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Terbium in PDB 6f2i: Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4

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

All present enzymatic activity of Crystal Structure of Hen Egg-White Lysozyme Co-Crystallized in Presence of 100 Mm Tb-XO4:
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, PDB code: 6f2i 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) 39.07 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.149, 78.149, 37.960, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.3

Other elements in 6f2i:

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

Chlorine (Cl) 4 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 (pdb code 6f2i). 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, PDB code: 6f2i:
Jump to Terbium binding site number: 1; 2; 3;

Terbium binding site 1 out of 3 in 6f2i

Go back to Terbium Binding Sites List in 6f2i
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb201

b:16.4
occ:0.20
 H011 A:7MT203 1.1 12.7 0.7
C01 A:7MT203 1.3 12.8 0.7
N02 A:7MT203 1.9 15.4 0.7
O25 A:7MT202 1.9 21.2 0.8
C03 A:7MT203 2.0 20.8 0.7
N09 A:7MT203 2.2 23.0 0.7
H012 A:7MT203 2.3 11.3 0.7
H301 A:7MT203 2.5 19.1 0.7
TB A:7MT203 2.5 17.5 0.7
H031 A:7MT203 2.6 20.3 0.7
C30 A:7MT203 2.6 18.1 0.7
H032 A:7MT203 2.9 20.7 0.7
C24 A:7MT202 3.0 22.1 0.8
H292 A:7MT203 3.0 25.7 0.7
C29 A:7MT203 3.0 25.7 0.7
N23 A:7MT203 3.2 26.0 0.7
C04 A:7MT203 3.2 16.6 0.7
H211 A:7MT202 3.2 23.6 0.8
O A:HOH461 3.4 38.0 1.0
H302 A:7MT203 3.4 18.4 0.7
C11 A:7MT203 3.4 24.0 0.7
H041 A:7MT203 3.5 16.7 0.7
O A:HOH377 3.5 30.7 1.0
C08 A:7MT203 3.6 18.9 0.7
N06 A:7MT203 3.6 18.4 0.7
C10 A:7MT203 3.7 20.3 0.7
N17 A:7MT203 3.7 22.6 0.7
O26 A:7MT202 3.8 20.9 0.8
C22 A:7MT202 3.9 20.2 0.8
H042 A:7MT203 3.9 17.8 0.7
C21 A:7MT202 3.9 23.0 0.8
C05 A:7MT203 3.9 15.6 0.7
H291 A:7MT203 4.0 25.8 0.7
C07 A:7MT203 4.1 17.5 0.7
H081 A:7MT203 4.2 19.2 0.7
O26 A:7MT203 4.2 29.3 0.7
C22 A:7MT203 4.2 27.2 0.7
H072 A:7MT203 4.2 19.2 0.7
H082 A:7MT203 4.3 19.0 0.7
H061 A:7MT203 4.4 18.8 0.7
H051 A:7MT203 4.4 15.3 0.7
C24 A:7MT203 4.7 29.3 0.7
C19 A:7MT203 4.7 23.4 0.7
H052 A:7MT203 4.9 15.0 0.7

Terbium binding site 2 out of 3 in 6f2i

Go back to Terbium Binding Sites List in 6f2i
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb202

b:18.9
occ:0.85
 TB A:7MT202 0.0 18.9 0.8
H061 A:7MT202 1.7 20.1 0.8
OD2 A:ASP101 2.3 23.7 1.0
N23 A:7MT202 2.4 24.9 0.8
O26 A:7MT202 2.5 20.9 0.8
OD1 A:ASP101 2.5 21.9 1.0
N02 A:7MT202 2.6 24.7 0.8
N09 A:7MT202 2.7 25.6 0.8
N17 A:7MT202 2.7 23.6 0.8
N06 A:7MT202 2.7 23.0 0.8
O28 A:7MT202 2.7 28.4 0.8
CG A:ASP101 2.8 24.0 1.0
H012 A:7MT202 3.2 25.4 0.8
C01 A:7MT202 3.2 25.9 0.8
C22 A:7MT202 3.3 20.2 0.8
C24 A:7MT202 3.3 22.1 0.8
C05 A:7MT202 3.3 25.4 0.8
C11 A:7MT202 3.3 25.7 0.8
C30 A:7MT202 3.3 24.7 0.8
H301 A:7MT202 3.4 25.3 0.8
H051 A:7MT202 3.4 26.2 0.8
C08 A:7MT202 3.4 24.0 0.8
C29 A:7MT202 3.4 25.8 0.8
C04 A:7MT202 3.4 24.1 0.8
C10 A:7MT202 3.5 23.4 0.8
C03 A:7MT202 3.5 28.1 0.8
H081 A:7MT202 3.5 22.8 0.8
C07 A:7MT202 3.6 23.3 0.8
C18 A:7MT202 3.6 28.3 0.8
C16 A:7MT202 3.6 27.3 0.8
H291 A:7MT202 3.7 25.6 0.8
H042 A:7MT202 4.1 24.1 0.8
H031 A:7MT202 4.1 27.5 0.8
H072 A:7MT202 4.2 23.6 0.8
H011 A:7MT202 4.2 27.2 0.8
H041 A:7MT202 4.3 24.3 0.8
H032 A:7MT202 4.3 28.2 0.8
CB A:ASP101 4.3 18.2 1.0
H052 A:7MT202 4.3 25.6 0.8
H302 A:7MT202 4.4 25.0 0.8
H071 A:7MT202 4.4 23.6 0.8
H292 A:7MT202 4.4 26.9 0.8
H082 A:7MT202 4.4 24.3 0.8
O25 A:7MT202 4.5 21.2 0.8
C21 A:7MT202 4.6 23.0 0.8
C19 A:7MT202 4.6 27.4 0.8
HH2 A:TRP63 4.6 15.9 1.0
H A:GLY102 4.7 22.1 1.0
HB2 A:ASP101 4.7 18.8 1.0
O A:HOH377 4.7 30.7 1.0
HB3 A:ASP101 4.7 18.1 1.0
H301 A:7MT203 4.8 19.1 0.7
O27 A:7MT202 4.8 29.1 0.8
C13 A:7MT202 4.8 23.2 0.8
HZ2 A:TRP63 4.9 16.9 1.0
C15 A:7MT202 4.9 26.6 0.8

Terbium binding site 3 out of 3 in 6f2i

Go back to Terbium Binding Sites List in 6f2i
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb203

b:17.5
occ:0.70
 TB A:7MT203 0.0 17.5 0.7
O25 A:7MT202 2.3 21.2 0.8
N06 A:7MT203 2.4 18.4 0.7
O26 A:7MT203 2.4 29.3 0.7
TB A:TB201 2.5 16.4 0.2
N17 A:7MT203 2.6 22.6 0.7
H061 A:7MT203 2.6 18.8 0.7
O28 A:7MT203 2.6 25.1 0.7
N23 A:7MT203 2.6 26.0 0.7
N02 A:7MT203 2.7 15.4 0.7
N09 A:7MT203 2.8 23.0 0.7
C05 A:7MT203 3.2 15.6 0.7
C24 A:7MT203 3.2 29.3 0.7
H051 A:7MT203 3.3 15.3 0.7
C08 A:7MT203 3.3 18.9 0.7
C01 A:7MT203 3.4 12.8 0.7
C22 A:7MT203 3.4 27.2 0.7
H081 A:7MT203 3.4 19.2 0.7
C07 A:7MT203 3.4 17.5 0.7
C18 A:7MT203 3.4 27.3 0.7
C24 A:7MT202 3.4 22.1 0.8
C16 A:7MT203 3.4 22.9 0.7
C10 A:7MT203 3.5 20.3 0.7
C04 A:7MT203 3.5 16.6 0.7
C30 A:7MT203 3.5 18.1 0.7
C03 A:7MT203 3.5 20.8 0.7
H011 A:7MT203 3.6 12.7 0.7
C11 A:7MT203 3.6 24.0 0.7
H301 A:7MT203 3.7 19.1 0.7
C29 A:7MT203 3.8 25.7 0.7
O26 A:7MT202 4.0 20.9 0.8
H032 A:7MT203 4.1 20.7 0.7
H072 A:7MT203 4.1 19.2 0.7
H071 A:7MT203 4.1 16.8 0.7
H041 A:7MT203 4.1 16.7 0.7
H052 A:7MT203 4.2 15.0 0.7
H211 A:7MT202 4.2 23.6 0.8
H042 A:7MT203 4.3 17.8 0.7
H012 A:7MT203 4.4 11.3 0.7
H082 A:7MT203 4.4 19.0 0.7
H292 A:7MT203 4.4 25.7 0.7
O25 A:7MT203 4.4 31.1 0.7
H031 A:7MT203 4.5 20.3 0.7
H301 A:7MT202 4.5 25.3 0.8
H302 A:7MT203 4.5 18.4 0.7
C22 A:7MT202 4.6 20.2 0.8
H291 A:7MT203 4.6 25.8 0.7
O27 A:7MT203 4.6 29.6 0.7
O A:HOH439 4.7 44.0 1.0
C21 A:7MT203 4.7 24.8 0.7
C15 A:7MT203 4.8 23.2 0.7
C13 A:7MT203 4.8 20.3 0.7
C21 A:7MT202 4.8 23.0 0.8
C19 A:7MT203 4.9 23.4 0.7

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 08:25:32 2024

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