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Ytterbium in PDB 4ms6: Human Leukotriene A4 Hydrolase in Complex with Pro-Gly-Pro Analogue

Enzymatic activity of Human Leukotriene A4 Hydrolase in Complex with Pro-Gly-Pro Analogue

All present enzymatic activity of Human Leukotriene A4 Hydrolase in Complex with Pro-Gly-Pro Analogue:
3.3.2.6;

Protein crystallography data

The structure of Human Leukotriene A4 Hydrolase in Complex with Pro-Gly-Pro Analogue, PDB code: 4ms6 was solved by A.Stsiapanava, A.Rinaldo-Matthis, J.Z.Haeggstrom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.90 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.766, 87.483, 98.964, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.5

Other elements in 4ms6:

The structure of Human Leukotriene A4 Hydrolase in Complex with Pro-Gly-Pro Analogue also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Human Leukotriene A4 Hydrolase in Complex with Pro-Gly-Pro Analogue (pdb code 4ms6). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 5 binding sites of Ytterbium where determined in the Human Leukotriene A4 Hydrolase in Complex with Pro-Gly-Pro Analogue, PDB code: 4ms6:
Jump to Ytterbium binding site number: 1; 2; 3; 4; 5;

Ytterbium binding site 1 out of 5 in 4ms6

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Ytterbium binding site 1 out of 5 in the Human Leukotriene A4 Hydrolase in Complex with Pro-Gly-Pro Analogue


Mono view


Stereo pair view

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

b:18.8
occ:0.50
 O A:HOH929 1.8 2.0 0.5
OD2 A:ASP47 2.6 21.5 1.0
OD1 A:ASP47 2.7 20.7 1.0
OXT A:ACY708 2.7 12.6 0.5
O A:ACY708 2.8 15.7 0.5
CG A:ASP47 3.0 21.8 1.0
C A:ACY708 3.1 15.2 0.5
OG A:SER95 4.4 28.2 1.0
CB A:ASP47 4.5 21.2 1.0
O A:HOH886 4.5 21.2 1.0
O A:HOH852 4.6 20.1 1.0
CH3 A:ACY708 4.6 14.7 0.5
N A:ASN48 4.7 19.3 1.0

Ytterbium binding site 2 out of 5 in 4ms6

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Ytterbium binding site 2 out of 5 in the Human Leukotriene A4 Hydrolase in Complex with Pro-Gly-Pro Analogue


Mono view


Stereo pair view

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

b:16.4
occ:0.50
 OXT A:ACY709 1.8 14.3 0.5
O A:ACY709 2.2 17.7 0.5
OD2 A:ASP481 2.2 22.3 1.0
C A:ACY709 2.3 15.9 0.5
OD1 A:ASP481 2.3 24.5 1.0
O A:HOH861 2.5 16.5 1.0
O A:HOH896 2.5 15.1 1.0
CG A:ASP481 2.6 26.3 1.0
CH3 A:ACY709 3.8 16.7 0.5
CB A:ASP481 4.2 20.7 1.0
OD2 A:ASP482 4.6 17.4 1.0
OD1 A:ASP482 4.6 20.6 1.0
CG A:LYS479 4.7 21.2 1.0
CB A:LYS479 4.8 19.1 1.0
CG A:ASP482 4.9 21.8 1.0

Ytterbium binding site 3 out of 5 in 4ms6

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Ytterbium binding site 3 out of 5 in the Human Leukotriene A4 Hydrolase in Complex with Pro-Gly-Pro Analogue


Mono view


Stereo pair view

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

b:84.0
occ:0.50
 O A:HOH1130 2.6 37.3 1.0
O A:HOH981 2.8 37.7 1.0
OE1 A:GLU46 4.4 40.4 1.0
OE2 A:GLU46 4.7 42.6 1.0
CD A:GLU46 5.0 36.5 1.0

Ytterbium binding site 4 out of 5 in 4ms6

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Ytterbium binding site 4 out of 5 in the Human Leukotriene A4 Hydrolase in Complex with Pro-Gly-Pro Analogue


Mono view


Stereo pair view

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

b:55.1
occ:0.50
 O A:HOH1221 2.3 19.5 0.5
OE2 A:GLU70 2.5 42.3 1.0
OE1 A:GLU70 2.7 48.7 1.0
CD A:GLU70 2.8 41.0 1.0
CG A:GLU70 4.1 36.8 1.0
O A:HOH1154 4.9 21.0 0.6
CB A:GLU70 5.0 29.7 1.0

Ytterbium binding site 5 out of 5 in 4ms6

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Ytterbium binding site 5 out of 5 in the Human Leukotriene A4 Hydrolase in Complex with Pro-Gly-Pro Analogue


Mono view


Stereo pair view

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

b:57.3
occ:0.50
 O A:HOH1273 2.6 31.3 1.0
OD1 A:ASP426 3.6 39.6 1.0
CG A:ASP426 4.0 35.8 1.0
CB A:ASP426 4.2 27.6 1.0
CA A:ASP426 4.3 25.4 1.0
O A:HOH1198 4.4 33.1 1.0
O A:ASP426 4.6 22.7 1.0
CB A:TYR429 4.7 25.1 1.0
OD2 A:ASP426 4.8 41.2 1.0
C A:ASP426 5.0 25.6 1.0

Reference:

A.Stsiapanava, U.Olsson, M.Wan, T.Kleinschmidt, D.Rutishauser, R.A.Zubarev, B.Samuelsson, A.Rinaldo-Matthis, J.Z.Haeggstrom. Binding of Pro-Gly-Pro at the Active Site of Leukotriene A4 Hydrolase/Aminopeptidase and Development of An Epoxide Hydrolase Selective Inhibitor. Proc.Natl.Acad.Sci.Usa V. 111 4227 2014.
ISSN: ISSN 0027-8424
PubMed: 24591641
DOI: 10.1073/PNAS.1402136111
Page generated: Sat Oct 12 21:11:54 2024

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