Magnesium in PDB 3ryw: Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811

The structure of Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811, PDB code: 3ryw was solved by J.H.No, 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)	35.22 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.744, 106.582, 139.031, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 26

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 (pdb code 3ryw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811, PDB code: 3ryw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811


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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:23.5 occ:1.00 OAF A:K9H2001 2.2 29.0 1.0 OAB A:K9H2001 2.3 30.5 1.0 OD1 A:ASP287 2.5 33.1 1.0 OD1 A:ASP305 3.5 40.0 1.0 CG A:ASP287 3.5 32.4 1.0 OD2 A:ASP305 3.8 44.4 1.0 PBA A:K9H2001 3.8 29.8 1.0 OD2 A:ASP291 3.8 38.4 1.0 PAZ A:K9H2001 3.9 33.1 1.0 OD2 A:ASP287 4.0 30.6 1.0 CG A:ASP305 4.0 39.2 1.0 O A:ASP287 4.2 27.3 1.0 OAC A:K9H2001 4.3 32.0 1.0 OD2 A:ASP288 4.3 37.3 1.0 CG A:ASP291 4.5 41.6 1.0 NE2 A:GLN284 4.5 31.2 1.0 CAY A:K9H2001 4.5 32.1 1.0 CB A:ASP291 4.6 39.3 1.0 C A:ASP287 4.6 28.8 1.0 OAD A:K9H2001 4.7 32.0 1.0 CB A:ASP287 4.7 29.6 1.0 OAG A:K9H2001 4.8 29.8 1.0 OAE A:K9H2001 4.8 36.5 1.0 MG A:MG2003 4.8 11.6 1.0 NZ A:LYS301 4.9 32.6 1.0

Magnesium binding site 2 out of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811


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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2003 b:11.6 occ:1.00 OD2 A:ASP130 2.0 33.1 1.0 OD2 A:ASP126 2.3 22.3 1.0 O A:HOH2108 2.5 20.6 1.0 OAC A:K9H2001 2.5 32.0 1.0 OAD A:K9H2001 2.7 32.0 1.0 CAY A:K9H2001 2.9 32.1 1.0 CG A:ASP130 3.1 33.2 1.0 CG A:ASP126 3.2 21.5 1.0 PBA A:K9H2001 3.3 29.8 1.0 PAZ A:K9H2001 3.4 33.1 1.0 OD1 A:ASP126 3.4 21.9 1.0 CB A:ASP130 3.5 30.6 1.0 MG A:MG2004 3.6 16.1 1.0 OAB A:K9H2001 3.8 30.5 1.0 OAF A:K9H2001 4.0 29.0 1.0 OD1 A:ASP130 4.2 38.4 1.0 CAT A:K9H2001 4.3 36.0 1.0 OAG A:K9H2001 4.6 29.8 1.0 CB A:ASP126 4.6 21.5 1.0 O A:ASP126 4.6 21.7 1.0 OAE A:K9H2001 4.8 36.5 1.0 MG A:MG2002 4.8 23.5 1.0 NH1 A:ARG135 4.9 23.5 1.0 C A:ASP126 5.0 23.2 1.0

Magnesium binding site 3 out of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811


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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2004 b:16.1 occ:1.00 OAD A:K9H2001 2.0 32.0 1.0 OD1 A:ASP126 2.3 21.9 1.0 OD2 A:ASP130 2.4 33.1 1.0 OD1 A:ASP130 2.8 38.4 1.0 CG A:ASP130 3.0 33.2 1.0 OE1 A:GLN195 3.1 29.3 1.0 OD2 A:ASP198 3.3 38.7 1.0 CG A:ASP126 3.3 21.5 1.0 PAZ A:K9H2001 3.5 33.1 1.0 MG A:MG2003 3.6 11.6 1.0 OD2 A:ASP126 3.8 22.3 1.0 OAE A:K9H2001 3.9 36.5 1.0 CD A:GLN195 3.9 28.0 1.0 NE2 A:GLN195 3.9 26.7 1.0 CG A:ASP198 4.2 33.8 1.0 CAY A:K9H2001 4.3 32.1 1.0 CE A:LYS310 4.4 35.2 1.0 CB A:ASP130 4.5 30.6 1.0 OAB A:K9H2001 4.6 30.5 1.0 NZ A:LYS310 4.6 38.0 1.0 CB A:ASP126 4.6 21.5 1.0 NZ A:LYS243 4.7 29.5 1.0 OD1 A:ASP198 4.8 36.5 1.0 CAJ A:K9H2001 4.9 37.7 1.0 O A:ASP126 5.0 21.7 1.0

Magnesium binding site 4 out of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2002 b:21.6 occ:1.00 OAF B:K9H2001 2.2 35.1 1.0 OD1 B:ASP287 2.3 50.1 1.0 OAB B:K9H2001 2.6 30.0 1.0 CG B:ASP287 3.3 43.2 1.0 OD1 B:ASP305 3.7 47.3 1.0 OD2 B:ASP287 3.7 42.8 1.0 OAD B:K9H2001 3.8 32.3 1.0 PBA B:K9H2001 3.8 32.0 1.0 PAZ B:K9H2001 3.8 33.3 1.0 OD2 B:ASP291 3.9 49.1 1.0 OD2 B:ASP305 3.9 42.1 1.0 O B:ASP287 4.1 33.2 1.0 CG B:ASP305 4.2 41.9 1.0 OD2 B:ASP288 4.3 53.3 1.0 NE2 B:GLN284 4.4 41.7 1.0 C B:ASP287 4.5 34.8 1.0 CB B:ASP287 4.5 38.6 1.0 OAC B:K9H2001 4.5 32.1 1.0 CAY B:K9H2001 4.5 32.3 1.0 CG B:ASP291 4.6 47.3 1.0 CB B:ASP291 4.6 43.1 1.0 OAG B:K9H2001 4.7 33.8 1.0 MG B:MG2003 4.9 19.1 1.0 N B:ASP288 4.9 35.1 1.0 NZ B:LYS301 5.0 42.2 1.0

Magnesium binding site 5 out of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2003 b:19.1 occ:1.00 OD2 B:ASP130 2.0 27.6 1.0 OAD B:K9H2001 2.1 32.3 1.0 OD2 B:ASP126 2.3 27.6 1.0 OAC B:K9H2001 2.4 32.1 1.0 CG B:ASP130 3.1 27.4 1.0 CG B:ASP126 3.2 26.7 1.0 CAY B:K9H2001 3.4 32.3 1.0 PBA B:K9H2001 3.4 32.0 1.0 OD1 B:ASP126 3.4 29.3 1.0 PAZ B:K9H2001 3.4 33.3 1.0 CB B:ASP130 3.5 27.8 1.0 MG B:MG2004 3.6 13.5 1.0 OAF B:K9H2001 3.8 35.1 1.0 OD1 B:ASP130 4.1 29.0 1.0 OAB B:K9H2001 4.4 30.0 1.0 OAE B:K9H2001 4.4 33.8 1.0 O B:HOH2104 4.5 22.0 1.0 CB B:ASP126 4.6 24.8 1.0 O B:ASP126 4.7 25.3 1.0 OAG B:K9H2001 4.7 33.8 1.0 CAT B:K9H2001 4.9 31.8 1.0 MG B:MG2002 4.9 21.6 1.0 NH1 B:ARG135 4.9 29.6 1.0

Magnesium binding site 6 out of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2004 b:13.5 occ:1.00 OD1 B:ASP126 2.4 29.3 1.0 OD2 B:ASP130 2.4 27.6 1.0 OAD B:K9H2001 2.7 32.3 1.0 OAE B:K9H2001 2.9 33.8 1.0 OD1 B:ASP130 3.0 29.0 1.0 CG B:ASP130 3.1 27.4 1.0 OE1 B:GLN195 3.2 33.8 1.0 OD2 B:ASP198 3.3 41.1 1.0 PAZ B:K9H2001 3.4 33.3 1.0 CG B:ASP126 3.5 26.7 1.0 MG B:MG2003 3.6 19.1 1.0 OD2 B:ASP126 3.8 27.6 1.0 CD B:GLN195 4.0 29.8 1.0 NE2 B:GLN195 4.1 29.8 1.0 CG B:ASP198 4.3 33.2 1.0 CE B:LYS310 4.4 27.6 1.0 CAY B:K9H2001 4.5 32.3 1.0 NZ B:LYS243 4.5 42.5 1.0 CB B:ASP130 4.6 27.8 1.0 OAB B:K9H2001 4.6 30.0 1.0 NZ B:LYS310 4.7 28.5 1.0 CB B:ASP126 4.8 24.8 1.0 OD1 B:ASP198 4.8 35.6 1.0 CAJ B:K9H2001 4.9 31.2 1.0

Magnesium binding site 7 out of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2002 b:29.1 occ:1.00 OAF C:K9H2001 1.9 29.5 1.0 OD1 C:ASP287 2.4 35.0 1.0 OAB C:K9H2001 2.6 27.2 1.0 CG C:ASP287 3.3 37.1 1.0 OD2 C:ASP287 3.6 38.9 1.0 PBA C:K9H2001 3.6 27.7 1.0 OD1 C:ASP305 3.7 49.2 1.0 OD2 C:ASP291 3.9 47.2 1.0 PAZ C:K9H2001 3.9 28.5 1.0 OD2 C:ASP305 4.0 51.9 1.0 O C:ASP287 4.2 31.4 1.0 CG C:ASP305 4.3 47.7 1.0 OAC C:K9H2001 4.3 28.6 1.0 OAD C:K9H2001 4.4 27.3 1.0 OAG C:K9H2001 4.5 28.6 1.0 CAY C:K9H2001 4.5 29.2 1.0 CB C:ASP287 4.6 34.3 1.0 NZ C:LYS301 4.6 47.2 1.0 OD2 C:ASP288 4.6 51.0 1.0 CG C:ASP291 4.6 45.2 1.0 C C:ASP287 4.6 33.1 1.0 NE2 C:GLN284 4.6 36.4 1.0 CB C:ASP291 4.7 43.0 1.0 CE C:LYS301 4.9 50.1 1.0 MG C:MG2003 5.0 15.5 1.0

Magnesium binding site 8 out of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2003 b:15.5 occ:1.00 OD2 C:ASP130 2.1 30.1 1.0 OAD C:K9H2001 2.1 27.3 1.0 OD2 C:ASP126 2.5 27.2 1.0 OAC C:K9H2001 2.5 28.6 1.0 CG C:ASP130 3.1 28.6 1.0 CAY C:K9H2001 3.4 29.2 1.0 CB C:ASP130 3.4 27.9 1.0 PBA C:K9H2001 3.4 27.7 1.0 PAZ C:K9H2001 3.4 28.5 1.0 CG C:ASP126 3.5 25.0 1.0 OD1 C:ASP126 3.7 25.5 1.0 OAF C:K9H2001 3.9 29.5 1.0 MG C:MG2004 4.0 22.9 1.0 OAB C:K9H2001 4.2 27.2 1.0 OD1 C:ASP130 4.2 31.3 1.0 OAE C:K9H2001 4.6 30.7 1.0 O C:ASP126 4.7 22.3 1.0 OAG C:K9H2001 4.8 28.6 1.0 NH1 C:ARG135 4.8 27.3 1.0 CB C:ASP126 4.8 23.3 1.0 CAT C:K9H2001 4.9 32.1 1.0 CA C:ASP130 4.9 29.6 1.0 OD1 C:ASP127 4.9 29.0 1.0 MG C:MG2002 5.0 29.1 1.0

Magnesium binding site 9 out of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2004 b:22.9 occ:1.00 OD1 C:ASP126 2.4 25.5 1.0 OAD C:K9H2001 2.4 27.3 1.0 OD2 C:ASP130 2.6 30.1 1.0 OAE C:K9H2001 2.9 30.7 1.0 OE1 C:GLN195 3.1 29.5 1.0 OD2 C:ASP198 3.1 44.4 1.0 PAZ C:K9H2001 3.2 28.5 1.0 OD1 C:ASP130 3.2 31.3 1.0 CG C:ASP130 3.3 28.6 1.0 CG C:ASP126 3.5 25.0 1.0 OD2 C:ASP126 3.9 27.2 1.0 CD C:GLN195 4.0 28.2 1.0 MG C:MG2003 4.0 15.5 1.0 CG C:ASP198 4.0 40.6 1.0 NE2 C:GLN195 4.1 29.1 1.0 OAB C:K9H2001 4.3 27.2 1.0 CAY C:K9H2001 4.4 29.2 1.0 CE C:LYS310 4.5 30.9 1.0 NZ C:LYS243 4.5 39.3 1.0 OD1 C:ASP198 4.5 43.0 1.0 NZ C:LYS310 4.7 33.9 1.0 CB C:ASP130 4.8 27.9 1.0 CB C:ASP126 4.8 23.3 1.0 CB C:ASP198 5.0 37.2 1.0

Magnesium binding site 10 out of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2002 b:30.0 occ:1.00 OD1 D:ASP287 2.1 53.0 1.0 OAF D:K9H2001 2.2 24.9 1.0 OAB D:K9H2001 2.6 25.0 1.0 CG D:ASP287 3.0 48.1 1.0 OD2 D:ASP287 3.4 52.9 1.0 O D:ASP287 3.8 32.3 1.0 PBA D:K9H2001 3.8 24.8 1.0 OD1 D:ASP305 3.8 54.3 1.0 OD2 D:ASP291 3.9 59.7 1.0 OD2 D:ASP305 4.0 58.1 1.0 PAZ D:K9H2001 4.0 26.6 1.0 CB D:ASP287 4.2 41.7 1.0 C D:ASP287 4.2 36.4 1.0 OD2 D:ASP288 4.3 41.9 1.0 NE2 D:GLN284 4.3 37.0 1.0 CG D:ASP305 4.3 52.4 1.0 CB D:ASP291 4.5 46.5 1.0 OAD D:K9H2001 4.6 23.4 1.0 CG D:ASP291 4.6 51.7 1.0 CAY D:K9H2001 4.6 26.7 1.0 NZ D:LYS301 4.6 47.6 1.0 OAC D:K9H2001 4.7 25.4 1.0 N D:ASP288 4.7 36.1 1.0 OAG D:K9H2001 4.7 26.5 1.0 CA D:ASP287 4.8 37.4 1.0 CA D:ASP288 4.9 36.6 1.0 CE D:LYS301 5.0 45.1 1.0

J.H.No, F.De Macedo Dossin, Y.Zhang, Y.L.Liu, W.Zhu, X.Feng, J.A.Yoo, E.Lee, K.Wang, R.Hui, L.H.Freitas-Junior, E.Oldfield. Lipophilic Analogs of Zoledronate and Risedronate Inhibit Plasmodium Geranylgeranyl Diphosphate Synthase (Ggpps) and Exhibit Potent Antimalarial Activity. Proc.Natl.Acad.Sci.Usa V. 109 4058 2012.
ISSN: ISSN 0027-8424
PubMed: 22392982
DOI: 10.1073/PNAS.1118215109