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Terbium in PDB 6y0e: Nbe Lbm

Protein crystallography data

The structure of Nbe Lbm, PDB code: 6y0e was solved by G.Pompidor, S.Zimmermann, C.Loew, T.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.76 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.477, 50.612, 93.528, 90, 90, 90
R / Rfree (%) 16.1 / 18

Terbium Binding Sites:

The binding sites of Terbium atom in the Nbe Lbm (pdb code 6y0e). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total 2 binding sites of Terbium where determined in the Nbe Lbm, PDB code: 6y0e:
Jump to Terbium binding site number: 1; 2;

Terbium binding site 1 out of 2 in 6y0e

Go back to Terbium Binding Sites List in 6y0e
Terbium binding site 1 out of 2 in the Nbe Lbm


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 1 of Nbe Lbm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb201

b:16.6
occ:0.95
OD1 A:ASP42C 2.3 20.5 1.0
O A:TRP42I 2.3 13.4 1.0
OD1 A:ASP42G 2.3 21.6 1.0
OD1 A:ASN42E 2.3 19.9 1.0
OE1 A:GLU42K 2.4 18.5 1.0
OE1 A:GLU42N 2.4 15.7 1.0
OE2 A:GLU42N 2.5 19.9 1.0
OE2 A:GLU42K 2.5 18.5 1.0
CD A:GLU42K 2.8 16.9 1.0
CD A:GLU42N 2.8 20.7 1.0
CG A:ASP42G 3.1 25.7 1.0
OD2 A:ASP42G 3.3 22.9 1.0
CG A:ASP42C 3.3 21.9 1.0
C A:TRP42I 3.4 17.3 1.0
CG A:ASN42E 3.4 31.5 1.0
HA A:ILE42J 3.6 15.4 1.0
H A:TRP42I 3.6 21.4 1.0
HA A:ASP42C 3.6 20.2 1.0
H A:ASN42E 3.6 30.1 1.0
HD21 A:ASN42E 3.7 36.7 1.0
H A:ASP42G 3.8 27.6 1.0
HB2 A:TRP42I 3.8 21.4 1.0
H A:GLU42K 3.9 18.2 1.0
ND2 A:ASN42E 4.0 30.6 1.0
OD2 A:ASP42C 4.1 22.9 1.0
CB A:ASP42C 4.2 16.4 1.0
N A:TRP42I 4.2 17.8 1.0
CA A:TRP42I 4.2 17.4 1.0
N A:ILE42J 4.2 14.0 1.0
HB2 A:ASP42C 4.3 19.6 1.0
CA A:ASP42C 4.3 16.8 1.0
CA A:ILE42J 4.3 12.8 1.0
CG A:GLU42K 4.3 17.4 1.0
CG A:GLU42N 4.3 17.7 1.0
N A:GLU42K 4.4 15.2 1.0
N A:ASN42E 4.5 25.1 1.0
CB A:TRP42I 4.5 17.9 1.0
CB A:ASP42G 4.5 24.3 1.0
H A:THR42D 4.5 25.8 1.0
N A:ASP42G 4.6 23.0 1.0
HE1 B:HIS116 4.6 43.3 1.0
CB A:ASN42E 4.6 31.7 1.0
HG3 A:GLU42N 4.6 21.2 1.0
HG2 A:GLU42K 4.6 20.9 1.0
C A:ASP42C 4.7 20.3 1.0
HG2 A:GLU42N 4.7 21.2 1.0
H A:GLY42H 4.7 22.0 1.0
N A:THR42D 4.7 21.5 1.0
HB3 A:TRP42I 4.8 21.4 1.0
HB3 A:ASP42G 4.8 29.2 1.0
HG3 A:GLU42K 4.8 20.9 1.0
HD22 A:ASN42E 4.8 36.7 1.0
C A:ILE42J 4.8 15.9 1.0
HB3 A:ASN42E 4.8 38.0 1.0
HB3 A:GLU42K 4.9 20.6 1.0
H A:ASN42F 4.9 34.5 1.0
HG13 A:ILE42J 4.9 18.8 1.0
CA A:ASN42E 4.9 31.4 1.0
HB2 A:GLU42N 4.9 19.8 1.0
CA A:ASP42G 4.9 21.6 1.0
C A:ASN42E 5.0 26.0 1.0
O A:HOH372 5.0 39.2 1.0

Terbium binding site 2 out of 2 in 6y0e

Go back to Terbium Binding Sites List in 6y0e
Terbium binding site 2 out of 2 in the Nbe Lbm


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 2 of Nbe Lbm within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb201

b:20.0
occ:0.57
OD1 B:ASN42E 2.1 39.9 1.0
O B:TRP42I 2.1 33.4 1.0
OD1 B:ASP42C 2.3 28.7 1.0
OE1 B:GLU42N 2.3 31.3 1.0
OE2 B:GLU42K 2.4 28.4 1.0
OE2 B:GLU42N 2.4 26.8 1.0
OD1 B:ASP42G 2.5 42.0 1.0
OE1 B:GLU42K 2.5 28.0 1.0
CD B:GLU42N 2.7 24.5 1.0
CD B:GLU42K 2.8 27.0 1.0
OD2 B:ASP42G 3.0 45.5 1.0
CG B:ASP42G 3.0 47.5 1.0
CG B:ASN42E 3.1 36.2 1.0
C B:TRP42I 3.2 34.0 1.0
CG B:ASP42C 3.3 39.5 1.0
H B:TRP42I 3.4 46.5 1.0
HD21 B:ASN42E 3.4 43.1 1.0
HA B:ILE42J 3.6 37.4 1.0
HA B:ASP42C 3.7 40.5 1.0
ND2 B:ASN42E 3.7 36.0 1.0
H B:ASN42E 3.7 44.0 1.0
H B:GLU42K 3.8 33.4 1.0
HB2 B:TRP42I 3.8 48.3 1.0
H B:ASP42G 3.8 54.1 1.0
HB2 B:ASP42C 4.0 40.3 1.0
N B:TRP42I 4.0 38.8 1.0
CB B:ASP42C 4.1 33.6 1.0
OD2 B:ASP42C 4.1 38.9 1.0
N B:ILE42J 4.1 27.5 1.0
CA B:TRP42I 4.1 38.7 1.0
O B:ASN42E 4.2 43.3 1.0
CG B:GLU42N 4.2 29.3 1.0
CA B:ILE42J 4.2 31.2 1.0
CA B:ASP42C 4.3 33.8 1.0
CG B:GLU42K 4.3 30.4 1.0
N B:GLU42K 4.3 27.8 1.0
CB B:ASN42E 4.3 39.2 1.0
CB B:ASP42G 4.5 41.6 1.0
CB B:TRP42I 4.5 40.2 1.0
N B:ASN42E 4.5 36.7 1.0
HD22 B:ASN42E 4.5 43.1 1.0
HG3 B:GLU42N 4.5 35.1 1.0
HB3 B:ASN42E 4.5 47.0 1.0
C B:ASN42E 4.6 43.4 1.0
N B:ASP42G 4.6 45.1 1.0
C B:ASP42C 4.7 34.0 1.0
HG2 B:GLU42N 4.7 35.1 1.0
HG3 B:GLU42K 4.7 36.5 1.0
HG2 B:GLU42K 4.7 36.5 1.0
CA B:ASN42E 4.7 34.1 1.0
H B:THR42D 4.7 40.4 1.0
H B:GLY42H 4.7 55.2 1.0
C B:ILE42J 4.8 28.7 1.0
HB3 B:ASP42G 4.8 49.9 1.0
HB2 B:GLU42N 4.9 36.7 1.0
N B:THR42D 4.9 33.7 1.0
H B:ILE42J 4.9 33.0 1.0
CA B:ASP42G 4.9 42.9 1.0
HB3 B:GLU42K 5.0 34.8 1.0
N B:GLY42H 5.0 46.0 1.0
HB3 B:ASP42C 5.0 40.3 1.0
HA B:TRP42I 5.0 46.4 1.0

Reference:

G.Pompidor, S.Zimmermann, C.Loew, T.Schneider. Engineered Nanobodies with A Lanthanide Binding Motif For Crystallographic Phasing To Be Published.
Page generated: Wed Mar 3 15:44:55 2021

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