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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: Wed Dec 16 02:26:37 2020

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