Magnesium in PDB 5rvy: Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z437516460

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z437516460:
1.2.4.2;

The structure of Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z437516460, PDB code: 5rvy 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)	85.32 / 1.61
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.112, 147.365, 87.431, 90.00, 102.61, 90.00
R / Rfree (%)	16.4 / 18.8

The binding sites of Magnesium atom in the Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z437516460 (pdb code 5rvy). 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 Z437516460, PDB code: 5rvy:
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 Z437516460


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 Z437516460 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:9.2 occ:1.00 O3B A:TPP1001 2.0 8.5 1.0 O2A A:TPP1001 2.0 9.1 1.0 O A:LEU368 2.1 13.9 1.0 OD1 A:ASP333 2.1 13.6 1.0 OD1 A:ASN366 2.1 14.0 1.0 O A:HOH1182 2.3 9.7 1.0 CG A:ASN366 3.1 13.9 1.0 PB A:TPP1001 3.1 9.5 1.0 PA A:TPP1001 3.1 9.5 1.0 CG A:ASP333 3.2 14.1 1.0 C A:LEU368 3.3 14.3 1.0 O3A A:TPP1001 3.3 8.8 1.0 ND2 A:ASN366 3.5 12.7 1.0 OD2 A:ASP333 3.7 15.6 1.0 O2B A:TPP1001 3.7 10.0 1.0 O7 A:TPP1001 3.9 10.0 1.0 N A:ASP333 4.0 9.6 1.0 N A:GLY369 4.1 13.6 1.0 N A:LEU368 4.1 14.5 1.0 O A:HOH1279 4.1 9.4 1.0 CA A:GLY369 4.2 13.8 1.0 CA A:LEU368 4.3 15.2 1.0 N A:ASN366 4.3 11.8 1.0 O A:VAL364 4.4 13.2 1.0 CB A:ASP333 4.4 11.5 1.0 O1A A:TPP1001 4.4 10.2 1.0 O1B A:TPP1001 4.4 9.2 1.0 CB A:ASN366 4.5 13.4 1.0 N A:ALA334 4.5 10.2 1.0 CA A:ASP333 4.7 9.9 1.0 CA A:ASN366 4.7 13.1 1.0 N A:GLN367 4.7 14.3 1.0 C A:ASN366 4.8 14.2 1.0 CA A:GLY332 4.8 10.7 1.0 C A:GLY332 4.8 10.6 1.0 CB A:LEU368 4.9 16.5 1.0

Magnesium binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z437516460


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 Z437516460 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:10.2 occ:1.00 O B:HOH1513 1.9 8.9 1.0 O A:HOH1475 2.1 6.9 1.0 OE1 B:GLU641 2.1 12.2 1.0 OE1 A:GLU641 2.1 9.8 1.0 O A:HOH1186 2.2 8.8 1.0 O B:HOH1221 2.2 7.2 1.0 CD B:GLU641 3.1 12.1 1.0 CD A:GLU641 3.2 11.2 1.0 OE2 B:GLU641 3.5 12.3 1.0 OE2 A:GLU641 3.6 11.4 1.0 O B:HOH1334 4.2 8.2 1.0 O A:HOH1491 4.3 8.3 1.0 O A:GLY671 4.3 6.8 1.0 O B:GLY671 4.3 10.6 1.0 CG B:GLU641 4.4 8.2 1.0 CG A:GLU641 4.4 9.1 1.0 OE2 A:GLU344 4.5 11.2 1.0 OE2 B:GLU344 4.5 11.7 1.0 CB B:GLU641 4.5 10.2 1.0 CB A:GLU641 4.5 8.8 1.0 O A:HOH1591 4.7 6.5 1.0 O B:HOH1468 4.8 7.1 1.0

Magnesium binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z437516460


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 Z437516460 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1003 b:11.2 occ:1.00 OD1 B:ASP333 2.0 12.9 1.0 O2B B:TPP1002 2.0 11.2 1.0 OD1 B:ASN366 2.1 16.8 1.0 O2A B:TPP1002 2.1 12.7 1.0 O B:LEU368 2.1 16.7 1.0 O B:HOH1191 2.2 17.5 1.0 CG B:ASN366 3.1 17.2 1.0 CG B:ASP333 3.1 13.9 1.0 PB B:TPP1002 3.2 12.3 1.0 PA B:TPP1002 3.2 11.8 1.0 O3A B:TPP1002 3.3 12.2 1.0 C B:LEU368 3.3 16.4 1.0 ND2 B:ASN366 3.5 17.1 1.0 OD2 B:ASP333 3.7 14.9 1.0 O3B B:TPP1002 3.7 11.5 1.0 N B:ASP333 3.9 12.3 1.0 O7 B:TPP1002 4.0 11.2 1.0 N B:LEU368 4.2 17.2 1.0 N B:GLY369 4.2 15.2 1.0 O B:HOH1296 4.2 12.2 1.0 CA B:GLY369 4.3 14.2 1.0 N B:ASN366 4.3 16.3 1.0 O B:VAL364 4.3 18.3 1.0 CB B:ASP333 4.3 12.6 1.0 CA B:LEU368 4.4 18.1 1.0 CB B:ASN366 4.4 16.3 1.0 O1B B:TPP1002 4.4 10.9 1.0 O1A B:TPP1002 4.4 11.4 1.0 N B:ALA334 4.5 11.3 1.0 CA B:ASP333 4.6 12.2 1.0 CA B:ASN366 4.7 16.2 1.0 N B:GLN367 4.7 16.5 1.0 C B:ASN366 4.7 16.7 1.0 CA B:GLY332 4.8 13.2 1.0 C B:GLY332 4.8 13.1 1.0 CB B:LEU368 4.9 20.5 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.