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Terbium in PDB 6xzf: Nanobody in Complex with Egfp

Protein crystallography data

The structure of Nanobody in Complex with Egfp, PDB code: 6xzf 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) 48.95 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.335, 69.335, 169.063, 90, 90, 120
R / Rfree (%) 17.3 / 20.4

Terbium Binding Sites:

The binding sites of Terbium atom in the Nanobody in Complex with Egfp (pdb code 6xzf). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total only one binding site of Terbium was determined in the Nanobody in Complex with Egfp, PDB code: 6xzf:

Terbium binding site 1 out of 1 in 6xzf

Go back to Terbium Binding Sites List in 6xzf
Terbium binding site 1 out of 1 in the Nanobody in Complex with Egfp


Mono view


Stereo pair view

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

b:57.3
occ:0.85
HD21 B:ASN42E 2.2 81.0 1.0
OD1 B:ASN42E 2.2 36.6 1.0
OD1 B:ASP42G 2.3 62.9 1.0
OE1 B:GLU42N 2.5 49.4 1.0
OE2 B:GLU42K 2.5 48.7 1.0
OE2 B:GLU42N 2.6 57.5 1.0
O B:TRP42I 2.6 56.2 1.0
OD1 B:ASP42C 2.6 53.0 1.0
OE1 B:GLU42K 2.7 50.8 1.0
ND2 B:ASN42E 2.7 67.5 1.0
CG B:ASN42E 2.8 70.6 1.0
CD B:GLU42N 2.9 49.9 1.0
CD B:GLU42K 3.0 53.4 1.0
CG B:ASP42G 3.0 75.4 1.0
OD2 B:ASP42G 3.2 73.7 1.0
H B:ASP42G 3.4 97.2 1.0
H B:TRP42I 3.4 77.0 1.0
CG B:ASP42C 3.5 63.4 1.0
C B:TRP42I 3.5 57.8 1.0
HD22 B:ASN42E 3.5 81.0 1.0
HA B:ILE42J 3.7 79.1 1.0
H B:ASN42E 3.7 99.8 1.0
HA B:ASP42C 3.8 71.8 1.0
H B:GLU42K 3.9 77.7 1.0
OD2 B:ASP42C 4.1 57.9 1.0
H B:ASN42F 4.2 107.5 1.0
N B:TRP42I 4.2 64.2 1.0
CB B:ASN42E 4.2 60.5 1.0
HD13 B:ILE42J 4.2 81.8 1.0
N B:ASP42G 4.2 81.0 1.0
HB2 B:TRP42I 4.2 93.1 1.0
N B:ILE42J 4.3 65.5 1.0
CG B:GLU42N 4.4 57.7 1.0
CB B:ASP42G 4.4 75.3 1.0
CA B:TRP42I 4.4 69.9 1.0
CA B:ILE42J 4.4 65.9 1.0
CB B:ASP42C 4.4 54.0 1.0
N B:ASN42E 4.4 83.2 1.0
CA B:ASP42C 4.4 59.8 1.0
H B:GLY42H 4.4 84.2 1.0
N B:GLU42K 4.4 64.8 1.0
HB2 B:ASP42C 4.5 64.9 1.0
CG B:GLU42K 4.5 52.6 1.0
N B:ASN42F 4.5 89.5 1.0
HB3 B:ASN42E 4.6 72.6 1.0
HB3 B:ASP42G 4.6 90.4 1.0
HG3 B:GLU42N 4.7 69.2 1.0
H B:THR42D 4.7 78.7 1.0
CA B:ASN42E 4.7 78.8 1.0
HB2 B:ASN42E 4.7 72.6 1.0
C B:ASP42C 4.7 63.4 1.0
CA B:ASP42G 4.8 76.7 1.0
CB B:TRP42I 4.8 77.6 1.0
HG2 B:GLU42K 4.8 63.2 1.0
C B:ASN42E 4.8 85.0 1.0
N B:GLY42H 4.8 70.2 1.0
HG2 B:GLU42N 4.8 69.2 1.0
N B:THR42D 4.8 65.6 1.0
C B:ILE42J 4.8 65.3 1.0
HB2 B:GLU42N 4.9 66.1 1.0
HG3 B:GLU42K 4.9 63.2 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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