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Ytterbium in PDB 3u9w: Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A

Enzymatic activity of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A

All present enzymatic activity of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A:
3.3.2.6;

Protein crystallography data

The structure of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A, PDB code: 3u9w was solved by D.Niegowski, M.Thunnissen, F.Tholander, A.Rinaldo-Matthis, A.Muroya, J.Z.Haeggstrom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.37 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.078, 86.799, 99.145, 90.00, 90.00, 90.00
R / Rfree (%) 13.4 / 16.1

Other elements in 3u9w:

The structure of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
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 SC57461A (pdb code 3u9w). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 8 binding sites of Ytterbium where determined in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A, PDB code: 3u9w:
Jump to Ytterbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Ytterbium binding site 1 out of 8 in 3u9w

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Ytterbium binding site 1 out of 8 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A


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 SC57461A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb2002

b:8.9
occ:1.00
 O A:HOH8062 2.2 11.2 1.0
OD1 A:ASP1481 2.3 8.3 1.0
O A:HOH8118 2.3 12.4 1.0
O A:HOH8066 2.3 9.1 1.0
O A:ACT1 2.4 8.5 1.0
OD2 A:ASP1481 2.5 7.0 1.0
OXT A:ACT1 2.5 14.0 1.0
CG A:ASP1481 2.8 7.2 1.0
C A:ACT1 2.8 11.9 1.0
CB A:ASP1481 4.3 7.2 1.0
CH3 A:ACT1 4.4 12.3 1.0
OD2 A:ASP1482 4.4 9.7 1.0
OD1 A:ASP1482 4.4 10.7 1.0
O A:HOH8740 4.4 47.4 1.0
O A:HOH8617 4.5 42.3 1.0
CG A:ASP1482 4.7 9.0 1.0
CB A:LYS1479 4.8 8.3 1.0

Ytterbium binding site 2 out of 8 in 3u9w

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Ytterbium binding site 2 out of 8 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A


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 SC57461A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb1611

b:14.9
occ:0.20
 O A:HOH8914 2.1 38.7 1.0
O A:HOH8913 2.2 54.7 1.0
OD2 A:ASP1426 2.3 17.6 0.5
O A:HOH8915 2.5 49.8 1.0
O A:HOH8920 2.7 58.1 1.0
CG A:ASP1426 3.3 13.0 0.5
OD1 A:ASP1426 3.4 13.3 0.5
YB A:YB2 3.6 12.6 0.2
OD2 A:ASP1426 4.1 22.0 0.5
YB A:YB7 4.2 21.7 0.2
CG A:ASP1426 4.4 16.1 0.5
O A:HOH8929 4.5 38.1 1.0
CB A:ASP1426 4.5 13.5 0.5
CB A:ASP1426 4.7 11.8 0.5
O A:HOH8648 4.8 38.6 1.0
O A:HOH8908 4.9 23.7 1.0

Ytterbium binding site 3 out of 8 in 3u9w

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Ytterbium binding site 3 out of 8 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A


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 SC57461A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb2

b:12.6
occ:0.25
 YB A:YB7 1.3 21.7 0.2
O A:HOH8908 2.1 23.7 1.0
OD1 A:ASP1426 2.3 13.3 0.5
O A:HOH8929 2.4 38.1 1.0
O A:HOH8914 2.5 38.7 1.0
O A:HOH8915 2.5 49.8 1.0
CG A:ASP1426 3.4 13.0 0.5
YB A:YB1611 3.6 14.9 0.2
OD2 A:ASP1426 3.8 17.6 0.5
O A:HOH8920 3.9 58.1 1.0
O A:ASP1426 4.4 12.6 1.0
CB A:ASP1426 4.6 13.5 0.5
CB A:ASP1426 4.6 11.8 0.5
CG A:ASP1426 4.7 16.1 0.5
OD1 A:ASP1426 4.8 19.2 0.5
CA A:ASP1426 4.8 12.5 0.5
CA A:ASP1426 4.8 11.6 0.5
O A:HOH8913 4.9 54.7 1.0

Ytterbium binding site 4 out of 8 in 3u9w

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Ytterbium binding site 4 out of 8 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A


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 SC57461A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb3

b:33.2
occ:0.15
 O A:HOH8925 1.9 4.5 0.2
O A:HOH8928 2.3 18.2 0.2
OD1 A:ASP1175 2.4 26.9 1.0
O A:HOH8927 2.7 50.0 1.0
CG A:ASP1175 3.6 21.7 1.0
O A:HOH8691 3.8 39.6 1.0
O A:HOH8916 3.9 64.7 1.0
OD2 A:ASP1175 4.3 30.4 1.0
CB A:ASP1175 4.7 14.6 1.0
CA A:ASP1175 4.7 12.4 1.0
O A:ASP1175 4.8 18.2 1.0
CD1 A:ILE1192 5.0 14.6 0.5

Ytterbium binding site 5 out of 8 in 3u9w

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Ytterbium binding site 5 out of 8 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A


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 SC57461A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb4

b:31.8
occ:0.20
 OE2 A:GLU1182 1.9 17.8 0.5
CD A:GLU1182 2.3 18.1 0.5
OE1 A:GLU1182 2.4 22.7 0.5
C4 A:IMD186 2.4 14.3 0.6
N3 A:IMD186 2.6 17.4 0.6
O A:HOH8226 2.6 21.2 1.0
O A:HOH8421 2.7 29.9 1.0
NH2 A:ARG1024 2.9 27.4 1.0
O A:HOH8505 3.4 32.8 1.0
CZ A:ARG1024 3.5 23.4 1.0
NH1 A:ARG1024 3.5 23.3 1.0
CG A:GLU1182 3.6 15.9 0.5
O A:HOH8624 3.7 28.2 1.0
C5 A:IMD186 3.8 17.7 0.6
C2 A:IMD186 3.8 15.9 0.6
CB A:GLU1182 4.1 14.6 0.5
CG A:GLU1182 4.2 18.9 0.5
CB A:GLU1182 4.4 15.0 0.5
OD1 A:ASP1180 4.4 13.3 1.0
N1 A:IMD186 4.4 14.7 0.6
OD2 A:ASP1180 4.5 13.2 1.0
NE A:ARG1024 4.6 24.3 1.0
O A:HOH8380 4.7 24.3 1.0
O A:HOH8763 4.7 56.5 1.0
O A:HOH8243 4.7 21.4 1.0
CG A:ASP1180 4.9 11.2 1.0

Ytterbium binding site 6 out of 8 in 3u9w

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Ytterbium binding site 6 out of 8 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 6 of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb5

b:37.8
occ:0.20
 OE2 A:GLU1070 2.3 24.1 1.0
O A:HOH8727 2.4 53.1 1.0
CD A:GLU1070 3.0 21.4 1.0
OE1 A:GLU1070 3.0 29.3 1.0
O A:HOH8700 4.2 51.0 1.0
CG A:GLU1070 4.4 16.8 1.0
O A:HOH8562 4.6 40.6 1.0

Ytterbium binding site 7 out of 8 in 3u9w

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Ytterbium binding site 7 out of 8 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 7 of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb6

b:40.1
occ:0.20
 OE2 A:GLU1590 2.8 25.7 0.5
OE1 A:GLU1590 2.9 27.4 0.5
CD A:GLU1590 3.2 23.4 0.5
O A:HOH8599 4.2 44.4 1.0
CE1 A:HIS1591 4.4 16.3 1.0
CG A:GLU1590 4.8 19.1 0.5

Ytterbium binding site 8 out of 8 in 3u9w

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Ytterbium binding site 8 out of 8 in the Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 8 of Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb7

b:21.7
occ:0.20
 YB A:YB2 1.3 12.6 0.2
OD1 A:ASP1426 2.1 13.3 0.5
O A:HOH8908 2.4 23.7 1.0
O A:HOH8914 2.7 38.7 1.0
CG A:ASP1426 3.3 13.0 0.5
O A:HOH8929 3.3 38.1 1.0
O A:HOH8915 3.6 49.8 1.0
O A:HOH8919 3.9 47.0 1.0
OD1 A:ASP1426 3.9 19.2 0.5
OD2 A:ASP1426 3.9 17.6 0.5
O A:HOH8912 4.1 47.0 1.0
CG A:ASP1426 4.1 16.1 0.5
YB A:YB1611 4.2 14.9 0.2
CB A:ASP1426 4.3 13.5 0.5
CB A:ASP1426 4.3 11.8 0.5
CA A:ASP1426 4.3 12.5 0.5
CA A:ASP1426 4.3 11.6 0.5
O A:ASP1426 4.4 12.6 1.0
C A:ASP1426 4.8 11.7 1.0
OD2 A:ASP1426 4.8 22.0 0.5
CB A:TYR1429 4.9 14.8 1.0

Reference:

U.Olsson, D.Niegowski, A.Stsiapanava, M.Thunnissen, J.Z.Haeggstrom, A.Rinaldo-Matthis. Structure of Human Leukotriene A4 Hydrolase in Complex with Inhibitor SC57461A To Be Published.
Page generated: Wed Dec 16 02:41:56 2020

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