Magnesium in PDB 4ga3: Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with Bph-1260

All present enzymatic activity of Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with Bph-1260:
2.5.1.1; 2.5.1.10;

The structure of Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with Bph-1260, PDB code: 4ga3 was solved by Y.-L.Liu, Y.Zhang, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.51 / 2.39
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	112.290, 112.290, 68.553, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 28.2

The binding sites of Magnesium atom in the Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with Bph-1260 (pdb code 4ga3). 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 Farnesyl Diphosphate Synthase in Complex with Bph-1260, PDB code: 4ga3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with Bph-1260


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 Farnesyl Diphosphate Synthase in Complex with Bph-1260 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:23.8 occ:1.00 OAG A:4GA1001 2.0 25.3 1.0 O A:HOH1105 2.1 24.5 1.0 OAD A:4GA1001 2.1 42.8 1.0 OAE A:4GA1001 2.2 24.9 1.0 O A:HOH1107 2.3 29.7 1.0 O A:HOH1106 2.3 29.1 1.0 OD2 A:ASP243 2.4 24.3 1.0 CAR A:4GA1001 2.9 28.9 1.0 PAS A:4GA1001 3.1 26.1 1.0 PAT A:4GA1001 3.3 26.1 1.0 CG A:ASP243 3.5 27.5 1.0 OAB A:4GA1001 3.7 26.1 1.0 O A:HOH1117 3.9 24.3 1.0 OD1 A:ASP243 3.9 27.8 1.0 O A:HOH1102 3.9 16.7 1.0 OAH A:4GA1001 4.0 21.0 1.0 CAO A:4GA1001 4.1 31.6 1.0 OD2 A:ASP247 4.2 35.9 1.0 OD2 A:ASP261 4.2 34.9 1.0 OD1 A:ASP261 4.3 33.9 1.0 OAF A:4GA1001 4.4 29.5 1.0 NE2 A:GLN240 4.4 26.0 1.0 OAC A:4GA1001 4.4 28.2 1.0 O A:HOH1111 4.5 29.4 1.0 O A:ASP243 4.5 35.6 1.0 OD1 A:ASP244 4.6 31.1 1.0 MG A:MG1004 4.7 24.9 1.0 CG A:ASP261 4.7 31.5 1.0 NZ A:LYS257 4.7 24.2 1.0 CB A:ASP243 4.7 24.5 1.0 CG A:ASP247 4.8 40.0 1.0 CB A:ASP247 4.8 36.8 1.0 C A:ASP243 4.8 30.6 1.0 CE A:LYS257 5.0 25.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with Bph-1260


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 Farnesyl Diphosphate Synthase in Complex with Bph-1260 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:12.4 occ:1.00 O A:HOH1104 1.9 24.6 1.0 OD2 A:ASP107 2.0 21.2 1.0 OAH A:4GA1001 2.1 21.0 1.0 OD2 A:ASP103 2.1 29.5 1.0 O A:HOH1103 2.2 19.8 1.0 CG A:ASP103 3.0 27.1 1.0 CG A:ASP107 3.1 24.0 1.0 OD1 A:ASP103 3.1 25.6 1.0 PAT A:4GA1001 3.2 26.1 1.0 MG A:MG1004 3.2 24.9 1.0 OAC A:4GA1001 3.3 28.2 1.0 OD1 A:ASP107 3.5 21.9 1.0 NE2 A:GLN171 3.9 27.6 1.0 NZ A:LYS266 4.1 29.1 1.0 OE1 A:GLN171 4.1 43.2 1.0 OAG A:4GA1001 4.1 25.3 1.0 OD2 A:ASP174 4.1 27.1 1.0 O A:HOH1102 4.2 16.7 1.0 CAI A:4GA1001 4.2 31.2 1.0 CAJ A:4GA1001 4.2 31.3 1.0 OD1 A:ASP174 4.2 25.8 1.0 O A:HOH1117 4.3 24.3 1.0 CB A:ASP103 4.4 23.9 1.0 CD A:GLN171 4.4 30.6 1.0 CG A:ASP174 4.4 27.2 1.0 CB A:ASP107 4.5 24.6 1.0 OAB A:4GA1001 4.7 26.1 1.0 O A:ASP103 4.8 24.8 1.0 NZ A:LYS200 4.8 24.7 1.0 CAR A:4GA1001 4.8 28.9 1.0 NAQ A:4GA1001 4.9 33.3 1.0 NAP A:4GA1001 4.9 30.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with Bph-1260


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 Farnesyl Diphosphate Synthase in Complex with Bph-1260 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1004 b:24.9 occ:1.00 OD1 A:ASP103 2.0 25.6 1.0 OAB A:4GA1001 2.0 26.1 1.0 OAH A:4GA1001 2.0 21.0 1.0 O A:HOH1102 2.1 16.7 1.0 O A:HOH1101 2.2 18.9 1.0 OD2 A:ASP107 2.4 21.2 1.0 CG A:ASP103 3.1 27.1 1.0 MG A:MG1003 3.2 12.4 1.0 CG A:ASP107 3.3 24.0 1.0 PAS A:4GA1001 3.3 26.1 1.0 PAT A:4GA1001 3.4 26.1 1.0 OD2 A:ASP103 3.6 29.5 1.0 CB A:ASP107 3.6 24.6 1.0 O A:HOH1111 3.7 29.4 1.0 OAG A:4GA1001 3.9 25.3 1.0 NH2 A:ARG112 4.0 25.6 1.0 CAR A:4GA1001 4.0 28.9 1.0 CAJ A:4GA1001 4.0 31.3 1.0 O A:ASP103 4.3 24.8 1.0 OAE A:4GA1001 4.3 24.9 1.0 OD1 A:ASP104 4.3 26.0 1.0 CB A:ASP103 4.4 23.9 1.0 OAF A:4GA1001 4.4 29.5 1.0 O A:HOH1103 4.4 19.8 1.0 OD1 A:ASP107 4.5 21.9 1.0 OG A:SER109 4.5 26.2 1.0 O A:HOH1112 4.6 26.0 1.0 O A:HOH1105 4.6 24.5 1.0 C A:ASP103 4.6 25.8 1.0 OAC A:4GA1001 4.7 28.2 1.0 MG A:MG1002 4.7 23.8 1.0 O A:HOH1104 4.7 24.6 1.0 CAI A:4GA1001 4.8 31.2 1.0 NAQ A:4GA1001 4.9 33.3 1.0

Y.Zhang, W.Zhu, Y.L.Liu, H.Wang, K.Wang, K.Li, J.H.No, L.Ayong, A.Gulati, R.Pang, L.Freitas-Junior, C.T.Morita, E.Old-Field. Chemo-Immunotherapeutic Anti-Malarials Targeting Isoprenoid Biosynthesis. Acs Med.Chem.Lett. V. 4 423 2013.
ISSN: ISSN 1948-5875
PubMed: 23610597
DOI: 10.1021/ML4000436