Magnesium in PDB 5rvx: Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z804566442

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z804566442:
1.2.4.2;

The structure of Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z804566442, PDB code: 5rvx was solved by G.A.Bezerra, W.R.Foster, H.J.Bailey, L.Shrestha, T.Krojer, J.Brandao-Neto, A.Douangamath, N.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, W.W.Yue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.44 / 1.66
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.145, 147.437, 87.559, 90.00, 102.63, 90.00
R / Rfree (%)	17.1 / 19.8

The binding sites of Magnesium atom in the Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z804566442 (pdb code 5rvx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z804566442, PDB code: 5rvx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z804566442


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z804566442 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:16.3 occ:1.00 O3B A:TPP1002 2.0 13.4 1.0 O2A A:TPP1002 2.0 13.4 1.0 O A:LEU368 2.0 20.1 1.0 OD1 A:ASN366 2.0 18.2 1.0 OD1 A:ASP333 2.1 14.9 1.0 O A:HOH1210 2.3 13.0 1.0 CG A:ASN366 3.1 17.6 1.0 PB A:TPP1002 3.2 14.6 1.0 PA A:TPP1002 3.2 13.6 1.0 CG A:ASP333 3.2 17.5 1.0 C A:LEU368 3.2 20.3 1.0 O3A A:TPP1002 3.3 13.6 1.0 ND2 A:ASN366 3.5 16.2 1.0 OD2 A:ASP333 3.7 20.2 1.0 O2B A:TPP1002 3.8 14.9 1.0 O7 A:TPP1002 3.9 13.4 1.0 N A:ASP333 4.1 14.8 1.0 N A:GLY369 4.1 19.7 1.0 N A:LEU368 4.1 20.9 1.0 O A:HOH1365 4.1 14.3 1.0 CA A:GLY369 4.2 19.7 1.0 CA A:LEU368 4.3 21.6 1.0 N A:ASN366 4.3 16.9 1.0 O A:VAL364 4.4 15.1 1.0 CB A:ASN366 4.4 17.3 1.0 O1A A:TPP1002 4.4 12.9 1.0 CB A:ASP333 4.4 16.0 1.0 O1B A:TPP1002 4.4 13.2 1.0 N A:ALA334 4.6 13.1 1.0 CA A:ASN366 4.7 18.2 1.0 C A:ASN366 4.7 19.4 1.0 CA A:ASP333 4.7 15.0 1.0 N A:GLN367 4.8 19.5 1.0 CA A:GLY332 4.8 14.5 1.0 CB A:LEU368 4.8 23.0 1.0 C A:GLY332 4.9 14.7 1.0

Magnesium binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z804566442


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z804566442 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1004 b:12.6 occ:1.00 O B:HOH1457 2.0 8.8 1.0 OE1 A:GLU641 2.1 11.2 1.0 O A:HOH1434 2.1 10.9 1.0 OE1 B:GLU641 2.2 14.2 1.0 O A:HOH1112 2.2 12.8 1.0 O B:HOH1172 2.2 12.7 1.0 CD A:GLU641 3.1 13.7 1.0 CD B:GLU641 3.2 14.8 1.0 OE2 B:GLU641 3.5 17.1 1.0 OE2 A:GLU641 3.5 13.8 1.0 O B:HOH1345 4.1 13.6 1.0 O A:GLY671 4.2 10.5 1.0 O A:HOH1448 4.2 12.6 1.0 O B:GLY671 4.3 13.1 1.0 CG A:GLU641 4.4 13.1 1.0 CB A:GLU641 4.5 11.1 1.0 CG B:GLU641 4.5 10.7 1.0 OE2 A:GLU344 4.5 12.2 1.0 CB B:GLU641 4.6 11.0 1.0 OE2 B:GLU344 4.6 14.2 1.0 O B:HOH1528 4.7 12.9 1.0 O A:HOH1493 4.8 13.9 1.0

Magnesium binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z804566442


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z804566442 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1003 b:20.9 occ:1.00 O2B B:TPP1002 2.0 17.9 1.0 OD1 B:ASP333 2.0 17.4 1.0 OD1 B:ASN366 2.0 19.3 1.0 O B:LEU368 2.1 23.9 1.0 O2A B:TPP1002 2.1 18.2 1.0 O B:HOH1168 2.2 20.6 1.0 CG B:ASN366 3.0 19.9 1.0 CG B:ASP333 3.1 17.9 1.0 PB B:TPP1002 3.2 18.7 1.0 PA B:TPP1002 3.3 17.4 1.0 C B:LEU368 3.3 23.7 1.0 O3A B:TPP1002 3.4 18.2 1.0 ND2 B:ASN366 3.5 19.3 1.0 OD2 B:ASP333 3.7 20.1 1.0 O3B B:TPP1002 3.8 19.5 1.0 N B:ASP333 4.0 15.0 1.0 O7 B:TPP1002 4.0 16.3 1.0 O B:HOH1233 4.1 17.6 1.0 N B:LEU368 4.1 24.7 1.0 N B:GLY369 4.2 22.4 1.0 N B:ASN366 4.2 20.6 1.0 CA B:GLY369 4.3 21.9 1.0 O B:VAL364 4.3 20.4 1.0 CA B:LEU368 4.3 25.1 1.0 CB B:ASP333 4.3 15.0 1.0 CB B:ASN366 4.4 20.8 1.0 O1B B:TPP1002 4.4 17.6 1.0 N B:ALA334 4.5 14.0 1.0 O1A B:TPP1002 4.5 16.4 1.0 CA B:ASN366 4.6 20.9 1.0 CA B:ASP333 4.6 14.6 1.0 C B:ASN366 4.7 22.0 1.0 N B:GLN367 4.7 22.8 1.0 CA B:GLY332 4.8 16.2 1.0 C B:GLY332 4.8 15.9 1.0 CB B:LEU368 4.9 26.3 1.0

G.A.Bezerra, W.R.Foster, H.J.Bailey, L.Shrestha, T.Krojer, J.Brandao-Neto, A.Douangamath, N.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, W.W.Yue. Pandda Analysis Group Deposition To Be Published.