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Magnesium in PDB 6r4v: Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate

Enzymatic activity of Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate

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

Protein crystallography data

The structure of Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate, PDB code: 6r4v was solved by M.Lisnyansky, M.Giladi, Y.Haitin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.65 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.450, 153.010, 198.590, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.5

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate (pdb code 6r4v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 17 binding sites of Magnesium where determined in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate, PDB code: 6r4v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 17 in 6r4v

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Magnesium binding site 1 out of 17 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate


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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 Bound to Ibandronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1301

b:45.4
occ:1.00
 OD2 A:ASP64 1.9 37.4 1.0
O12 A:BFQ1304 2.0 45.8 1.0
O A:HOH1427 2.1 31.2 1.0
O2 A:BFQ1304 2.1 76.0 1.0
OD1 A:ASP68 2.2 30.5 1.0
O A:HOH1422 2.3 42.0 1.0
CG A:ASP64 2.7 27.7 1.0
MG A:MG1303 2.8 26.6 1.0
OD1 A:ASP64 3.0 36.6 1.0
CG A:ASP68 3.3 31.0 1.0
P8 A:BFQ1304 3.3 63.9 1.0
P1 A:BFQ1304 3.4 72.1 1.0
C7 A:BFQ1304 3.8 82.2 1.0
O A:HOH1411 3.9 47.1 1.0
CB A:ASP68 3.9 32.2 1.0
O A:HOH1418 3.9 27.6 1.0
NZ A:LYS202 4.0 42.9 1.0
NH1 A:ARG73 4.0 40.1 1.0
O A:ASP64 4.1 24.0 1.0
O5 A:BFQ1304 4.1 73.0 1.0
CB A:ASP64 4.1 26.4 1.0
O10 A:BFQ1304 4.2 75.3 1.0
C16 A:BFQ1304 4.3 77.6 1.0
O9 A:BFQ1304 4.3 60.5 1.0
OD2 A:ASP68 4.3 33.4 1.0
OE2 A:GLU210 4.4 32.5 1.0
C A:ASP64 4.4 29.1 1.0
O3 A:BFQ1304 4.5 67.0 1.0
OG A:SER70 4.5 25.3 1.0
OD1 A:ASP65 4.6 33.1 1.0
O A:HOH1423 4.7 32.3 1.0
CE A:LYS202 4.8 50.8 1.0
O A:HOH1405 4.8 25.1 1.0
CA A:ASP64 4.8 23.2 1.0
MG A:MG1302 4.9 67.7 1.0
N A:ASP65 5.0 23.2 1.0
OE1 A:GLU210 5.0 32.9 1.0

Magnesium binding site 2 out of 17 in 6r4v

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Magnesium binding site 2 out of 17 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate


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 Bound to Ibandronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1302

b:67.7
occ:1.00
 O A:HOH1519 2.2 53.7 1.0
O5 A:BFQ1304 2.4 73.0 1.0
O9 A:BFQ1304 2.4 60.5 1.0
OD2 A:ASP188 2.6 63.7 1.0
O A:HOH1411 2.7 47.1 1.0
O14 A:BFQ1304 3.2 96.7 1.0
P8 A:BFQ1304 3.3 63.9 1.0
P1 A:BFQ1304 3.4 72.1 1.0
C7 A:BFQ1304 3.4 82.2 1.0
ND2 A:ASN192 3.4 41.0 1.0
NE2 A:GLN185 3.5 32.4 1.0
CG A:ASP188 3.8 54.5 1.0
O12 A:BFQ1304 3.8 45.8 1.0
O2 A:BFQ1304 4.1 76.0 1.0
OD1 A:ASP189 4.1 28.2 1.0
NZ A:LYS212 4.1 42.5 1.0
O A:HOH1422 4.3 42.0 1.0
NZ A:LYS202 4.5 42.9 1.0
CB A:ASP188 4.5 41.2 1.0
O3 A:BFQ1304 4.6 67.0 1.0
O10 A:BFQ1304 4.6 75.3 1.0
CD A:GLN185 4.6 33.4 1.0
OD2 A:ASP207 4.6 30.6 1.0
OD1 A:ASP207 4.6 46.6 1.0
OD1 A:ASP188 4.7 56.8 1.0
CG A:ASN192 4.7 49.7 1.0
OE1 A:GLN185 4.9 37.5 1.0
MG A:MG1301 4.9 45.4 1.0
C16 A:BFQ1304 4.9 77.6 1.0
C A:ASP188 5.0 26.4 1.0

Magnesium binding site 3 out of 17 in 6r4v

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Magnesium binding site 3 out of 17 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate


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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 Bound to Ibandronate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1303

b:26.6
occ:1.00
 OD1 A:ASP64 2.0 36.6 1.0
OD1 A:ASP68 2.1 30.5 1.0
O12 A:BFQ1304 2.2 45.8 1.0
O A:HOH1418 2.2 27.6 1.0
O A:HOH1423 2.2 32.3 1.0
O A:HOH1405 2.2 25.1 1.0
MG A:MG1301 2.8 45.4 1.0
CG A:ASP64 3.0 27.7 1.0
O10 A:BFQ1304 3.0 75.3 1.0
CG A:ASP68 3.0 31.0 1.0
P8 A:BFQ1304 3.1 63.9 1.0
OD2 A:ASP64 3.3 37.4 1.0
OD2 A:ASP68 3.3 33.4 1.0
O A:HOH1422 3.7 42.0 1.0
NE2 A:GLN126 3.9 34.0 1.0
OD2 A:ASP129 4.0 39.7 1.0
O9 A:BFQ1304 4.1 60.5 1.0
OE1 A:GLU210 4.1 32.9 1.0
OE1 A:GLN126 4.2 40.9 1.0
CB A:ASP64 4.4 26.4 1.0
CD A:GLN126 4.4 41.3 1.0
CB A:ASP68 4.4 32.2 1.0
O2 A:BFQ1304 4.4 76.0 1.0
C7 A:BFQ1304 4.5 82.2 1.0
O A:ASP64 4.6 24.0 1.0
NZ A:LYS212 4.6 42.5 1.0
O A:HOH1427 4.6 31.2 1.0
C16 A:BFQ1304 4.7 77.6 1.0
OE2 A:GLU210 4.8 32.5 1.0
CD A:GLU210 4.9 34.4 1.0
NZ A:LYS151 4.9 39.1 1.0
CA A:ASP64 4.9 23.2 1.0

Magnesium binding site 4 out of 17 in 6r4v

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Magnesium binding site 4 out of 17 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate


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 Bound to Ibandronate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1301

b:37.5
occ:1.00
 O10 C:BFQ1303 1.7 33.9 1.0
MG C:MG1302 2.1 25.1 1.0
OD2 C:ASP68 2.2 27.4 1.0
OD2 C:ASP64 2.2 24.9 1.0
O2 C:BFQ1303 2.4 70.5 1.0
O C:HOH1479 2.4 43.1 1.0
OD1 C:ASP64 2.7 24.2 1.0
CG C:ASP64 2.8 21.3 1.0
O C:HOH1439 2.9 25.2 1.0
P8 C:BFQ1303 3.1 61.1 1.0
O C:HOH1467 3.2 25.7 1.0
CG C:ASP68 3.4 30.2 1.0
P1 C:BFQ1303 3.4 71.9 1.0
C7 C:BFQ1303 3.6 73.7 1.0
O C:HOH1431 3.6 24.9 1.0
C16 C:BFQ1303 3.6 71.9 1.0
O12 C:BFQ1303 3.8 74.4 1.0
O5 C:BFQ1303 4.0 73.2 1.0
O C:HOH1419 4.2 23.4 1.0
O9 C:BFQ1303 4.2 70.2 1.0
OD1 C:ASP68 4.2 31.6 1.0
CB C:ASP64 4.3 23.3 1.0
CB C:ASP68 4.3 23.1 1.0
OE1 C:GLU210 4.4 30.0 1.0
NZ C:LYS212 4.5 42.7 1.0
O C:ASP64 4.5 23.6 1.0
NZ C:LYS202 4.6 37.0 1.0
OE2 C:GLU210 4.6 27.6 1.0
NH1 C:ARG73 4.7 31.1 1.0
O3 C:BFQ1303 4.7 76.5 1.0
C C:ASP64 4.8 26.3 1.0
CD C:GLU210 4.9 31.7 1.0
O14 C:BFQ1303 4.9 75.0 1.0
CE C:LYS212 5.0 48.8 1.0

Magnesium binding site 5 out of 17 in 6r4v

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Magnesium binding site 5 out of 17 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate


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 Bound to Ibandronate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1302

b:25.1
occ:1.00
 O C:HOH1431 2.0 24.9 1.0
O C:HOH1467 2.0 25.7 1.0
OD1 C:ASP64 2.1 24.2 1.0
MG C:MG1301 2.1 37.5 1.0
OD2 C:ASP68 2.1 27.4 1.0
O C:HOH1419 2.2 23.4 1.0
O10 C:BFQ1303 2.3 33.9 1.0
CG C:ASP68 3.0 30.2 1.0
CG C:ASP64 3.1 21.3 1.0
OD1 C:ASP68 3.2 31.6 1.0
OD2 C:ASP64 3.3 24.9 1.0
P8 C:BFQ1303 3.7 61.1 1.0
O C:HOH1479 3.9 43.1 1.0
OD2 C:ASP129 3.9 33.2 1.0
NE2 C:GLN126 3.9 29.0 1.0
OE2 C:GLU210 4.1 27.6 1.0
OE1 C:GLN126 4.1 30.7 1.0
O9 C:BFQ1303 4.1 70.2 1.0
C16 C:BFQ1303 4.3 71.9 1.0
CD C:GLN126 4.4 33.2 1.0
CB C:ASP64 4.4 23.3 1.0
O2 C:BFQ1303 4.4 70.5 1.0
CB C:ASP68 4.4 23.1 1.0
O C:ASP64 4.5 23.6 1.0
O C:HOH1439 4.6 25.2 1.0
NZ C:LYS151 4.6 62.7 1.0
C7 C:BFQ1303 4.6 73.7 1.0
O12 C:BFQ1303 4.7 74.4 1.0
NZ C:LYS212 4.8 42.7 1.0
OE1 C:GLU210 4.8 30.0 1.0
CD C:GLU210 4.9 31.7 1.0
CA C:ASP64 4.9 23.7 1.0
CG C:ASP129 5.0 32.5 1.0

Magnesium binding site 6 out of 17 in 6r4v

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Magnesium binding site 6 out of 17 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate


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 Bound to Ibandronate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1301

b:26.4
occ:1.00
 OD2 F:ASP64 2.0 33.8 1.0
O5 F:BFQ1304 2.1 31.5 1.0
OD1 F:ASP68 2.1 36.0 1.0
O9 F:BFQ1304 2.1 30.9 1.0
O F:HOH1413 2.2 31.4 1.0
O F:HOH1412 2.3 22.3 1.0
CG F:ASP64 3.0 31.3 1.0
MG F:MG1303 3.1 30.0 1.0
CG F:ASP68 3.2 31.0 1.0
P8 F:BFQ1304 3.4 34.3 1.0
P1 F:BFQ1304 3.4 40.1 1.0
OD1 F:ASP64 3.4 34.0 1.0
CB F:ASP68 3.7 29.9 1.0
C7 F:BFQ1304 3.8 49.5 1.0
C16 F:BFQ1304 4.0 59.8 1.0
O12 F:BFQ1304 4.1 51.0 1.0
NH1 F:ARG73 4.1 32.0 1.0
MG F:MG1302 4.2 69.8 1.0
O F:HOH1460 4.2 29.2 1.0
O F:ASP64 4.2 30.4 1.0
O3 F:BFQ1304 4.3 40.7 1.0
OD2 F:ASP68 4.3 32.9 1.0
OE2 F:GLU210 4.3 36.5 1.0
CB F:ASP64 4.3 27.5 1.0
O2 F:BFQ1304 4.4 42.4 1.0
OG F:SER70 4.4 27.7 1.0
O10 F:BFQ1304 4.5 43.0 1.0
C F:ASP64 4.6 30.3 1.0
OD1 F:ASP65 4.6 30.0 1.0
NZ F:LYS202 4.6 47.7 1.0
CE F:LYS202 4.7 53.8 1.0
O F:HOH1417 4.8 31.1 1.0
O F:HOH1429 5.0 26.1 1.0
O F:HOH1506 5.0 42.0 1.0

Magnesium binding site 7 out of 17 in 6r4v

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Magnesium binding site 7 out of 17 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate


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 Bound to Ibandronate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1302

b:69.8
occ:1.00
 O12 F:BFQ1304 2.2 51.0 1.0
O3 F:BFQ1304 2.3 40.7 1.0
O F:HOH1430 2.5 34.2 1.0
O F:HOH1520 3.0 47.3 1.0
P1 F:BFQ1304 3.2 40.1 1.0
P8 F:BFQ1304 3.3 34.3 1.0
NZ F:LYS212 3.3 53.9 1.0
O F:HOH1413 3.3 31.4 1.0
O5 F:BFQ1304 3.4 31.5 1.0
OD1 F:ASP207 3.6 31.6 1.0
O9 F:BFQ1304 3.6 30.9 1.0
C7 F:BFQ1304 3.7 49.5 1.0
CE F:LYS202 3.9 53.8 1.0
O14 F:BFQ1304 4.0 68.4 1.0
OD2 F:ASP207 4.1 40.8 1.0
MG F:MG1301 4.2 26.4 1.0
CG F:ASP207 4.3 38.5 1.0
CE F:LYS212 4.4 48.0 1.0
NE2 F:GLN185 4.5 50.0 1.0
O F:HOH1506 4.6 42.0 1.0
O2 F:BFQ1304 4.6 42.4 1.0
NZ F:LYS202 4.6 47.7 1.0
O10 F:BFQ1304 4.6 43.0 1.0
CD F:LYS212 4.6 48.7 1.0
ND2 F:ASN192 4.8 51.0 1.0
O F:HOH1416 4.8 50.3 1.0
OD1 F:ASP189 4.9 38.0 1.0

Magnesium binding site 8 out of 17 in 6r4v

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Magnesium binding site 8 out of 17 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate


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 Bound to Ibandronate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1303

b:30.0
occ:1.00
 O F:HOH1417 2.0 31.1 1.0
O F:HOH1460 2.1 29.2 1.0
OD1 F:ASP64 2.1 34.0 1.0
O F:HOH1429 2.1 26.1 1.0
O9 F:BFQ1304 2.2 30.9 1.0
OD1 F:ASP68 2.2 36.0 1.0
CG F:ASP68 3.0 31.0 1.0
CG F:ASP64 3.0 31.3 1.0
OD2 F:ASP68 3.1 32.9 1.0
MG F:MG1301 3.1 26.4 1.0
OD2 F:ASP64 3.3 33.8 1.0
P8 F:BFQ1304 3.3 34.3 1.0
O10 F:BFQ1304 3.3 43.0 1.0
NE2 F:GLN126 3.8 52.8 1.0
OD1 F:ASP129 4.0 26.4 1.0
O F:HOH1413 4.0 31.4 1.0
O12 F:BFQ1304 4.2 51.0 1.0
OE1 F:GLU210 4.2 29.7 1.0
CD F:GLN126 4.4 44.2 1.0
OE1 F:GLN126 4.4 40.2 1.0
CB F:ASP64 4.4 27.5 1.0
CB F:ASP68 4.4 29.9 1.0
C16 F:BFQ1304 4.6 59.8 1.0
O F:ASP64 4.6 30.4 1.0
C7 F:BFQ1304 4.7 49.5 1.0
NZ F:LYS212 4.7 53.9 1.0
O5 F:BFQ1304 4.7 31.5 1.0
OE2 F:GLU210 4.9 36.5 1.0
NZ F:LYS151 4.9 40.8 1.0
CD F:GLU210 5.0 35.6 1.0
CA F:ASP64 5.0 30.9 1.0

Magnesium binding site 9 out of 17 in 6r4v

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Magnesium binding site 9 out of 17 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate


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 Bound to Ibandronate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1301

b:25.9
occ:1.00
 O5 E:BFQ1304 1.9 31.8 1.0
O E:HOH1463 2.0 27.5 1.0
OD2 E:ASP64 2.1 26.8 1.0
O12 E:BFQ1304 2.1 33.8 1.0
O E:HOH1408 2.3 18.3 1.0
OD2 E:ASP68 2.3 30.3 1.0
CG E:ASP64 3.1 26.7 1.0
P1 E:BFQ1304 3.2 32.0 1.0
MG E:MG1303 3.2 24.2 1.0
P8 E:BFQ1304 3.3 35.9 1.0
CG E:ASP68 3.4 26.6 1.0
OD1 E:ASP64 3.5 28.7 1.0
NZ E:LYS202 3.7 39.7 1.0
C7 E:BFQ1304 3.8 50.1 1.0
O9 E:BFQ1304 3.8 54.2 1.0
CB E:ASP68 3.9 26.9 1.0
NH1 E:ARG73 4.0 26.6 1.0
O3 E:BFQ1304 4.1 45.8 1.0
O E:HOH1405 4.1 53.3 1.0
C16 E:BFQ1304 4.2 59.2 1.0
O E:HOH1462 4.2 34.0 1.0
O2 E:BFQ1304 4.2 45.7 1.0
O E:ASP64 4.2 22.5 1.0
OE1 E:GLU210 4.4 36.8 1.0
OG E:SER70 4.4 27.7 1.0
OD1 E:ASP65 4.4 29.4 1.0
CB E:ASP64 4.4 19.7 1.0
OD1 E:ASP68 4.5 25.0 1.0
O10 E:BFQ1304 4.6 50.3 1.0
C E:ASP64 4.6 26.7 1.0
C19 E:BFQ1304 4.7 51.0 1.0
CE E:LYS202 4.7 41.4 1.0
MG E:MG1302 4.9 58.5 1.0
O E:HOH1409 5.0 26.5 1.0

Magnesium binding site 10 out of 17 in 6r4v

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Magnesium binding site 10 out of 17 in the Crystal Structure of Human Geranylgeranyl Diphosphate Synthase Bound to Ibandronate


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 Bound to Ibandronate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1302

b:58.5
occ:1.00
 O3 E:BFQ1304 2.0 45.8 1.0
O E:HOH1405 2.1 53.3 1.0
O E:HOH1425 2.4 38.2 1.0
OD2 E:ASP188 2.5 92.5 1.0
O E:HOH1509 2.6 50.0 1.0
O9 E:BFQ1304 2.7 54.2 1.0
CG E:ASP188 3.3 84.3 1.0
P1 E:BFQ1304 3.3 32.0 1.0
O5 E:BFQ1304 3.8 31.8 1.0
O14 E:BFQ1304 3.8 66.8 1.0
P8 E:BFQ1304 3.8 35.9 1.0
CE E:LYS202 3.9 41.4 1.0
C7 E:BFQ1304 3.9 50.1 1.0
OD1 E:ASP188 3.9 99.2 1.0
CB E:ASP188 4.0 55.8 1.0
OD1 E:ASP207 4.1 34.5 1.0
OD2 E:ASP207 4.1 32.7 1.0
O E:HOH1463 4.1 27.5 1.0
NE2 E:GLN185 4.4 34.1 1.0
NZ E:LYS212 4.4 39.1 1.0
O2 E:BFQ1304 4.5 45.7 1.0
NZ E:LYS202 4.5 39.7 1.0
CG E:ASP207 4.5 37.9 1.0
O12 E:BFQ1304 4.6 33.8 1.0
OD1 E:ASP189 4.6 23.4 1.0
CD E:LYS202 4.7 46.7 1.0
O E:HOH1478 4.7 36.5 1.0
ND2 E:ASN192 4.7 54.3 1.0
O E:ASP188 4.8 29.9 1.0
C E:ASP188 4.9 29.3 1.0
MG E:MG1301 4.9 25.9 1.0
O10 E:BFQ1304 4.9 50.3 1.0

Reference:

M.Lisnyansky, E.Yariv, O.Segal, M.Marom, A.Loewenstein, N.Ben-Tal, M.Giladi, Y.Haitin. Metal Coordination Is Crucial For Geranylgeranyl Diphosphate Synthase-Bisphosphonate Interactions: A Crystallographic and Computational Analysis. Mol.Pharmacol. V. 96 580 2019.
ISSN: ESSN 1521-0111
PubMed: 31427399
DOI: 10.1124/MOL.119.117499
Page generated: Tue Oct 1 16:34:27 2024

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