Magnesium in PDB 6u3j: Structure of the 2-Oxoadipate Dehydrogenase DHTKD1

All present enzymatic activity of Structure of the 2-Oxoadipate Dehydrogenase DHTKD1:
1.2.4.2;

The structure of Structure of the 2-Oxoadipate Dehydrogenase DHTKD1, PDB code: 6u3j was solved by S.Khamrui, M.B.Lazarus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.01 / 2.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	332.314, 72.612, 79.675, 90.00, 91.87, 90.00
R / Rfree (%)	20.9 / 24.1

The binding sites of Magnesium atom in the Structure of the 2-Oxoadipate Dehydrogenase DHTKD1 (pdb code 6u3j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the 2-Oxoadipate Dehydrogenase DHTKD1, PDB code: 6u3j:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the 2-Oxoadipate Dehydrogenase DHTKD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the 2-Oxoadipate Dehydrogenase DHTKD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:36.8 occ:1.00 O A:HOH1327 2.1 27.4 1.0 OE2 B:GLU641 2.2 19.6 1.0 O B:HOH1139 2.2 26.7 1.0 O A:HOH1133 2.2 22.6 1.0 O A:HOH1291 2.3 27.5 1.0 OE2 A:GLU641 2.3 24.1 1.0 CD B:GLU641 3.1 21.0 1.0 CD A:GLU641 3.2 23.2 1.0 OE1 B:GLU641 3.3 24.2 1.0 OE1 A:GLU641 3.5 25.9 1.0 O B:GLY671 4.2 25.1 1.0 O A:GLY671 4.2 25.9 1.0 O B:HOH1332 4.3 22.9 1.0 O A:HOH1341 4.3 23.6 1.0 CG B:GLU641 4.4 28.9 1.0 CG A:GLU641 4.5 26.9 1.0 CB B:GLU641 4.6 23.8 1.0 CB A:GLU641 4.6 26.2 1.0 O B:HOH1207 4.7 36.1 1.0 O A:HOH1189 4.8 35.9 1.0 OE2 A:GLU344 4.8 28.5 1.0 OE2 B:GLU344 4.8 28.5 1.0 O B:HOH1194 4.9 20.7 1.0 O A:HOH1177 4.9 25.0 1.0

Magnesium binding site 2 out of 3 in the Structure of the 2-Oxoadipate Dehydrogenase DHTKD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the 2-Oxoadipate Dehydrogenase DHTKD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:28.8 occ:1.00 OD1 A:ASN366 2.0 29.1 1.0 O1A A:TPP1001 2.1 32.8 1.0 OD1 A:ASP333 2.1 34.2 1.0 O A:LEU368 2.1 30.7 1.0 O3B A:TPP1001 2.2 37.7 1.0 O A:HOH1181 2.5 31.2 1.0 CG A:ASN366 3.0 35.7 1.0 CG A:ASP333 3.1 42.3 1.0 C A:LEU368 3.3 37.8 1.0 PA A:TPP1001 3.3 40.5 1.0 ND2 A:ASN366 3.4 39.0 1.0 PB A:TPP1001 3.4 39.3 1.0 OD2 A:ASP333 3.5 42.0 1.0 O3A A:TPP1001 3.7 43.3 1.0 N A:LEU368 4.0 35.6 1.0 O2B A:TPP1001 4.0 29.6 1.0 N A:GLY369 4.1 44.6 1.0 N A:ASP333 4.1 24.8 1.0 O7 A:TPP1001 4.2 40.4 1.0 CA A:GLY369 4.2 28.3 1.0 CA A:LEU368 4.2 38.0 1.0 N A:ASN366 4.3 28.4 1.0 CB A:ASN366 4.3 25.5 1.0 CB A:ASP333 4.4 25.3 1.0 N A:ALA334 4.4 27.2 1.0 O A:HOH1131 4.5 31.9 1.0 O2A A:TPP1001 4.5 40.2 1.0 O A:VAL364 4.5 24.2 1.0 N A:GLN367 4.6 30.4 1.0 O1B A:TPP1001 4.6 28.5 1.0 CA A:ASN366 4.6 35.0 1.0 C A:ASN366 4.6 32.8 1.0 CA A:ASP333 4.7 24.7 1.0 CD2 A:LEU368 4.8 49.2 1.0 CB A:ALA334 4.9 22.5 1.0

Magnesium binding site 3 out of 3 in the Structure of the 2-Oxoadipate Dehydrogenase DHTKD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the 2-Oxoadipate Dehydrogenase DHTKD1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:27.5 occ:0.90 O B:LEU368 2.0 30.5 1.0 OD1 B:ASN366 2.0 27.1 1.0 O2A B:TPP1001 2.0 29.8 1.0 OD1 B:ASP333 2.1 33.0 1.0 O3B B:TPP1001 2.2 38.3 1.0 O B:HOH1190 2.4 21.9 1.0 CG B:ASN366 3.0 35.0 1.0 CG B:ASP333 3.1 43.1 1.0 C B:LEU368 3.2 37.1 1.0 PA B:TPP1001 3.3 37.6 1.0 PB B:TPP1001 3.4 36.9 1.0 ND2 B:ASN366 3.4 37.7 1.0 OD2 B:ASP333 3.5 40.9 1.0 O3A B:TPP1001 3.7 43.8 1.0 N B:LEU368 3.9 34.4 1.0 N B:GLY369 4.1 45.6 1.0 O1B B:TPP1001 4.1 28.6 1.0 CA B:GLY369 4.1 32.7 1.0 O7 B:TPP1001 4.1 38.8 1.0 N B:ASP333 4.2 21.3 1.0 O B:HOH1117 4.2 34.6 1.0 CA B:LEU368 4.2 39.0 1.0 N B:ASN366 4.3 28.5 1.0 CB B:ASN366 4.4 26.0 1.0 N B:ALA334 4.4 26.7 1.0 CB B:ASP333 4.4 25.4 1.0 O1A B:TPP1001 4.5 40.2 1.0 O B:VAL364 4.6 26.3 1.0 N B:GLN367 4.6 29.3 1.0 O2B B:TPP1001 4.6 29.2 1.0 C B:ASN366 4.7 33.0 1.0 CA B:ASN366 4.7 35.0 1.0 CA B:ASP333 4.8 25.4 1.0 CD2 B:LEU368 4.8 49.7 1.0 CB B:ALA334 4.9 21.5 1.0

J.Leandro, S.Khamrui, H.Wang, C.Suebsuwong, N.S.Nemeria, K.Huynh, M.Moustakim, C.Secor, M.Wang, T.Dodatko, B.Stauffer, C.G.Wilson, C.Yu, M.R.Arkin, F.Jordan, R.Sanchez, R.J.Devita, M.B.Lazarus, S.M.Houten. Inhibition and Crystal Structure of the Human DHTKD1-Thiamin Diphosphate Complex. Acs Chem.Biol. V. 15 2041 2020.
ISSN: ESSN 1554-8937
PubMed: 32633484
DOI: 10.1021/ACSCHEMBIO.0C00114