Atomistry » Terbium » PDB 1m9s-6xym » 6xym
Atomistry »
  Terbium »
    PDB 1m9s-6xym »
      6xym »

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: Fri Oct 11 08:43:33 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy