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Ytterbium in PDB 5fwq: Apo Structure of Human Leukotriene A4 Hydrolase

Enzymatic activity of Apo Structure of Human Leukotriene A4 Hydrolase

All present enzymatic activity of Apo Structure of Human Leukotriene A4 Hydrolase:
3.3.2.6;

Protein crystallography data

The structure of Apo Structure of Human Leukotriene A4 Hydrolase, PDB code: 5fwq was solved by S.K.Wittmann, L.Kalinowsky, J.Kramer, R.Bloecher, D.Steinhilber, D.Pogoryelov, E.Proschak, J.Heering, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.29 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.337, 86.980, 96.310, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.3

Other elements in 5fwq:

The structure of Apo Structure of Human Leukotriene A4 Hydrolase also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Apo Structure of Human Leukotriene A4 Hydrolase (pdb code 5fwq). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 6 binding sites of Ytterbium where determined in the Apo Structure of Human Leukotriene A4 Hydrolase, PDB code: 5fwq:
Jump to Ytterbium binding site number: 1; 2; 3; 4; 5; 6;

Ytterbium binding site 1 out of 6 in 5fwq

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Ytterbium binding site 1 out of 6 in the Apo Structure of Human Leukotriene A4 Hydrolase


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Apo Structure of Human Leukotriene A4 Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb1613

b:22.8
occ:0.50
 O A:HOH2406 2.5 16.0 1.0
O A:HOH2331 2.6 13.2 1.0
O A:HOH2330 2.7 16.7 1.0
O A:HOH2407 2.8 18.7 1.0
OD1 A:ASP481 2.8 24.6 1.0
OD2 A:ASP481 2.8 23.0 1.0
CG A:ASP481 3.2 22.3 1.0
OD1 A:ASP482 4.4 19.2 1.0
O A:HOH2324 4.4 31.8 1.0
OD2 A:ASP482 4.5 21.1 1.0
CB A:ASP481 4.7 19.2 1.0
CB A:LYS479 4.8 18.5 1.0
O A:HOH2325 4.8 18.1 1.0
CG A:LYS479 4.8 23.4 1.0
CG A:ASP482 4.8 19.4 1.0

Ytterbium binding site 2 out of 6 in 5fwq

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Ytterbium binding site 2 out of 6 in the Apo Structure of Human Leukotriene A4 Hydrolase


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Apo Structure of Human Leukotriene A4 Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb1614

b:96.5
occ:0.50
 OE1 A:GLU121 2.2 69.4 1.0
CD A:GLU121 3.4 56.5 1.0
OE2 A:GLU121 3.9 59.7 1.0
CG A:GLU121 4.6 44.0 1.0

Ytterbium binding site 3 out of 6 in 5fwq

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Ytterbium binding site 3 out of 6 in the Apo Structure of Human Leukotriene A4 Hydrolase


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Apo Structure of Human Leukotriene A4 Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb1615

b:26.2
occ:0.50
 O A:HOH2294 2.4 30.8 1.0
OD1 A:ASP426 2.5 33.2 1.0
OD1 A:ASP422 2.6 22.9 1.0
OD2 A:ASP422 2.6 32.9 1.0
OD2 A:ASP426 2.6 28.0 1.0
CG A:ASP426 2.9 24.3 1.0
CG A:ASP422 3.0 21.9 1.0
CB A:ASP426 4.4 24.7 1.0
CB A:ASP422 4.4 22.5 1.0
O A:ASP422 4.5 22.3 1.0
C A:ASP422 5.0 19.8 1.0

Ytterbium binding site 4 out of 6 in 5fwq

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Ytterbium binding site 4 out of 6 in the Apo Structure of Human Leukotriene A4 Hydrolase


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 4 of Apo Structure of Human Leukotriene A4 Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb1616

b:31.6
occ:0.50
 O A:HOH2036 2.6 18.3 1.0
OD2 A:ASP47 2.7 17.5 1.0
OD1 A:ASP47 2.8 15.5 1.0
CG A:ASP47 3.1 16.4 1.0
N A:ASN48 4.4 20.6 1.0
OG A:SER95 4.5 27.8 1.0
CB A:ASP47 4.5 20.5 1.0
CB A:ASN48 4.6 20.1 1.0
O A:HOH2037 4.8 25.9 1.0
CA A:ASN48 4.8 17.0 1.0

Ytterbium binding site 5 out of 6 in 5fwq

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Ytterbium binding site 5 out of 6 in the Apo Structure of Human Leukotriene A4 Hydrolase


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 5 of Apo Structure of Human Leukotriene A4 Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb1617

b:82.1
occ:0.50
 OE2 A:GLU46 2.2 55.2 1.0
O A:HOH2032 2.7 31.7 0.9
OE1 A:GLU46 2.7 24.3 1.0
CD A:GLU46 2.7 36.4 1.0
O A:HOH2031 3.1 30.9 1.0
O A:HOH2033 3.7 42.6 1.0
CG A:GLU46 4.1 37.3 1.0
O A:HOH2008 4.5 48.9 1.0
O A:HOH2034 4.7 26.8 1.0
CB A:GLU46 4.9 30.0 1.0

Ytterbium binding site 6 out of 6 in 5fwq

Go back to Ytterbium Binding Sites List in 5fwq
Ytterbium binding site 6 out of 6 in the Apo Structure of Human Leukotriene A4 Hydrolase


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 6 of Apo Structure of Human Leukotriene A4 Hydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb2612

b:70.5
occ:0.50
 OD1 A:ASP175 2.5 42.1 1.0
O A:ASP175 3.1 37.2 1.0
O A:HOH2138 3.2 47.0 1.0
CG A:ASP175 3.5 29.8 1.0
C A:ASP175 3.7 31.0 1.0
CA A:ASP175 4.0 27.4 1.0
OD2 A:ASP175 4.3 34.9 1.0
CB A:ASP175 4.4 29.3 1.0
O A:HOH2055 4.5 53.4 1.0
N A:GLY176 4.6 28.3 1.0
O A:HOH2139 4.8 39.2 1.0
CA A:GLY176 5.0 28.4 1.0

Reference:

S.K.Wittmann, L.Kalinowsky, J.S.Kramer, R.Bloecher, S.Knapp, D.Steinhilber, D.Pogoryelov, E.Proschak, J.Heering. Thermodynamic Properties of Leukotriene A4HYDROLASE Inhibitors. Bioorg.Med.Chem. V. 24 5243 2016.
ISSN: ESSN 1464-3391
PubMed: 27651294
DOI: 10.1016/J.BMC.2016.08.047
Page generated: Wed Dec 16 02:42:03 2020

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