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Ytterbium in PDB 5l2o: Crystal Structure of ALDH1A1 in Complex with BUC22

Enzymatic activity of Crystal Structure of ALDH1A1 in Complex with BUC22

All present enzymatic activity of Crystal Structure of ALDH1A1 in Complex with BUC22:
1.2.1.36;

Protein crystallography data

The structure of Crystal Structure of ALDH1A1 in Complex with BUC22, PDB code: 5l2o was solved by C.D.Buchman, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 90.984, 98.292, 127.322, 80.55, 86.23, 64.36
R / Rfree (%) 17.4 / 20.5

Other elements in 5l2o:

The structure of Crystal Structure of ALDH1A1 in Complex with BUC22 also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Crystal Structure of ALDH1A1 in Complex with BUC22 (pdb code 5l2o). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 8 binding sites of Ytterbium where determined in the Crystal Structure of ALDH1A1 in Complex with BUC22, PDB code: 5l2o:
Jump to Ytterbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Ytterbium binding site 1 out of 8 in 5l2o

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Ytterbium binding site 1 out of 8 in the Crystal Structure of ALDH1A1 in Complex with BUC22


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Crystal Structure of ALDH1A1 in Complex with BUC22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb602

b:29.1
occ:1.00
 O A:HOH731 2.2 22.7 1.0
O A:HOH907 2.2 34.1 1.0
O A:HOH924 2.3 31.5 1.0
OE1 A:GLU46 2.3 29.4 1.0
CD A:GLU46 3.4 29.3 1.0
OE2 A:GLU46 3.8 30.7 1.0
OH A:TYR380 4.7 20.4 1.0
CG A:GLU46 4.7 25.9 1.0
O A:HOH879 4.7 32.4 1.0

Ytterbium binding site 2 out of 8 in 5l2o

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Ytterbium binding site 2 out of 8 in the Crystal Structure of ALDH1A1 in Complex with BUC22


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Crystal Structure of ALDH1A1 in Complex with BUC22 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Yb602

b:27.5
occ:1.00
 O B:HOH834 2.2 27.6 1.0
OD1 B:ASP356 2.2 25.0 1.0
O B:HOH925 2.3 21.3 1.0
O B:HOH772 2.3 24.4 1.0
OE1 B:GLU359 2.3 27.2 1.0
CD B:GLU359 3.4 28.5 1.0
CG B:ASP356 3.4 24.1 1.0
OE2 B:GLU359 3.7 32.5 1.0
OD2 B:ASP356 4.0 27.3 1.0
O B:HOH730 4.5 21.7 1.0
CB B:ASP356 4.7 20.9 1.0
CA B:ASP356 4.8 19.6 1.0
CG B:GLU359 4.8 28.1 1.0

Ytterbium binding site 3 out of 8 in 5l2o

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Ytterbium binding site 3 out of 8 in the Crystal Structure of ALDH1A1 in Complex with BUC22


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Crystal Structure of ALDH1A1 in Complex with BUC22 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Yb602

b:35.8
occ:1.00
 OE2 D:GLU46 2.5 42.2 1.0
CD D:GLU46 3.7 43.2 1.0
OE1 D:GLU46 4.3 51.4 1.0

Ytterbium binding site 4 out of 8 in 5l2o

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Ytterbium binding site 4 out of 8 in the Crystal Structure of ALDH1A1 in Complex with BUC22


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 4 of Crystal Structure of ALDH1A1 in Complex with BUC22 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Yb602

b:32.3
occ:1.00
 OE2 E:GLU359 2.3 42.2 1.0
OE1 E:GLU359 2.4 39.6 1.0
OD1 E:ASP356 2.4 36.2 1.0
O E:HOH961 2.4 19.0 1.0
CD E:GLU359 2.9 34.1 1.0
CG E:ASP356 3.6 34.5 1.0
O E:HOH939 4.0 47.4 1.0
OD2 E:ASP356 4.2 44.9 1.0
CG E:GLU359 4.5 32.5 1.0
O E:HOH717 4.7 24.3 1.0
O E:HOH738 4.7 29.7 1.0
CB E:ASP356 4.8 28.6 1.0
CA E:ASP356 5.0 24.8 1.0

Ytterbium binding site 5 out of 8 in 5l2o

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Ytterbium binding site 5 out of 8 in the Crystal Structure of ALDH1A1 in Complex with BUC22


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 5 of Crystal Structure of ALDH1A1 in Complex with BUC22 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Yb603

b:56.9
occ:1.00
 O E:HOH946 2.3 26.9 1.0
O E:HOH952 4.2 24.0 1.0
OD1 E:ASP15 4.4 46.2 1.0
OD2 E:ASP15 4.9 49.8 1.0

Ytterbium binding site 6 out of 8 in 5l2o

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Ytterbium binding site 6 out of 8 in the Crystal Structure of ALDH1A1 in Complex with BUC22


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 6 of Crystal Structure of ALDH1A1 in Complex with BUC22 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Yb602

b:49.9
occ:1.00
 O F:HOH804 2.3 41.2 1.0
OE1 F:GLU48 3.6 39.8 1.0
OE2 F:GLU48 3.9 38.0 1.0
CD F:GLU48 3.9 38.2 1.0
CG F:GLU48 4.9 33.7 1.0
CB F:GLU48 4.9 34.0 1.0

Ytterbium binding site 7 out of 8 in 5l2o

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Ytterbium binding site 7 out of 8 in the Crystal Structure of ALDH1A1 in Complex with BUC22


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 7 of Crystal Structure of ALDH1A1 in Complex with BUC22 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Yb602

b:31.5
occ:1.00
 OE1 G:GLU359 2.2 37.8 1.0
O G:HOH724 2.2 29.6 1.0
O G:HOH873 2.3 33.0 1.0
OD1 G:ASP356 2.3 27.9 1.0
CD G:GLU359 3.3 33.6 1.0
CG G:ASP356 3.6 26.3 1.0
OE2 G:GLU359 3.6 33.6 1.0
O G:HOH715 3.6 27.9 1.0
OD2 G:ASP356 4.2 28.1 1.0
O G:HOH721 4.3 22.9 1.0
CG G:GLU359 4.6 31.5 1.0
CB G:ASP356 4.7 22.6 1.0
CA G:ASP356 4.8 20.4 1.0
CB G:GLU359 4.9 29.1 1.0

Ytterbium binding site 8 out of 8 in 5l2o

Go back to Ytterbium Binding Sites List in 5l2o
Ytterbium binding site 8 out of 8 in the Crystal Structure of ALDH1A1 in Complex with BUC22


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 8 of Crystal Structure of ALDH1A1 in Complex with BUC22 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Yb602

b:25.5
occ:1.00
 O H:HOH853 2.2 22.2 1.0
O H:HOH830 2.3 20.8 1.0
OE1 H:GLU46 2.4 28.2 1.0
CD H:GLU46 3.4 24.6 1.0
OE2 H:GLU46 3.9 22.5 1.0
O H:HOH978 4.5 21.3 1.0
CG H:GLU46 4.7 22.9 1.0
OH H:TYR380 4.8 19.5 1.0

Reference:

C.D.Buchman, T.D.Hurley. Inhibition of the Aldehyde Dehydrogenase 1/2 Family By Psoralen and Coumarin Derivatives. J. Med. Chem. V. 60 2439 2017.
ISSN: ISSN 1520-4804
PubMed: 28219011
DOI: 10.1021/ACS.JMEDCHEM.6B01825
Page generated: Sat Oct 12 21:20:11 2024

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