Magnesium in PDB 6g31: Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate

All present enzymatic activity of Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate:
2.5.1.1; 2.5.1.10; 2.5.1.29;

The structure of Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate, PDB code: 6g31 was solved by M.Lisnyansky, N.Kapelushnik, A.Ben-Bassat, M.Marom, A.Loewenstein, D.Khananshvili, M.Giladi, Y.Haitin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.62 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	116.800, 134.240, 134.460, 90.00, 102.67, 90.00
R / Rfree (%)	25.6 / 30.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate (pdb code 6g31). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 36 binding sites of Magnesium where determined in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate, PDB code: 6g31:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 36 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate


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 Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:57.6 occ:1.00 O16 A:ZOL401 1.9 63.3 1.0 O10 A:ZOL401 2.3 64.4 1.0 P14 A:ZOL401 3.2 66.6 1.0 O13 A:ZOL401 3.6 65.1 1.0 P9 A:ZOL401 3.6 63.1 1.0 C8 A:ZOL401 3.7 65.2 1.0 NE2 A:GLN185 3.7 72.9 1.0 NZ A:LYS212 3.8 77.0 1.0 OD1 A:ASP189 3.8 77.0 1.0 O17 A:ZOL401 4.0 68.3 1.0 OD1 A:ASP207 4.2 76.3 1.0 O15 A:ZOL401 4.3 62.5 1.0 CB A:TYR188 4.4 89.3 1.0 O12 A:ZOL401 4.4 62.6 1.0 OD2 A:ASP207 4.6 75.7 1.0 O11 A:ZOL401 4.7 61.7 1.0 CD A:GLN185 4.7 75.6 1.0 CG A:ASP207 4.8 75.2 1.0 OE1 A:GLN185 4.9 77.6 1.0 CE A:LYS212 4.9 72.9 1.0 C A:TYR188 4.9 84.2 1.0 O A:TYR188 5.0 86.2 1.0 OD1 A:ASN192 5.0 82.5 1.0

Magnesium binding site 2 out of 36 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate


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 Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:54.3 occ:1.00 OD2 A:ASP64 1.9 57.1 1.0 O15 A:ZOL401 2.1 62.5 1.0 O12 A:ZOL401 2.2 62.6 1.0 OD1 A:ASP68 2.8 56.6 1.0 CG A:ASP64 3.0 57.4 1.0 P14 A:ZOL401 3.3 66.6 1.0 P9 A:ZOL401 3.5 63.1 1.0 OD1 A:ASP64 3.5 57.3 1.0 CG A:ASP68 3.6 56.8 1.0 C7 A:ZOL401 3.7 67.4 1.0 C8 A:ZOL401 3.7 65.2 1.0 CB A:ASP68 3.7 56.8 1.0 OD1 A:ASP65 3.8 55.9 1.0 MG A:MG404 3.9 47.9 1.0 O16 A:ZOL401 4.1 63.3 1.0 CB A:ASP64 4.3 58.3 1.0 O10 A:ZOL401 4.3 64.4 1.0 NH1 A:ARG73 4.4 60.6 1.0 O17 A:ZOL401 4.5 68.3 1.0 O11 A:ZOL401 4.5 61.7 1.0 NH2 A:ARG73 4.5 61.9 1.0 O A:ASP64 4.6 58.5 1.0 C A:ASP64 4.7 59.0 1.0 OD2 A:ASP68 4.7 57.1 1.0 N15 A:ZOL401 4.8 70.2 1.0 CZ A:ARG73 4.9 61.5 1.0

Magnesium binding site 3 out of 36 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate


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 Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:47.9 occ:1.00 OD1 A:ASP64 2.1 57.3 1.0 OD1 A:ASP68 2.2 56.6 1.0 O12 A:ZOL401 2.5 62.6 1.0 O11 A:ZOL401 2.8 61.7 1.0 CG A:ASP68 3.1 56.8 1.0 OE1 A:GLN126 3.1 64.8 1.0 CG A:ASP64 3.2 57.4 1.0 P9 A:ZOL401 3.2 63.1 1.0 OD2 A:ASP68 3.3 57.1 1.0 OD2 A:ASP64 3.5 57.1 1.0 MG A:MG403 3.9 54.3 1.0 OD2 A:ASP129 3.9 65.6 1.0 CD A:GLN126 4.1 64.1 1.0 O10 A:ZOL401 4.3 64.4 1.0 C19 A:ZOL401 4.3 68.1 1.0 NE2 A:GLN126 4.3 64.9 1.0 N15 A:ZOL401 4.5 70.2 1.0 CB A:ASP68 4.5 56.8 1.0 CB A:ASP64 4.5 58.3 1.0 C7 A:ZOL401 4.5 67.4 1.0 C8 A:ZOL401 4.6 65.2 1.0 NH2 A:ARG133 4.7 68.4 1.0 C18 A:ZOL401 5.0 68.5 1.0 CD A:LYS151 5.0 72.3 1.0

Magnesium binding site 4 out of 36 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate


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 Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:68.3 occ:1.00 O16 B:ZOL401 2.0 62.9 1.0 O10 B:ZOL401 3.3 64.1 1.0 P14 B:ZOL401 3.5 66.2 1.0 OD2 B:ASP207 3.8 62.7 1.0 OD2 B:ASP189 4.0 64.5 1.0 O13 B:ZOL401 4.0 64.8 1.0 CB B:TYR188 4.1 73.0 1.0 O15 B:ZOL401 4.2 62.2 1.0 C8 B:ZOL401 4.2 64.8 1.0 OD1 B:ASP207 4.3 61.8 1.0 P9 B:ZOL401 4.4 62.7 1.0 O B:TYR188 4.4 75.4 1.0 C B:TYR188 4.4 75.0 1.0 CG B:ASP207 4.4 63.2 1.0 O17 B:ZOL401 4.5 67.9 1.0 OD1 B:ASN192 4.7 67.9 1.0 N B:ASP189 4.7 68.5 1.0 CB B:ASN192 4.7 66.1 1.0 OE1 B:GLN185 4.9 65.4 1.0 CA B:TYR188 4.9 74.9 1.0 CA B:ASP189 5.0 68.9 1.0

Magnesium binding site 5 out of 36 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate


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 Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:59.1 occ:1.00 OD2 B:ASP64 2.0 57.0 1.0 O12 B:ZOL401 2.0 62.2 1.0 O15 B:ZOL401 2.1 62.2 1.0 OD1 B:ASP68 3.0 57.4 1.0 CG B:ASP64 3.1 58.7 1.0 P9 B:ZOL401 3.3 62.7 1.0 P14 B:ZOL401 3.4 66.2 1.0 CG B:ASP68 3.4 55.6 1.0 OD1 B:ASP64 3.4 60.8 1.0 CB B:ASP68 3.6 52.6 1.0 C8 B:ZOL401 3.8 64.8 1.0 MG B:MG404 3.9 51.8 1.0 NH1 B:ARG73 3.9 63.1 1.0 O10 B:ZOL401 4.0 64.1 1.0 OG B:SER70 4.1 54.7 1.0 C7 B:ZOL401 4.1 67.1 1.0 O16 B:ZOL401 4.2 62.9 1.0 OD1 B:ASP65 4.3 54.4 1.0 OD2 B:ASP68 4.3 56.7 1.0 O17 B:ZOL401 4.4 67.9 1.0 O11 B:ZOL401 4.4 61.3 1.0 CB B:ASP64 4.4 59.7 1.0 O B:ASP64 4.7 51.5 1.0 C B:ASP64 4.8 53.4 1.0

Magnesium binding site 6 out of 36 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate


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 Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:51.8 occ:1.00 OD1 B:ASP64 2.0 60.8 1.0 OD1 B:ASP68 2.3 57.4 1.0 O12 B:ZOL401 2.3 62.2 1.0 O11 B:ZOL401 2.5 61.3 1.0 OD2 B:ASP68 2.8 56.7 1.0 CG B:ASP68 2.9 55.6 1.0 P9 B:ZOL401 2.9 62.7 1.0 CG B:ASP64 3.1 58.7 1.0 OD2 B:ASP64 3.6 57.0 1.0 MG B:MG403 3.9 59.1 1.0 O10 B:ZOL401 3.9 64.1 1.0 OE1 B:GLN126 3.9 58.0 1.0 OD2 B:ASP129 4.2 51.4 1.0 C19 B:ZOL401 4.3 67.8 1.0 CB B:ASP68 4.4 52.6 1.0 NE2 B:GLN126 4.4 55.2 1.0 CD B:GLN126 4.4 57.3 1.0 CB B:ASP64 4.4 59.7 1.0 C8 B:ZOL401 4.5 64.8 1.0 C7 B:ZOL401 4.7 67.1 1.0 N15 B:ZOL401 4.8 69.8 1.0 CG B:ASP129 4.9 52.0 1.0

Magnesium binding site 7 out of 36 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate


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 Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:60.7 occ:1.00 O16 C:ZOL401 2.2 65.3 1.0 O11 C:ZOL401 2.4 66.5 1.0 O13 C:ZOL401 3.1 67.2 1.0 P14 C:ZOL401 3.3 68.7 1.0 OD2 C:ASP189 3.3 76.4 1.0 C8 C:ZOL401 3.4 67.2 1.0 P9 C:ZOL401 3.4 65.1 1.0 OE1 C:GLN185 3.9 77.3 1.0 CB C:TYR188 3.9 81.6 1.0 O15 C:ZOL401 4.2 70.4 1.0 O17 C:ZOL401 4.4 64.6 1.0 O10 C:ZOL401 4.4 64.7 1.0 O12 C:ZOL401 4.4 63.8 1.0 CG C:ASP189 4.5 75.3 1.0 C C:TYR188 4.8 80.9 1.0 N C:ASP189 4.8 79.9 1.0 CD C:GLN185 4.8 76.0 1.0 C7 C:ZOL401 4.9 69.5 1.0

Magnesium binding site 8 out of 36 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate


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 Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:62.4 occ:1.00 OD2 C:ASP64 1.9 64.9 1.0 O10 C:ZOL401 2.0 64.7 1.0 O17 C:ZOL401 2.1 64.6 1.0 OD1 C:ASP68 2.2 67.3 1.0 CG C:ASP64 2.8 65.0 1.0 OD1 C:ASP64 3.0 67.6 1.0 CG C:ASP68 3.1 65.8 1.0 P9 C:ZOL401 3.4 65.1 1.0 NH1 C:ARG73 3.4 74.3 1.0 P14 C:ZOL401 3.4 68.7 1.0 CB C:ASP68 3.5 63.7 1.0 C8 C:ZOL401 3.8 67.2 1.0 MG C:MG404 3.8 53.8 1.0 C7 C:ZOL401 3.9 69.5 1.0 O11 C:ZOL401 4.1 66.5 1.0 OG C:SER70 4.1 69.2 1.0 O16 C:ZOL401 4.1 65.3 1.0 OD2 C:ASP68 4.2 66.2 1.0 CB C:ASP64 4.3 62.7 1.0 CZ C:ARG73 4.3 71.1 1.0 O C:ASP64 4.4 60.2 1.0 OD1 C:ASP65 4.4 59.7 1.0 O12 C:ZOL401 4.4 63.8 1.0 NH2 C:ARG73 4.5 71.9 1.0 O15 C:ZOL401 4.6 70.4 1.0 C C:ASP64 4.6 59.4 1.0 N15 C:ZOL401 5.0 72.2 1.0 CA C:ASP68 5.0 62.5 1.0

Magnesium binding site 9 out of 36 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate


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 Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg404 b:53.8 occ:1.00 OD1 C:ASP68 2.3 67.3 1.0 OD1 C:ASP64 2.4 67.6 1.0 OD2 C:ASP68 2.5 66.2 1.0 CG C:ASP68 2.7 65.8 1.0 O10 C:ZOL401 2.8 64.7 1.0 NE2 C:GLN126 2.8 75.8 1.0 OD2 C:ASP129 3.2 73.9 1.0 O12 C:ZOL401 3.3 63.8 1.0 P9 C:ZOL401 3.6 65.1 1.0 CG C:ASP64 3.6 65.0 1.0 MG C:MG403 3.8 62.4 1.0 CD C:GLN126 4.0 76.2 1.0 OD2 C:ASP64 4.2 64.9 1.0 CB C:ASP68 4.2 63.7 1.0 O11 C:ZOL401 4.3 66.5 1.0 CG C:ASP129 4.4 73.2 1.0 CG C:GLN126 4.7 76.1 1.0 C19 C:ZOL401 4.7 70.2 1.0 OE1 C:GLN126 4.8 76.8 1.0 CB C:ASP64 4.8 62.7 1.0

Magnesium binding site 10 out of 36 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate


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 Human Geranylgeranyl Diphosphate Synthase Mutant D188Y Bound to Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:63.1 occ:1.00 O16 D:ZOL401 2.3 62.2 1.0 O11 D:ZOL401 2.5 63.3 1.0 P14 D:ZOL401 3.8 65.5 1.0 OD1 D:ASP207 3.8 73.1 1.0 P9 D:ZOL401 3.9 62.0 1.0 OD2 D:ASP189 4.1 69.8 1.0 OD2 D:ASP207 4.1 75.3 1.0 CB D:TYR188 4.3 72.5 1.0 C8 D:ZOL401 4.3 64.0 1.0 O13 D:ZOL401 4.3 64.0 1.0 CG D:ASP207 4.4 73.9 1.0 OE1 D:GLN185 4.4 69.5 1.0 O10 D:ZOL401 4.6 61.5 1.0 O17 D:ZOL401 4.6 61.4 1.0 OD1 D:ASN192 4.6 75.0 1.0 O15 D:ZOL401 4.7 67.2 1.0 C D:TYR188 4.8 75.8 1.0 O D:TYR188 4.9 77.2 1.0 O12 D:ZOL401 5.0 60.6 1.0

M.Lisnyansky, N.Kapelushnik, A.Ben-Bassat, M.Marom, A.Loewenstein, D.Khananshvili, M.Giladi, Y.Haitin. Reduced Activity of Geranylgeranyl Diphosphate Synthase Mutant Is Involved in Bisphosphonate-Induced Atypical Fractures. Mol. Pharmacol. V. 94 1391 2018.
ISSN: ESSN 1521-0111
PubMed: 30275041
DOI: 10.1124/MOL.118.113670