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Europium in PDB 3tf6: Crystal Structure of Neutrophil Gelatinase-Associated Lipocalin (C87S Mutant) in Complex with Europium and the Siderophore Analog Tren(Cam)(1,2-Hopo)2

Protein crystallography data

The structure of Crystal Structure of Neutrophil Gelatinase-Associated Lipocalin (C87S Mutant) in Complex with Europium and the Siderophore Analog Tren(Cam)(1,2-Hopo)2, PDB code: 3tf6 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.95 / 2.35
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 114.090, 114.090, 118.190, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.6

Other elements in 3tf6:

The structure of Crystal Structure of Neutrophil Gelatinase-Associated Lipocalin (C87S Mutant) in Complex with Europium and the Siderophore Analog Tren(Cam)(1,2-Hopo)2 also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Europium Binding Sites:

The binding sites of Europium atom in the Crystal Structure of Neutrophil Gelatinase-Associated Lipocalin (C87S Mutant) in Complex with Europium and the Siderophore Analog Tren(Cam)(1,2-Hopo)2 (pdb code 3tf6). This binding sites where shown within 5.0 Angstroms radius around Europium atom.
In total 3 binding sites of Europium where determined in the Crystal Structure of Neutrophil Gelatinase-Associated Lipocalin (C87S Mutant) in Complex with Europium and the Siderophore Analog Tren(Cam)(1,2-Hopo)2, PDB code: 3tf6:
Jump to Europium binding site number: 1; 2; 3;

Europium binding site 1 out of 3 in 3tf6

Go back to Europium Binding Sites List in 3tf6
Europium binding site 1 out of 3 in the Crystal Structure of Neutrophil Gelatinase-Associated Lipocalin (C87S Mutant) in Complex with Europium and the Siderophore Analog Tren(Cam)(1,2-Hopo)2


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 1 of Crystal Structure of Neutrophil Gelatinase-Associated Lipocalin (C87S Mutant) in Complex with Europium and the Siderophore Analog Tren(Cam)(1,2-Hopo)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Eu206

b:65.3
occ:0.50
O6 A:DBH216 2.3 52.1 1.0
O3 A:DBH216 2.7 67.6 1.0
C6 A:DBH216 3.2 53.6 1.0
C3 A:DBH216 3.4 53.5 1.0
NZ A:LYS125 3.8 36.5 1.0
NZ A:LYS134 4.0 38.3 1.0
C9 A:DBH216 4.5 48.0 1.0
NE1 A:TRP79 4.7 65.5 1.0
C18 A:DBH216 4.7 50.6 1.0
OH A:TYR106 4.9 26.5 1.0
CE A:LYS125 4.9 33.2 1.0
CE A:LYS134 5.0 35.3 1.0

Europium binding site 2 out of 3 in 3tf6

Go back to Europium Binding Sites List in 3tf6
Europium binding site 2 out of 3 in the Crystal Structure of Neutrophil Gelatinase-Associated Lipocalin (C87S Mutant) in Complex with Europium and the Siderophore Analog Tren(Cam)(1,2-Hopo)2


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 2 of Crystal Structure of Neutrophil Gelatinase-Associated Lipocalin (C87S Mutant) in Complex with Europium and the Siderophore Analog Tren(Cam)(1,2-Hopo)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Eu206

b:78.6
occ:0.50
O3 B:DBH216 2.1 79.9 1.0
O6 B:DBH216 3.0 53.9 1.0
C3 B:DBH216 3.1 68.3 1.0
C6 B:DBH216 3.5 65.3 1.0
NZ B:LYS125 3.6 44.4 1.0
C18 B:DBH216 4.3 66.7 1.0
NZ B:LYS134 4.6 49.8 1.0
C21 B:DBH216 4.7 70.2 1.0
C9 B:DBH216 4.8 62.5 1.0
CE B:LYS125 4.9 42.2 1.0

Europium binding site 3 out of 3 in 3tf6

Go back to Europium Binding Sites List in 3tf6
Europium binding site 3 out of 3 in the Crystal Structure of Neutrophil Gelatinase-Associated Lipocalin (C87S Mutant) in Complex with Europium and the Siderophore Analog Tren(Cam)(1,2-Hopo)2


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 3 of Crystal Structure of Neutrophil Gelatinase-Associated Lipocalin (C87S Mutant) in Complex with Europium and the Siderophore Analog Tren(Cam)(1,2-Hopo)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Eu206

b:83.5
occ:0.50
O6 C:DBH216 2.0 52.1 1.0
O3 C:DBH216 2.8 68.3 1.0
C6 C:DBH216 3.0 52.9 1.0
C3 C:DBH216 3.3 52.2 1.0
NZ C:LYS125 3.8 35.6 1.0
NZ C:LYS134 3.9 32.9 1.0
OH C:TYR106 4.3 28.5 1.0
C9 C:DBH216 4.3 46.4 1.0
NE1 C:TRP79 4.3 49.0 1.0
CE2 C:TYR106 4.6 25.6 1.0
C18 C:DBH216 4.7 49.0 1.0
CZ2 C:TRP79 4.8 51.4 1.0
CE C:LYS125 4.8 33.4 1.0
CE C:LYS134 4.8 29.4 1.0
CE2 C:TRP79 4.9 51.2 1.0
CZ C:TYR106 5.0 26.1 1.0
CD C:LYS125 5.0 30.8 1.0

Reference:

M.C.Clifton, P.B.Rupert, T.M.Hoette, K.N.Raymond, R.J.Abergel, R.K.Strong. Parsing the Functional Specificity of Siderocalin / Lipocalin 2 / Ngal For Siderophores and Related Small-Molecule Ligands To Be Published V. 7.
Page generated: Sun Dec 13 11:27:50 2020

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