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Ytterbium in PDB 4dpr: Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril

Enzymatic activity of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril

All present enzymatic activity of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril:
3.3.2.6;

Protein crystallography data

The structure of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril, PDB code: 4dpr was solved by A.Stsiapanava, J.Z.Haeggstrom, A.Rinaldo-Matthis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.69 / 2.02
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.552, 87.398, 99.592, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 22.8

Other elements in 4dpr:

The structure of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril (pdb code 4dpr). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 5 binding sites of Ytterbium where determined in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril, PDB code: 4dpr:
Jump to Ytterbium binding site number: 1; 2; 3; 4; 5;

Ytterbium binding site 1 out of 5 in 4dpr

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Ytterbium binding site 1 out of 5 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb703

b:9.6
occ:0.50
 O A:ACY708 2.0 5.2 0.5
O A:ACY708 2.3 13.1 0.5
OD1 A:ASP47 2.5 12.0 1.0
O A:HOH1213 2.6 2.0 0.5
C A:ACY708 2.6 7.2 0.5
OXT A:ACY708 2.6 8.1 0.5
OD2 A:ASP47 2.6 14.3 1.0
OXT A:ACY708 2.9 16.4 0.5
C A:ACY708 2.9 14.2 0.5
CG A:ASP47 2.9 14.1 1.0
CH3 A:ACY708 4.1 6.5 0.5
N A:ASN48 4.3 14.0 1.0
CH3 A:ACY708 4.4 13.5 0.5
OG A:SER95 4.4 21.8 1.0
CB A:ASP47 4.5 14.4 1.0
CB A:ASN48 4.5 13.8 1.0
CA A:ASN48 4.7 13.9 1.0
O A:HOH924 4.8 15.0 1.0
C A:ASP47 5.0 15.3 1.0

Ytterbium binding site 2 out of 5 in 4dpr

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Ytterbium binding site 2 out of 5 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb704

b:10.5
occ:0.50
 O A:HOH941 1.5 2.0 0.5
O A:HOH1214 1.8 2.0 0.5
O A:HOH825 2.3 2.0 0.5
OD1 A:ASP481 2.7 12.7 1.0
OD2 A:ASP481 2.7 9.1 1.0
CG A:ASP481 3.1 10.7 1.0
OD1 A:ASP482 4.4 13.3 1.0
OD2 A:ASP482 4.5 12.4 1.0
CB A:ASP481 4.6 11.4 1.0
O A:HOH942 4.8 4.6 1.0
CG A:ASP482 4.8 13.5 1.0
CB A:LYS479 5.0 11.9 1.0

Ytterbium binding site 3 out of 5 in 4dpr

Go back to Ytterbium Binding Sites List in 4dpr
Ytterbium binding site 3 out of 5 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb705

b:62.3
occ:0.65
 OD1 A:ASP175 2.9 28.7 1.0
OD2 A:ASP175 3.2 37.5 1.0
CG A:ASP175 3.3 28.1 1.0
O A:HOH959 3.4 26.9 1.0
O A:ASP175 4.5 21.7 1.0
CB A:ASP175 4.6 22.9 1.0
CA A:ASP175 4.7 22.1 1.0
C A:ASP175 4.9 21.9 1.0

Ytterbium binding site 4 out of 5 in 4dpr

Go back to Ytterbium Binding Sites List in 4dpr
Ytterbium binding site 4 out of 5 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 4 of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb706

b:84.9
occ:0.55
 OE2 A:GLU70 2.9 32.4 1.0
OE1 A:GLU70 3.1 30.0 1.0
O A:HOH930 3.2 28.8 1.0
CD A:GLU70 3.3 27.9 1.0
CG A:GLU70 4.8 27.3 1.0

Ytterbium binding site 5 out of 5 in 4dpr

Go back to Ytterbium Binding Sites List in 4dpr
Ytterbium binding site 5 out of 5 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 5 of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor Captopril within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb707

b:84.2
occ:0.65
 O A:HOH1155 2.8 33.2 1.0
OD1 A:ASP426 3.6 27.4 1.0
O A:HOH971 3.6 32.2 1.0
CG A:ASP426 4.3 24.1 1.0
CA A:ASP426 4.4 15.0 1.0
CB A:TYR429 4.6 14.5 1.0
CB A:ASP426 4.6 16.5 1.0
O A:ASP426 4.7 15.5 1.0

Reference:

A.Stsiapanava, B.Samuelsson, J.Z.Haeggstrom. Capturing LTA4HYDROLASE in Action: Insights to the Chemistry and Dynamics of Chemotactic LTB4SYNTHESIS. Proc. Natl. Acad. Sci. V. 114 9689 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28827365
DOI: 10.1073/PNAS.1710850114
Page generated: Tue Aug 19 18:51:50 2025

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