Magnesium in PDB 2q58: Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate

The structure of Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate, PDB code: 2q58 was solved by M.Chruszcz, J.Artz, H.Zheng, A.Dong, J.Dunford, J.Lew, Y.Zhao, I.Kozieradski, K.L.Kavanaugh, U.Opperman, M.Sundstrom, J.Weigelt, A.Edwards, C.Arrowsmith, A.Bochkarev, R.Hui, W.Minor, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.46 / 2.37
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	101.776, 101.776, 75.275, 90.00, 90.00, 120.00
R / Rfree (%)	21.6 / 23.8

The binding sites of Magnesium atom in the Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate (pdb code 2q58). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate, PDB code: 2q58:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3 b:33.4 occ:1.00 O12 A:ZOL1 2.0 44.9 1.0 O17 A:ZOL1 2.0 41.0 1.0 O A:HOH8002 2.3 20.0 1.0 OD2 A:ASP1119 2.3 51.1 1.0 OD2 A:ASP1115 2.3 66.3 1.0 MG A:MG4 3.1 35.0 1.0 CG A:ASP1115 3.1 68.9 1.0 P9 A:ZOL1 3.1 58.3 1.0 P14 A:ZOL1 3.2 61.3 1.0 OD1 A:ASP1115 3.2 83.9 1.0 CG A:ASP1119 3.4 45.3 1.0 C8 A:ZOL1 3.5 61.0 1.0 C7 A:ZOL1 3.7 58.0 1.0 NH1 A:ARG1124 3.7 43.5 1.0 O A:HOH8006 3.9 31.0 1.0 CB A:ASP1119 3.9 33.9 1.0 O16 A:ZOL1 4.0 86.7 1.0 O11 A:ZOL1 4.0 60.1 1.0 O10 A:ZOL1 4.4 70.3 1.0 MG A:MG5 4.4 30.2 1.0 O15 A:ZOL1 4.5 50.2 1.0 OD1 A:ASP1119 4.5 79.8 1.0 CB A:ASP1115 4.5 58.3 1.0 O A:ASP1115 4.7 57.3 1.0 OD1 A:ASP1116 4.7 64.6 1.0 O A:HOH8001 4.8 20.0 1.0 N15 A:ZOL1 4.8 51.5 1.0 C A:ASP1115 4.9 46.0 1.0 O13 A:ZOL1 4.9 50.4 1.0

Magnesium binding site 2 out of 6 in the Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4 b:35.0 occ:1.00 O12 A:ZOL1 2.1 44.9 1.0 O A:HOH8001 2.1 20.0 1.0 OD2 A:ASP1119 2.1 51.1 1.0 OD1 A:ASP1115 2.3 83.9 1.0 CG A:ASP1119 3.0 45.3 1.0 MG A:MG3 3.1 33.4 1.0 OD1 A:ASP1119 3.1 79.8 1.0 P9 A:ZOL1 3.2 58.3 1.0 O10 A:ZOL1 3.3 70.3 1.0 CG A:ASP1115 3.3 68.9 1.0 OD2 A:ASP1115 3.7 66.3 1.0 OD1 A:ASP1187 4.1 66.3 1.0 C19 A:ZOL1 4.3 48.9 1.0 OE1 A:GLN1184 4.3 49.6 1.0 O11 A:ZOL1 4.3 60.1 1.0 NE2 A:GLN1184 4.3 43.3 1.0 C7 A:ZOL1 4.4 58.0 1.0 CB A:ASP1119 4.4 33.9 1.0 OD2 A:ASP1187 4.4 54.2 1.0 CG A:ASP1187 4.4 58.9 1.0 C8 A:ZOL1 4.4 61.0 1.0 N15 A:ZOL1 4.5 51.5 1.0 CB A:ASP1115 4.6 58.3 1.0 O17 A:ZOL1 4.7 41.0 1.0 O A:HOH8002 4.7 20.0 1.0 CD A:GLN1184 4.8 44.4 1.0 O A:ASP1115 4.9 57.3 1.0 CA A:ASP1115 5.0 50.7 1.0

Magnesium binding site 3 out of 6 in the Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg5 b:30.2 occ:1.00 O11 A:ZOL1 2.0 60.1 1.0 O16 A:ZOL1 2.0 86.7 1.0 O A:HOH8008 2.1 29.6 1.0 O A:HOH8006 2.2 31.0 1.0 O A:HOH8007 2.2 32.6 1.0 OD1 A:ASN1254 2.5 32.4 1.0 P9 A:ZOL1 3.2 58.3 1.0 P14 A:ZOL1 3.2 61.3 1.0 CG A:ASN1254 3.3 37.3 1.0 ND2 A:ASN1254 3.5 38.4 1.0 C8 A:ZOL1 3.6 61.0 1.0 O17 A:ZOL1 3.8 41.0 1.0 O12 A:ZOL1 3.8 44.9 1.0 O13 A:ZOL1 3.8 50.4 1.0 OD1 A:ASP1255 4.1 69.1 1.0 O A:ASN1254 4.2 45.7 1.0 MG A:MG3 4.4 33.4 1.0 O15 A:ZOL1 4.5 50.2 1.0 O10 A:ZOL1 4.5 70.3 1.0 OE1 A:GLN1251 4.6 63.9 1.0 C A:ASN1254 4.7 53.3 1.0 CB A:ASN1254 4.8 49.4 1.0

Magnesium binding site 4 out of 6 in the Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg6 b:33.0 occ:1.00 O17 B:ZOL2 2.0 66.8 1.0 O B:HOH8003 2.1 20.0 1.0 OD2 B:ASP2119 2.5 59.8 1.0 OD2 B:ASP2115 2.6 60.9 1.0 O B:HOH8004 2.6 20.0 1.0 O12 B:ZOL2 2.8 65.3 1.0 P14 B:ZOL2 3.2 60.5 1.0 CG B:ASP2119 3.4 33.4 1.0 CB B:ASP2119 3.6 33.6 1.0 CG B:ASP2115 3.7 50.4 1.0 O16 B:ZOL2 3.7 56.3 1.0 P9 B:ZOL2 3.7 48.8 1.0 NH2 B:ARG2271 4.0 56.8 1.0 MG B:MG7 4.1 33.3 1.0 O11 B:ZOL2 4.1 40.1 1.0 C8 B:ZOL2 4.1 41.6 1.0 NH1 B:ARG2124 4.1 31.1 1.0 OD1 B:ASP2115 4.1 53.9 1.0 O B:HOH8009 4.2 29.3 1.0 NZ B:LYS2273 4.3 62.1 1.0 O15 B:ZOL2 4.5 53.1 1.0 C7 B:ZOL2 4.6 47.9 1.0 O B:ASP2115 4.6 63.3 1.0 OD1 B:ASP2119 4.6 54.2 1.0 OD1 B:ASP2116 4.7 39.8 1.0 CB B:ASP2115 4.9 53.6 1.0 CZ B:ARG2271 4.9 62.9 1.0

Magnesium binding site 5 out of 6 in the Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg7 b:33.3 occ:1.00 O B:HOH8005 2.2 20.0 1.0 OD2 B:ASP2119 2.4 59.8 1.0 O12 B:ZOL2 2.5 65.3 1.0 OD2 B:ASP2187 2.9 52.0 1.0 OD1 B:ASP2115 3.1 53.9 1.0 CG B:ASP2119 3.2 33.4 1.0 OD1 B:ASP2119 3.3 54.2 1.0 CG B:ASP2187 3.6 44.9 1.0 NZ B:LYS2273 3.6 62.1 1.0 OD1 B:ASP2187 3.7 50.0 1.0 P9 B:ZOL2 3.7 48.8 1.0 CG B:ASP2115 4.0 50.4 1.0 O10 B:ZOL2 4.0 61.1 1.0 MG B:MG6 4.1 33.0 1.0 OD2 B:ASP2115 4.1 60.9 1.0 CE B:LYS2273 4.1 77.1 1.0 NH2 B:ARG2271 4.4 56.8 1.0 O11 B:ZOL2 4.5 40.1 1.0 OE1 B:GLN2184 4.6 47.9 1.0 CD B:LYS2273 4.7 72.6 1.0 NZ B:LYS2210 4.7 35.9 1.0 CB B:ASP2119 4.7 33.6 1.0 CB B:ASP2187 4.7 44.7 1.0 NE2 B:GLN2184 4.8 65.8 1.0 O B:HOH8003 4.8 20.0 1.0

Magnesium binding site 6 out of 6 in the Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryptosporidium Parvum Putative Polyprenyl Pyrophosphate Synthase (CGD4_2550) in Complex with Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg8 b:30.7 occ:1.00 OD1 B:ASN2254 1.9 48.6 1.0 O11 B:ZOL2 2.0 40.1 1.0 O B:HOH8009 2.0 29.3 1.0 O B:HOH8010 2.4 34.5 1.0 O B:HOH8011 2.4 29.0 1.0 O16 B:ZOL2 2.5 56.3 1.0 CG B:ASN2254 3.0 44.5 1.0 P9 B:ZOL2 3.5 48.8 1.0 O13 B:ZOL2 3.5 53.7 1.0 P14 B:ZOL2 3.7 60.5 1.0 OD1 B:ASP2255 3.8 65.1 1.0 C8 B:ZOL2 3.8 41.6 1.0 O B:ASN2254 3.8 49.6 1.0 NE2 B:GLN2251 3.8 47.1 1.0 ND2 B:ASN2254 3.9 64.0 1.0 C B:ASN2254 4.0 51.2 1.0 CB B:ASN2254 4.0 48.1 1.0 OD1 B:ASP2268 4.2 90.3 1.0 O B:HOH8003 4.2 20.0 1.0 N B:ASP2255 4.3 52.9 1.0 O10 B:ZOL2 4.4 61.1 1.0 OD1 B:ASP2258 4.4 78.5 1.0 NZ B:LYS2273 4.4 62.1 1.0 CA B:ASP2255 4.4 46.2 1.0 O12 B:ZOL2 4.5 65.3 1.0 CA B:ASN2254 4.6 50.3 1.0 CB B:ASP2258 4.6 51.8 1.0 O17 B:ZOL2 4.7 66.8 1.0 CG B:ASP2258 4.8 57.6 1.0 CG B:ASP2255 4.8 58.7 1.0 O15 B:ZOL2 4.8 53.1 1.0

J.D.Artz, J.E.Dunford, M.J.Arrowood, A.Dong, M.Chruszcz, K.L.Kavanagh, W.Minor, R.G.Russell, F.H.Ebetino, U.Oppermann, R.Hui. Targeting A Uniquely Nonspecific Prenyl Synthase with Bisphosphonates to Combat Cryptosporidiosis Chem.Biol. V. 15 1296 2008.
ISSN: ISSN 1074-5521
PubMed: 19101474
DOI: 10.1016/J.CHEMBIOL.2008.10.017