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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: Fri Oct 11 08:26:27 2024

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