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

Enzymatic activity of Structure of the 2-Oxoadipate Dehydrogenase DHTKD1

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

Protein crystallography data

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

Magnesium Binding Sites:

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 6u3j

Go back to Magnesium Binding Sites List in 6u3j
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 6u3j

Go back to Magnesium Binding Sites List in 6u3j
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 6u3j

Go back to Magnesium Binding Sites List in 6u3j
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

Reference:

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
Page generated: Tue Oct 1 20:49:08 2024

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