0
|
CD
|
A:GLU82
|
2.9
|
57.6
|
1.0
|
CG
|
A:ASN73
|
3.1
|
59.0
|
1.0
|
CG
|
A:ASP75
|
3.1
|
59.7
|
1.0
|
OD2
|
A:ASP75
|
3.2
|
58.5
|
1.0
|
C
|
A:TRP77
|
3.3
|
60.3
|
1.0
|
CG
|
A:ASP71
|
3.3
|
58.4
|
1.0
|
ND2
|
A:ASN73
|
3.3
|
58.0
|
1.0
|
N
|
A:TRP77
|
4.0
|
60.7
|
1.0
|
N
|
A:ILE78
|
4.1
|
60.2
|
1.0
|
CB
|
A:ASP71
|
4.1
|
59.0
|
1.0
|
N
|
A:ASP75
|
4.1
|
61.5
|
1.0
|
CA
|
A:ASP71
|
4.1
|
59.5
|
1.0
|
CG
|
A:GLU79
|
4.1
|
61.4
|
1.0
|
CA
|
A:TRP77
|
4.2
|
60.7
|
1.0
|
OD2
|
A:ASP71
|
4.2
|
55.0
|
1.0
|
CA
|
A:ILE78
|
4.2
|
60.4
|
1.0
|
CB
|
A:ASP75
|
4.3
|
60.8
|
1.0
|
CG
|
A:GLU82
|
4.4
|
58.2
|
1.0
|
N
|
A:GLU79
|
4.4
|
60.9
|
1.0
|
CB
|
A:ASN73
|
4.4
|
59.8
|
1.0
|
N
|
A:ASN73
|
4.5
|
60.1
|
1.0
|
N
|
A:ASN74
|
4.5
|
61.1
|
1.0
|
C
|
A:ASP71
|
4.5
|
59.3
|
1.0
|
CB
|
A:TRP77
|
4.6
|
61.3
|
1.0
|
CA
|
A:ASP75
|
4.6
|
61.0
|
1.0
|
C
|
A:ILE78
|
4.7
|
60.5
|
1.0
|
N
|
A:THR72
|
4.7
|
59.5
|
1.0
|
N
|
A:GLY76
|
4.8
|
60.7
|
1.0
|
CA
|
A:ASN73
|
4.8
|
60.2
|
1.0
|
CB
|
A:GLU79
|
4.8
|
61.0
|
1.0
|
C
|
A:ASN73
|
4.9
|
60.7
|
1.0
|
C
|
A:ASP75
|
4.9
|
60.7
|
1.0
|
|
Terbium binding site 2 out
of 2 in 2ojr
Go back to
Terbium Binding Sites List in 2ojr
Terbium binding site 2 out
of 2 in the Structure of Ubiquitin Solved By Sad Using the Lanthanide-Binding Tag
Mono view
Stereo pair view
|
A full contact list of Terbium with other atoms in the Tb binding
site number 2 of Structure of Ubiquitin Solved By Sad Using the Lanthanide-Binding Tag within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tb501
b:49.5
occ:1.00
|
OE2
|
A:GLU97
|
2.0
|
54.2
|
1.0
|
OE2
|
A:GLU94
|
2.0
|
30.9
|
1.0
|
OD2
|
A:ASP86
|
2.1
|
51.7
|
1.0
|
OE1
|
A:GLU94
|
2.1
|
36.7
|
1.0
|
OD1
|
A:ASP90
|
2.2
|
49.3
|
1.0
|
OD1
|
A:ASN88
|
2.3
|
56.0
|
1.0
|
CD
|
A:GLU94
|
2.4
|
38.4
|
1.0
|
O
|
A:TRP92
|
2.4
|
48.8
|
1.0
|
CD
|
A:GLU97
|
2.7
|
51.3
|
1.0
|
OE1
|
A:GLU97
|
2.9
|
51.9
|
1.0
|
CG
|
A:ASP90
|
3.0
|
51.0
|
1.0
|
OD2
|
A:ASP90
|
3.0
|
48.6
|
1.0
|
CG
|
A:ASN88
|
3.1
|
52.8
|
1.0
|
CG
|
A:ASP86
|
3.1
|
53.9
|
1.0
|
C
|
A:TRP92
|
3.2
|
49.0
|
1.0
|
ND2
|
A:ASN88
|
3.4
|
51.4
|
1.0
|
OD1
|
A:ASP86
|
3.7
|
53.7
|
1.0
|
CG
|
A:GLU94
|
3.9
|
43.0
|
1.0
|
N
|
A:ILE93
|
4.0
|
47.9
|
1.0
|
CA
|
A:ILE93
|
4.0
|
47.2
|
1.0
|
CA
|
A:TRP92
|
4.1
|
50.0
|
1.0
|
O
|
A:HOH17
|
4.1
|
55.6
|
1.0
|
CG
|
A:GLU97
|
4.1
|
50.6
|
1.0
|
N
|
A:GLU94
|
4.1
|
46.4
|
1.0
|
N
|
A:TRP92
|
4.2
|
50.6
|
1.0
|
CB
|
A:ASP86
|
4.3
|
53.9
|
1.0
|
CB
|
A:ASP90
|
4.4
|
52.4
|
1.0
|
N
|
A:ASP90
|
4.4
|
53.4
|
1.0
|
CB
|
A:ASN88
|
4.4
|
52.9
|
1.0
|
CB
|
A:TRP92
|
4.4
|
49.9
|
1.0
|
N
|
A:ASN88
|
4.4
|
53.0
|
1.0
|
C
|
A:ILE93
|
4.5
|
46.7
|
1.0
|
CA
|
A:ASP86
|
4.5
|
53.8
|
1.0
|
O
|
A:ASP90
|
4.5
|
53.2
|
1.0
|
CD1
|
A:ILE93
|
4.6
|
47.4
|
1.0
|
N
|
A:ASN89
|
4.7
|
53.2
|
1.0
|
CB
|
A:GLU94
|
4.7
|
45.4
|
1.0
|
C
|
A:ASP90
|
4.7
|
52.8
|
1.0
|
CA
|
A:ASP90
|
4.8
|
52.7
|
1.0
|
CA
|
A:ASN88
|
4.8
|
52.9
|
1.0
|
C
|
A:ASP86
|
4.8
|
53.4
|
1.0
|
C
|
A:ASN88
|
4.9
|
52.9
|
1.0
|
|
Reference:
N.R.Silvaggi,
L.J.Martin,
H.Schwalbe,
B.Imperiali,
K.N.Allen.
Double-Lanthanide-Binding Tags For Macromolecular Crystallographic Structure Determination. J.Am.Chem.Soc. V. 129 7114 2007.
ISSN: ISSN 0002-7863
PubMed: 17497863
DOI: 10.1021/JA070481N
Page generated: Fri Oct 11 08:11:52 2024
|