Atomistry » Europium » PDB 1bub-6fkw » 3tf6
Atomistry »
  Europium »
    PDB 1bub-6fkw »
      3tf6 »

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

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy