Atomistry » Terbium » PDB 1m9s-6xym » 6f2j
Atomistry »
  Terbium »
    PDB 1m9s-6xym »
      6f2j »

Terbium in PDB 6f2j: Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate

Enzymatic activity of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate

All present enzymatic activity of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate, PDB code: 6f2j was solved by S.Engilberge, F.Riobe, S.Di Pietro, E.Girard, E.Dumont, O.Maury, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.84 / 1.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.915, 77.915, 37.738, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 17.9

Other elements in 6f2j:

The structure of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Terbium Binding Sites:

The binding sites of Terbium atom in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate (pdb code 6f2j). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total 3 binding sites of Terbium where determined in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate, PDB code: 6f2j:
Jump to Terbium binding site number: 1; 2; 3;

Terbium binding site 1 out of 3 in 6f2j

Go back to Terbium Binding Sites List in 6f2j
Terbium binding site 1 out of 3 in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 1 of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb201

b:15.3
occ:0.25
H012 A:7MT206 1.3 12.4 0.7
C01 A:7MT206 1.5 13.5 0.7
O25 A:7MT205 1.8 20.7 0.8
N02 A:7MT206 1.9 15.2 0.7
N09 A:7MT206 2.1 17.9 0.7
C03 A:7MT206 2.2 16.4 0.7
H301 A:7MT206 2.4 18.6 0.7
H292 A:7MT206 2.4 22.5 0.7
H011 A:7MT206 2.5 10.8 0.7
TB A:7MT206 2.5 15.4 0.7
C30 A:7MT206 2.6 17.3 0.7
C29 A:7MT206 2.6 21.2 0.7
H032 A:7MT206 2.7 18.1 0.7
H031 A:7MT206 2.9 17.5 0.7
C24 A:7MT205 3.0 19.4 0.8
N23 A:7MT206 3.0 20.1 0.7
C11 A:7MT206 3.2 20.9 0.7
C04 A:7MT206 3.2 14.6 0.7
H302 A:7MT206 3.3 17.9 0.7
O A:HOH486 3.4 43.1 1.0
H211 A:7MT205 3.4 21.2 0.8
H042 A:7MT206 3.5 13.7 0.7
C08 A:7MT206 3.5 15.3 0.7
H291 A:7MT206 3.5 22.1 0.7
O A:HOH361 3.5 29.8 1.0
N06 A:7MT206 3.6 14.8 0.7
C10 A:7MT206 3.6 17.5 0.7
N17 A:7MT206 3.6 18.0 0.7
O26 A:7MT205 3.8 23.1 0.8
H041 A:7MT206 3.9 15.5 0.7
C05 A:7MT206 4.0 14.4 0.7
C22 A:7MT205 4.0 17.5 0.8
H081 A:7MT206 4.0 14.9 0.7
C21 A:7MT205 4.0 21.1 0.8
C07 A:7MT206 4.1 13.0 0.7
H082 A:7MT206 4.1 15.1 0.7
O26 A:7MT206 4.2 22.6 0.7
C22 A:7MT206 4.2 20.9 0.7
H061 A:7MT206 4.3 13.2 0.7
H072 A:7MT206 4.4 12.7 0.7
O A:HOH321 4.4 22.7 1.0
H051 A:7MT206 4.4 14.6 0.7
C19 A:7MT206 4.5 21.2 0.7
C24 A:7MT206 4.7 23.1 0.7
H052 A:7MT206 4.8 14.1 0.7
O28 A:7MT206 4.9 17.4 0.7
H071 A:7MT206 4.9 11.7 0.7
C13 A:7MT206 4.9 18.4 0.7
C16 A:7MT206 5.0 18.0 0.7
H191 A:7MT206 5.0 21.6 0.7

Terbium binding site 2 out of 3 in 6f2j

Go back to Terbium Binding Sites List in 6f2j
Terbium binding site 2 out of 3 in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 2 of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb205

b:15.8
occ:0.85
TB A:7MT205 0.0 15.8 0.8
OD2 A:ASP101 2.3 23.0 1.0
N23 A:7MT205 2.4 22.1 0.8
OD1 A:ASP101 2.5 21.5 1.0
O26 A:7MT205 2.5 23.1 0.8
N06 A:7MT205 2.5 19.5 0.8
O28 A:7MT205 2.6 23.1 0.8
N17 A:7MT205 2.6 18.4 0.8
N02 A:7MT205 2.7 19.9 0.8
CG A:ASP101 2.7 23.2 1.0
N09 A:7MT205 2.8 23.4 0.8
H061 A:7MT205 2.8 19.4 0.8
H301 A:7MT205 3.3 21.0 0.8
C22 A:7MT205 3.3 17.5 0.8
C24 A:7MT205 3.3 19.4 0.8
C05 A:7MT205 3.3 19.6 0.8
C30 A:7MT205 3.3 20.7 0.8
C11 A:7MT205 3.3 23.2 0.8
H051 A:7MT205 3.4 20.1 0.8
H012 A:7MT205 3.4 20.2 0.8
C01 A:7MT205 3.4 21.4 0.8
C10 A:7MT205 3.4 19.6 0.8
C18 A:7MT205 3.4 23.1 0.8
C16 A:7MT205 3.5 22.4 0.8
C29 A:7MT205 3.5 24.9 0.8
C08 A:7MT205 3.5 19.5 0.8
C04 A:7MT205 3.5 20.8 0.8
C07 A:7MT205 3.5 19.0 0.8
H081 A:7MT205 3.6 19.5 0.8
H291 A:7MT205 3.6 25.1 0.8
C03 A:7MT205 3.6 23.8 0.8
H042 A:7MT205 4.1 21.7 0.8
H072 A:7MT205 4.2 18.9 0.8
H031 A:7MT205 4.2 23.7 0.8
H071 A:7MT205 4.2 20.3 0.8
H052 A:7MT205 4.2 20.4 0.8
CB A:ASP101 4.2 17.1 1.0
H041 A:7MT205 4.2 20.7 0.8
H302 A:7MT205 4.3 21.5 0.8
H011 A:7MT205 4.3 22.5 0.8
H032 A:7MT205 4.3 24.4 0.8
H292 A:7MT205 4.4 25.5 0.8
H A:GLY102 4.4 19.4 1.0
H082 A:7MT205 4.4 20.5 0.8
HH2 A:TRP63 4.4 16.6 1.0
O25 A:7MT205 4.5 20.7 0.8
HB2 A:ASP101 4.6 17.2 1.0
C21 A:7MT205 4.6 21.1 0.8
O27 A:7MT205 4.6 25.2 0.8
O A:HOH361 4.7 29.8 1.0
C19 A:7MT205 4.7 23.1 0.8
HB3 A:ASP101 4.7 15.8 1.0
C13 A:7MT205 4.8 22.5 0.8
C15 A:7MT205 4.8 23.6 0.8
HZ2 A:TRP63 4.8 17.7 1.0
HA A:ASP101 4.9 14.8 1.0
H301 A:7MT206 5.0 18.6 0.7

Terbium binding site 3 out of 3 in 6f2j

Go back to Terbium Binding Sites List in 6f2j
Terbium binding site 3 out of 3 in the Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 3 of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4 and 100 Mm Sodium Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb206

b:15.4
occ:0.70
TB A:7MT206 0.0 15.4 0.7
O A:HOH321 2.3 22.7 1.0
N06 A:7MT206 2.4 14.8 0.7
O25 A:7MT205 2.4 20.7 0.8
O26 A:7MT206 2.4 22.6 0.7
TB A:TB201 2.5 15.3 0.2
N17 A:7MT206 2.5 18.0 0.7
H061 A:7MT206 2.5 13.2 0.7
O28 A:7MT206 2.5 17.4 0.7
N23 A:7MT206 2.6 20.1 0.7
N02 A:7MT206 2.7 15.2 0.7
N09 A:7MT206 2.8 17.9 0.7
C05 A:7MT206 3.2 14.4 0.7
C24 A:7MT206 3.3 23.1 0.7
H051 A:7MT206 3.3 14.6 0.7
C22 A:7MT206 3.3 20.9 0.7
C08 A:7MT206 3.3 15.3 0.7
C07 A:7MT206 3.4 13.0 0.7
C18 A:7MT206 3.4 21.5 0.7
C24 A:7MT205 3.4 19.4 0.8
C16 A:7MT206 3.4 18.0 0.7
C10 A:7MT206 3.4 17.5 0.7
H081 A:7MT206 3.4 14.9 0.7
C30 A:7MT206 3.5 17.3 0.7
C04 A:7MT206 3.5 14.6 0.7
C01 A:7MT206 3.5 13.5 0.7
C11 A:7MT206 3.5 20.9 0.7
H301 A:7MT206 3.6 18.6 0.7
C29 A:7MT206 3.7 21.2 0.7
C03 A:7MT206 3.7 16.4 0.7
H012 A:7MT206 3.7 12.4 0.7
O26 A:7MT205 3.9 23.1 0.8
H071 A:7MT206 3.9 11.7 0.7
H292 A:7MT206 4.0 22.5 0.7
H031 A:7MT206 4.1 17.5 0.7
H072 A:7MT206 4.1 12.7 0.7
H042 A:7MT206 4.1 13.7 0.7
H052 A:7MT206 4.1 14.1 0.7
H041 A:7MT206 4.2 15.5 0.7
H082 A:7MT206 4.3 15.1 0.7
H211 A:7MT205 4.3 21.2 0.8
H302 A:7MT206 4.4 17.9 0.7
H011 A:7MT206 4.4 10.8 0.7
O25 A:7MT206 4.5 25.4 0.7
H291 A:7MT206 4.5 22.1 0.7
H032 A:7MT206 4.5 18.1 0.7
C22 A:7MT205 4.6 17.5 0.8
O27 A:7MT206 4.6 25.7 0.7
H301 A:7MT205 4.6 21.0 0.8
C21 A:7MT206 4.7 19.1 0.7
O A:HOH463 4.7 36.4 1.0
C15 A:7MT206 4.8 19.7 0.7
C13 A:7MT206 4.8 18.4 0.7
O A:HOH403 4.8 38.7 1.0
C19 A:7MT206 4.8 21.2 0.7
C21 A:7MT205 4.8 21.1 0.8

Reference:

S.Engilberge, F.Riobe, T.Wagner, S.Di Pietro, C.Breyton, B.Franzetti, S.Shima, E.Girard, E.Dumont, O.Maury. Unveiling the Binding Modes of the Crystallophore, A Terbium-Based Nucleating and Phasing Molecular Agent For Protein Crystallography. Chemistry V. 24 9739 2018.
ISSN: ISSN 1521-3765
PubMed: 29806881
DOI: 10.1002/CHEM.201802172
Page generated: Wed Dec 16 02:27:05 2020

Last articles

Zn in 7RE3
Zn in 7RDX
Zn in 7RDZ
Zn in 7RWM
Zn in 7PGU
Zn in 7PGR
Zn in 7PGT
Zn in 7PGS
Zn in 7SQE
Zn in 7RWK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy