Ytterbium in PDB 5ac2: Human Aldehyde Dehydrogenase 1A1 with Duocarmycin Analog

All present enzymatic activity of Human Aldehyde Dehydrogenase 1A1 with Duocarmycin Analog:
1.2.1.36;

The structure of Human Aldehyde Dehydrogenase 1A1 with Duocarmycin Analog, PDB code: 5ac2 was solved by M.F.Koch, S.Harteis, I.D.Blank, G.Pestel, L.F.Tietze, C.Ochsenfeld, S.Schneider, S.A.Sieber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.80 / 1.85
Space group	P 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	109.123, 109.123, 83.175, 90.00, 90.00, 90.00
R / Rfree (%)	19.927 / 25.122

The binding sites of Ytterbium atom in the Human Aldehyde Dehydrogenase 1A1 with Duocarmycin Analog (pdb code 5ac2). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 3 binding sites of Ytterbium where determined in the Human Aldehyde Dehydrogenase 1A1 with Duocarmycin Analog, PDB code: 5ac2:
Jump to Ytterbium binding site number: 1; 2; 3;

Ytterbium binding site 1 out of 3 in the Human Aldehyde Dehydrogenase 1A1 with Duocarmycin Analog


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Human Aldehyde Dehydrogenase 1A1 with Duocarmycin Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb1503 b:0.6 occ:1.00 OD2 A:ASP283 3.0 50.4 1.0 OD1 A:ASP283 3.0 52.0 1.0 CG A:ASP283 3.4 49.0 1.0 CB A:ASP285 4.1 51.7 1.0 O A:HOH2105 4.1 31.5 1.0 N A:ASN286 4.3 41.7 1.0 CB A:ASN286 4.7 39.6 1.0 OD2 A:ASP285 4.8 62.8 1.0 CB A:ASP283 4.9 49.1 1.0 C A:ASP285 4.9 45.1 1.0 CA A:ASP285 5.0 46.9 1.0 CA A:ASN286 5.0 39.3 1.0

Ytterbium binding site 2 out of 3 in the Human Aldehyde Dehydrogenase 1A1 with Duocarmycin Analog


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Human Aldehyde Dehydrogenase 1A1 with Duocarmycin Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb1507 b:35.4 occ:1.00 O A:HOH2164 1.9 19.4 1.0 O A:HOH2018 2.1 24.4 1.0 O A:HOH2165 2.5 29.7 1.0 O A:HOH2124 2.5 33.5 1.0 O A:HOH2130 2.5 12.0 1.0 O A:HOH2016 2.7 34.1 1.0 O A:HOH2017 2.7 21.2 1.0 OE2 A:GLU46 4.2 37.9 1.0 O A:ASN377 4.2 46.7 1.0 OE1 A:GLU46 4.5 42.6 1.0 O A:HOH2129 4.7 34.2 1.0 CD A:GLU46 4.8 36.6 1.0

Ytterbium binding site 3 out of 3 in the Human Aldehyde Dehydrogenase 1A1 with Duocarmycin Analog


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Human Aldehyde Dehydrogenase 1A1 with Duocarmycin Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb1508 b:34.7 occ:1.00 O1N A:TXE1504 2.0 28.8 1.0 O A:HOH2123 2.3 28.5 1.0 O A:HOH2091 2.3 25.6 1.0 O A:HOH2089 2.4 33.6 1.0 O A:HOH2163 2.4 34.1 1.0 O2P A:TXE1504 2.6 27.9 1.0 O A:HOH2122 2.7 50.0 1.0 O A:HOH2167 2.9 50.0 1.0 O A:HOH2166 2.9 35.9 1.0 PN A:TXE1504 3.5 30.5 1.0 PA A:TXE1504 3.6 31.9 1.0 O3 A:TXE1504 3.9 30.5 1.0 OE1 A:GLU249 4.0 70.9 1.0 OE2 A:GLU349 4.2 42.0 1.0 OE1 A:GLU349 4.4 42.5 1.0 O1P A:TXE1504 4.5 31.5 1.0 O2N A:TXE1504 4.6 32.9 1.0 C5B A:TXE1504 4.6 30.6 1.0 O5B A:TXE1504 4.6 33.0 1.0 C8A A:TXE1504 4.7 29.6 1.0 CG2 A:VAL250 4.7 44.0 1.0 CD A:GLU349 4.7 42.4 1.0 OG A:SER247 4.8 34.4 1.0 O5' A:TXE1504 4.9 36.7 1.0 N7A A:TXE1504 5.0 32.0 1.0

M.F.Koch, S.Harteis, I.D.Blank, G.Pestel, L.F.Tietze, C.Ochsenfeld, S.Schneider, S.A.Sieber. Structural, Biochemical, and Computational Studies Reveal the Mechanism of Selective Aldehyde Dehydrogenase 1A1 Inhibition By Cytotoxic Duocarmycin Analogues. Angew.Chem.Int.Ed.Engl. V. 54 13550 2015.
ISSN: ISSN 1433-7851
PubMed: 26373694
DOI: 10.1002/ANIE.201505749