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
Go back to
Magnesium Binding Sites List in 6r4v
Magnesium binding site 1 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 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
Go back to
Magnesium Binding Sites List in 6r4v
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
Go back to
Magnesium Binding Sites List in 6r4v
Magnesium binding site 3 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 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
Go back to
Magnesium Binding Sites List in 6r4v
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
Go back to
Magnesium Binding Sites List in 6r4v
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
Go back to
Magnesium Binding Sites List in 6r4v
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
Go back to
Magnesium Binding Sites List in 6r4v
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
Go back to
Magnesium Binding Sites List in 6r4v
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
Go back to
Magnesium Binding Sites List in 6r4v
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
Go back to
Magnesium Binding Sites List in 6r4v
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
|