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Terbium in PDB 6xym: Nbe-Lbm

Protein crystallography data

The structure of Nbe-Lbm, PDB code: 6xym 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) 60.73 / 1.20
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.731, 63.855, 66.792, 90, 90, 90
R / Rfree (%) 15.4 / 19.8

Terbium Binding Sites:

The binding sites of Terbium atom in the Nbe-Lbm (pdb code 6xym). 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: 6xym:
Jump to Terbium binding site number: 1; 2;

Terbium binding site 1 out of 2 in 6xym

Go back to Terbium Binding Sites List in 6xym
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:16.1
occ:1.00
OD1 A:ASP42G 2.3 17.2 1.0
OD1 A:ASN42E 2.3 16.2 1.0
O A:TRP42I 2.3 15.7 1.0
OE2 A:GLU42K 2.4 17.7 1.0
OD1 A:ASP42C 2.4 14.5 1.0
OE1 A:GLU42N 2.4 15.4 1.0
OE1 A:GLU42K 2.5 16.2 1.0
OE2 A:GLU42N 2.5 16.6 1.0
CD A:GLU42K 2.7 17.4 1.0
CD A:GLU42N 2.8 15.8 1.0
CG A:ASP42G 3.1 16.9 1.0
OD2 A:ASP42G 3.3 18.9 1.0
CG A:ASN42E 3.4 17.9 1.0
C A:TRP42I 3.4 15.3 1.0
CG A:ASP42C 3.4 15.2 1.0
ND2 A:ASN42E 3.9 21.5 1.0
OD2 A:ASP42C 4.2 16.9 1.0
N A:TRP42I 4.2 14.6 1.0
CG A:GLU42K 4.2 18.7 1.0
CB A:ASP42C 4.3 15.7 1.0
CA A:TRP42I 4.3 15.8 1.0
N A:ILE42J 4.3 14.7 1.0
CG A:GLU42N 4.3 16.2 1.0
CA A:ASP42C 4.3 14.9 1.0
CA A:ILE42J 4.4 15.0 1.0
N A:ASP42G 4.4 15.4 1.0
CB A:ASP42G 4.4 18.8 1.0
N A:GLU42K 4.4 15.7 1.0
N A:ASN42E 4.4 15.8 1.0
CB A:ASN42E 4.5 19.3 1.0
C A:ASP42C 4.6 15.3 1.0
CB A:TRP42I 4.6 18.3 1.0
N A:ASN42F 4.7 17.0 1.0
O A:HOH361 4.7 34.3 1.0
C A:ILE42J 4.7 13.6 1.0
CA A:ASN42E 4.8 17.2 1.0
C A:ASN42E 4.8 17.2 1.0
N A:THR42D 4.9 16.9 1.0
CA A:ASP42G 4.9 16.6 1.0

Terbium binding site 2 out of 2 in 6xym

Go back to Terbium Binding Sites List in 6xym
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:23.8
occ:1.00
OD1 B:ASP42C 2.2 28.9 1.0
O B:TRP42I 2.2 28.5 0.5
OD1 B:ASP42G 2.3 27.1 1.0
OD1 B:ASN42E 2.4 26.6 1.0
OE1 B:GLU42K 2.4 24.1 1.0
O B:TRP42I 2.4 28.6 0.5
OE2 B:GLU42K 2.4 22.0 1.0
OE1 B:GLU42N 2.4 24.2 1.0
OE2 B:GLU42N 2.5 26.7 1.0
CD B:GLU42K 2.7 21.3 1.0
CD B:GLU42N 2.8 25.0 1.0
CG B:ASP42G 3.0 24.8 1.0
OD2 B:ASP42G 3.3 26.5 1.0
CG B:ASP42C 3.3 26.7 1.0
CG B:ASN42E 3.4 28.8 1.0
C B:TRP42I 3.4 26.6 0.5
C B:TRP42I 3.5 25.1 0.5
ND2 B:ASN42E 3.9 28.4 1.0
OD2 B:ASP42C 4.2 28.2 1.0
N B:TRP42I 4.2 24.9 0.5
N B:TRP42I 4.2 24.7 0.5
CG B:GLU42K 4.2 20.8 1.0
CB B:ASP42C 4.3 28.8 1.0
N B:ASP42G 4.3 31.7 1.0
CA B:ASP42C 4.3 27.0 1.0
CG B:GLU42N 4.3 25.2 1.0
N B:ILE42J 4.3 21.6 1.0
CA B:TRP42I 4.3 25.7 0.5
CB B:ASP42G 4.3 29.1 1.0
CA B:TRP42I 4.3 26.4 0.5
N B:GLU42K 4.4 21.3 1.0
CA B:ILE42J 4.4 21.5 1.0
N B:ASN42E 4.5 30.9 1.0
CB B:ASN42E 4.6 31.4 1.0
CB B:TRP42I 4.6 26.2 0.5
C B:ASP42C 4.6 29.6 1.0
N B:ASN42F 4.7 33.3 1.0
C B:ILE42J 4.7 19.7 1.0
CB B:TRP42I 4.7 29.1 0.5
O B:HOH325 4.7 37.0 1.0
CA B:ASP42G 4.8 32.0 1.0
N B:THR42D 4.8 30.3 1.0
CA B:ASN42E 4.8 30.3 1.0
C B:ASN42E 4.9 28.6 1.0
N B:GLY42H 4.9 30.1 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 15:44:42 2021

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