Magnesium in PDB 1dci: Dienoyl-Coa Isomerase

All present enzymatic activity of Dienoyl-Coa Isomerase:
4.2.1.17;

The structure of Dienoyl-Coa Isomerase, PDB code: 1dci was solved by Y.Modis, S.A.Filppula, D.Novikov, B.Norledge, J.K.Hiltunen, R.K.Wierenga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	131.543, 131.543, 96.731, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 20.5

The binding sites of Magnesium atom in the Dienoyl-Coa Isomerase (pdb code 1dci). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Dienoyl-Coa Isomerase, PDB code: 1dci:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Dienoyl-Coa Isomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dienoyl-Coa Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg17 b:24.8 occ:1.00 O A:HOH640 2.1 23.9 1.0 O A:HOH643 2.1 20.5 1.0 O A:HOH641 2.1 27.1 1.0 O A:HOH644 2.1 24.2 1.0 O A:HOH639 2.1 22.7 1.0 O A:HOH642 2.1 23.4 1.0 O A:HOH328 3.9 17.0 1.0 O A:HOH379 3.9 18.7 1.0 OD2 A:ASP121 4.0 18.4 1.0 O A:HOH397 4.1 24.3 1.0 OD1 A:ASP121 4.1 18.9 1.0 O A:HOH624 4.2 29.3 1.0 ND2 A:ASN81 4.3 18.9 1.0 CG A:ASP121 4.5 21.4 1.0 O1 A:SO49 4.7 21.7 1.0

Magnesium binding site 2 out of 4 in the Dienoyl-Coa Isomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dienoyl-Coa Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg19 b:27.1 occ:1.00 O C:HOH652 2.1 27.3 1.0 O B:HOH650 2.1 29.2 1.0 O B:HOH649 2.1 26.2 1.0 O A:HOH645 2.1 27.0 1.0 O C:HOH651 2.1 28.5 1.0 O A:HOH646 2.1 29.9 1.0 OD1 C:ASP238 4.1 33.5 1.0 OD1 B:ASP238 4.1 27.8 1.0 O C:ASP238 4.1 22.1 1.0 OD1 A:ASP238 4.1 28.6 1.0 O B:ASP238 4.2 20.2 1.0 O C:HOH506 4.2 31.7 1.0 O C:HOH425 4.2 27.3 1.0 O A:ASP238 4.2 19.4 1.0 O A:HOH489 4.2 36.8 1.0 O A:HOH438 4.3 25.3 1.0 O B:HOH459 4.3 34.9 1.0 O A:HOH462 4.3 27.5 1.0 CG C:ASP238 4.6 31.9 1.0 CG B:ASP238 4.7 26.4 1.0 CG A:ASP238 4.7 26.9 1.0 OD2 C:ASP238 4.8 33.0 1.0 OD2 B:ASP238 4.8 28.1 1.0 OD2 A:ASP238 5.0 28.5 1.0

Magnesium binding site 3 out of 4 in the Dienoyl-Coa Isomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dienoyl-Coa Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg18 b:12.9 occ:0.50 O C:HOH645 2.1 18.7 1.0 O C:HOH646 2.1 18.9 0.5 O C:HOH647 2.1 17.6 1.0 O C:HOH650 2.1 13.2 0.0 O C:HOH649 2.1 20.4 0.5 O C:HOH648 2.1 12.0 0.0 OE1 C:GLU75 4.2 18.5 1.0 OE2 C:GLU75 4.2 18.3 1.0 O C:ASN72 4.3 19.1 1.0 O C:HOH546 4.3 42.5 1.0 OE2 C:GLU55 4.3 25.2 1.0 O C:GLU55 4.5 25.2 1.0 CD C:GLU75 4.6 17.8 1.0 CA C:ARG73 4.9 18.3 1.0 CG C:ARG73 5.0 21.5 1.0

Magnesium binding site 4 out of 4 in the Dienoyl-Coa Isomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dienoyl-Coa Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg20 b:36.8 occ:1.00 O C:HOH655 2.1 40.6 1.0 O C:HOH658 2.1 38.3 1.0 O C:HOH657 2.1 39.1 1.0 O C:HOH653 2.1 38.2 1.0 O C:HOH654 2.1 37.9 1.0 O C:HOH656 2.1 40.3 1.0 OE1 C:GLU315 3.9 35.2 1.0 OE2 C:GLU315 4.0 30.9 1.0 O C:HOH400 4.1 25.8 1.0 O3 C:SO411 4.2 45.6 1.0 OE1 C:GLN311 4.3 28.1 1.0 O2 C:SO411 4.3 43.6 1.0 CD C:GLU315 4.4 32.8 1.0 S C:SO411 4.7 44.6 1.0 O1 C:SO411 4.7 43.8 1.0 CD C:GLN311 4.8 28.1 1.0 CB C:GLN311 4.9 17.8 1.0

Y.Modis, S.A.Filppula, D.K.Novikov, B.Norledge, J.K.Hiltunen, R.K.Wierenga. The Crystal Structure of Dienoyl-Coa Isomerase at 1.5 A Resolution Reveals the Importance of Aspartate and Glutamate Sidechains For Catalysis. Structure V. 6 957 1998.
ISSN: ISSN 0969-2126
PubMed: 9739087
DOI: 10.1016/S0969-2126(98)00098-7