Magnesium in PDB 5ygi: Crystal Structure of Human Fpps in Complex with An Inhibitor THZ93

All present enzymatic activity of Crystal Structure of Human Fpps in Complex with An Inhibitor THZ93:
2.5.1.1; 2.5.1.10;

The structure of Crystal Structure of Human Fpps in Complex with An Inhibitor THZ93, PDB code: 5ygi was solved by X.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.47 / 2.18
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.743, 111.743, 66.191, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 27.2

The binding sites of Magnesium atom in the Crystal Structure of Human Fpps in Complex with An Inhibitor THZ93 (pdb code 5ygi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Fpps in Complex with An Inhibitor THZ93, PDB code: 5ygi:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human Fpps in Complex with An Inhibitor THZ93


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Fpps in Complex with An Inhibitor THZ93 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:41.2 occ:1.00 O7 A:T93506 2.0 43.7 1.0 O3 A:T93506 2.1 42.4 1.0 O A:HOH606 2.1 37.8 1.0 OD2 A:ASP243 2.1 41.3 1.0 O A:HOH626 2.2 36.1 1.0 O A:HOH635 2.2 37.4 1.0 CG A:ASP243 3.1 41.0 1.0 P6 A:T93506 3.3 42.0 1.0 P2 A:T93506 3.3 40.8 1.0 OD1 A:ASP243 3.5 40.4 1.0 O A:HOH618 3.5 43.6 1.0 C5 A:T93506 3.7 40.2 1.0 H051 A:T93506 3.7 18.7 1.0 O9 A:T93506 4.0 42.2 1.0 O A:HOH624 4.0 42.0 1.0 O4 A:T93506 4.1 41.2 1.0 OD1 A:ASP247 4.2 44.7 1.0 NE2 A:GLN240 4.2 45.2 1.0 OD2 A:ASP261 4.3 40.6 1.0 NZ A:LYS257 4.3 43.4 1.0 O A:HOH641 4.3 40.6 1.0 OD1 A:ASP261 4.4 40.5 1.0 OD1 A:ASP244 4.4 37.2 1.0 O A:ASP243 4.4 44.6 1.0 CB A:ASP243 4.4 41.1 1.0 O8 A:T93506 4.4 41.9 1.0 O1 A:T93506 4.4 39.7 1.0 O A:HOH637 4.5 35.7 1.0 C A:ASP243 4.5 43.9 1.0 CB A:ASP247 4.6 45.4 1.0 CG A:ASP247 4.7 46.5 1.0 CG A:ASP261 4.7 41.5 1.0 N A:ASP244 4.8 36.3 1.0 MG A:MG504 4.9 38.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Fpps in Complex with An Inhibitor THZ93


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Fpps in Complex with An Inhibitor THZ93 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:38.8 occ:1.00 O A:HOH641 2.0 40.6 1.0 O4 A:T93506 2.1 41.2 1.0 OD2 A:ASP103 2.2 39.0 1.0 O9 A:T93506 2.2 42.2 1.0 OD2 A:ASP107 2.2 42.5 1.0 O A:HOH608 2.2 38.5 1.0 MG A:MG505 3.1 24.3 1.0 CG A:ASP103 3.2 38.5 1.0 CG A:ASP107 3.2 42.9 1.0 P2 A:T93506 3.3 40.8 1.0 P6 A:T93506 3.5 42.0 1.0 H101 A:T93506 3.5 18.7 1.0 OD1 A:ASP103 3.6 39.1 1.0 CB A:ASP107 3.7 44.0 1.0 O A:HOH637 3.8 35.7 1.0 C5 A:T93506 3.8 40.2 1.0 N10 A:T93506 3.8 38.9 1.0 O3 A:T93506 4.0 42.4 1.0 O A:HOH631 4.1 33.0 1.0 O7 A:T93506 4.2 43.7 1.0 O A:HOH626 4.3 36.1 1.0 NH2 A:ARG112 4.3 39.0 1.0 O A:HOH634 4.3 41.7 1.0 OD1 A:ASP107 4.3 43.0 1.0 OG A:SER109 4.4 39.8 1.0 O A:ASP103 4.4 40.3 1.0 CB A:ASP103 4.5 37.2 1.0 O1 A:T93506 4.5 39.7 1.0 OD1 A:ASP104 4.6 37.5 1.0 O8 A:T93506 4.6 41.9 1.0 O A:HOH627 4.7 47.0 1.0 H051 A:T93506 4.7 18.7 1.0 O A:HOH621 4.7 43.0 1.0 O A:HOH623 4.7 34.1 1.0 C A:ASP103 4.8 39.4 1.0 MG A:MG503 4.9 41.2 1.0 H231 A:T93506 5.0 18.7 1.0 C11 A:T93506 5.0 38.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Fpps in Complex with An Inhibitor THZ93


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Fpps in Complex with An Inhibitor THZ93 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:24.3 occ:1.00 O A:HOH623 1.9 34.1 1.0 O A:HOH621 1.9 43.0 1.0 O A:HOH631 1.9 33.0 1.0 OD1 A:ASP103 2.1 39.1 1.0 OD2 A:ASP107 2.2 42.5 1.0 O9 A:T93506 2.2 42.2 1.0 CG A:ASP103 2.9 38.5 1.0 OD2 A:ASP103 3.0 39.0 1.0 CG A:ASP107 3.1 42.9 1.0 MG A:MG504 3.1 38.8 1.0 OD1 A:ASP107 3.2 43.0 1.0 P6 A:T93506 3.4 42.0 1.0 O8 A:T93506 3.4 41.9 1.0 OE1 A:GLN171 3.9 36.9 1.0 OD1 A:ASP174 4.0 43.2 1.0 NE2 A:GLN171 4.0 37.4 1.0 H231 A:T93506 4.2 18.7 1.0 NZ A:LYS266 4.2 36.8 1.0 N10 A:T93506 4.2 38.9 1.0 O A:HOH641 4.3 40.6 1.0 H101 A:T93506 4.3 18.7 1.0 CB A:ASP103 4.3 37.2 1.0 O A:HOH624 4.3 42.0 1.0 CD A:GLN171 4.4 36.9 1.0 O7 A:T93506 4.4 43.7 1.0 C5 A:T93506 4.5 40.2 1.0 C23 A:T93506 4.5 37.5 1.0 CB A:ASP107 4.5 44.0 1.0 CG A:ASP174 4.5 43.5 1.0 C11 A:T93506 4.5 38.3 1.0 OD2 A:ASP174 4.6 44.3 1.0 O4 A:T93506 4.7 41.2 1.0 H171 A:T93506 4.7 18.7 1.0 NZ A:LYS200 4.9 44.3 1.0 O A:ASP103 4.9 40.3 1.0 O A:HOH634 4.9 41.7 1.0 O A:HOH608 4.9 38.5 1.0

Y.Xia, Y.Xie, Z.Yu, H.Xiao, G.Jiang, X.Zhou, Y.Yang, X.Li, M.Zhao, L.Li, M.Zheng, S.Han, Z.Zong, X.Meng, H.Deng, H.Ye, Y.Fa, H.Wu, E.Oldfield, X.Hu, W.Liu, Y.Shi, Y.Zhang. The Mevalonate Pathway Is A Druggable Target For Vaccine Adjuvant Discovery. Cell V. 175 1059 2018.
ISSN: ISSN 1097-4172
PubMed: 30270039
DOI: 10.1016/J.CELL.2018.08.070