Magnesium in PDB 3ldw: Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound
Protein crystallography data
The structure of Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound, PDB code: 3ldw
was solved by
A.K.Wernimont,
J.Lew,
Y.Zhao,
I.Kozieradzki,
D.Cossar,
M.Schapira,
A.Bochkarev,
C.H.Arrowsmith,
C.Bountra,
J.Weigelt,
A.M.Edwards,
R.Hui,
J.D.Artz,
Structural Genomics Consortium (Sgc),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.24 /
2.47
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
111.264,
139.543,
109.711,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.9 /
28.6
|
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Magnesium atom in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound
(pdb code 3ldw). 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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound, PDB code: 3ldw:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 12 in 3ldw
Go back to
Magnesium Binding Sites List in 3ldw
Magnesium binding site 1 out
of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound
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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1102
b:21.6
occ:1.00
|
O17
|
A:ZOL397
|
2.0
|
43.9
|
1.0
|
OD2
|
A:ASP130
|
2.0
|
36.7
|
1.0
|
OD2
|
A:ASP126
|
2.1
|
22.2
|
1.0
|
O12
|
A:ZOL397
|
2.1
|
20.3
|
1.0
|
O
|
A:HOH1164
|
2.2
|
27.4
|
1.0
|
O
|
A:HOH1142
|
2.4
|
22.2
|
1.0
|
OD1
|
A:ASP126
|
2.6
|
21.0
|
1.0
|
CG
|
A:ASP126
|
2.7
|
22.8
|
1.0
|
MG
|
A:MG1103
|
3.0
|
22.8
|
1.0
|
CG
|
A:ASP130
|
3.1
|
30.6
|
1.0
|
P14
|
A:ZOL397
|
3.2
|
30.7
|
1.0
|
P9
|
A:ZOL397
|
3.4
|
30.7
|
1.0
|
C8
|
A:ZOL397
|
3.6
|
15.1
|
1.0
|
CB
|
A:ASP130
|
3.7
|
23.0
|
1.0
|
C7
|
A:ZOL397
|
3.9
|
20.0
|
1.0
|
O11
|
A:ZOL397
|
4.0
|
21.5
|
1.0
|
O
|
A:HOH1162
|
4.0
|
38.1
|
1.0
|
O16
|
A:ZOL397
|
4.1
|
22.8
|
1.0
|
CB
|
A:ASP126
|
4.1
|
22.9
|
1.0
|
OD1
|
A:ASP130
|
4.2
|
29.9
|
1.0
|
O
|
A:ASP126
|
4.2
|
21.6
|
1.0
|
O
|
A:HOH1155
|
4.2
|
37.7
|
1.0
|
O
|
A:HOH1161
|
4.4
|
50.1
|
1.0
|
O15
|
A:ZOL397
|
4.4
|
17.1
|
1.0
|
C
|
A:ASP126
|
4.5
|
23.0
|
1.0
|
NH1
|
A:ARG135
|
4.5
|
11.5
|
1.0
|
OD1
|
A:ASP127
|
4.5
|
19.0
|
1.0
|
O10
|
A:ZOL397
|
4.6
|
37.5
|
1.0
|
O
|
A:HOH1154
|
4.7
|
39.3
|
1.0
|
O
|
A:HOH1130
|
4.7
|
23.1
|
1.0
|
O
|
A:HOH1251
|
4.8
|
15.2
|
1.0
|
CA
|
A:ASP126
|
4.8
|
21.6
|
1.0
|
N15
|
A:ZOL397
|
4.9
|
30.3
|
1.0
|
O
|
A:HOH1132
|
4.9
|
25.2
|
1.0
|
|
Magnesium binding site 2 out
of 12 in 3ldw
Go back to
Magnesium Binding Sites List in 3ldw
Magnesium binding site 2 out
of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound
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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1103
b:22.8
occ:1.00
|
OD1
|
A:ASP126
|
2.0
|
21.0
|
1.0
|
O
|
A:HOH1162
|
2.0
|
38.1
|
1.0
|
OD2
|
A:ASP130
|
2.1
|
36.7
|
1.0
|
O
|
A:HOH1161
|
2.2
|
50.1
|
1.0
|
O12
|
A:ZOL397
|
2.2
|
20.3
|
1.0
|
O
|
A:HOH1143
|
2.4
|
20.6
|
1.0
|
O
|
A:HOH1130
|
2.4
|
23.1
|
1.0
|
CG
|
A:ASP130
|
2.8
|
30.6
|
1.0
|
OD1
|
A:ASP130
|
2.8
|
29.9
|
1.0
|
MG
|
A:MG1102
|
3.0
|
21.6
|
1.0
|
CG
|
A:ASP126
|
3.2
|
22.8
|
1.0
|
P9
|
A:ZOL397
|
3.6
|
30.7
|
1.0
|
OD2
|
A:ASP198
|
3.8
|
44.6
|
1.0
|
OD2
|
A:ASP126
|
3.8
|
22.2
|
1.0
|
O10
|
A:ZOL397
|
3.9
|
37.5
|
1.0
|
NE2
|
A:GLN195
|
4.1
|
30.5
|
1.0
|
O
|
A:HOH1164
|
4.2
|
27.4
|
1.0
|
CB
|
A:ASP130
|
4.2
|
23.0
|
1.0
|
OE1
|
A:GLN195
|
4.3
|
27.9
|
1.0
|
CB
|
A:ASP126
|
4.3
|
22.9
|
1.0
|
CG
|
A:ASP198
|
4.4
|
30.4
|
1.0
|
O
|
A:ASP126
|
4.4
|
21.6
|
1.0
|
OD1
|
A:ASP198
|
4.5
|
29.3
|
1.0
|
C19
|
A:ZOL397
|
4.5
|
21.6
|
1.0
|
NZ
|
A:LYS310
|
4.6
|
31.8
|
1.0
|
CD
|
A:GLN195
|
4.6
|
33.4
|
1.0
|
O11
|
A:ZOL397
|
4.7
|
21.5
|
1.0
|
C7
|
A:ZOL397
|
4.7
|
20.0
|
1.0
|
CA
|
A:ASP126
|
4.7
|
21.6
|
1.0
|
C8
|
A:ZOL397
|
4.7
|
15.1
|
1.0
|
O17
|
A:ZOL397
|
4.7
|
43.9
|
1.0
|
N15
|
A:ZOL397
|
4.8
|
30.3
|
1.0
|
CE
|
A:LYS310
|
4.8
|
29.1
|
1.0
|
C
|
A:ASP126
|
4.9
|
23.0
|
1.0
|
O
|
A:HOH1117
|
4.9
|
17.6
|
1.0
|
|
Magnesium binding site 3 out
of 12 in 3ldw
Go back to
Magnesium Binding Sites List in 3ldw
Magnesium binding site 3 out
of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound
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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1104
b:23.6
occ:1.00
|
O
|
A:HOH1144
|
2.0
|
16.4
|
1.0
|
O11
|
A:ZOL397
|
2.0
|
21.5
|
1.0
|
O16
|
A:ZOL397
|
2.0
|
22.8
|
1.0
|
O
|
A:HOH1116
|
2.1
|
19.0
|
1.0
|
O
|
A:HOH1251
|
2.4
|
15.2
|
1.0
|
OD1
|
A:ASP287
|
2.4
|
26.7
|
1.0
|
CG
|
A:ASP287
|
3.3
|
28.7
|
1.0
|
P14
|
A:ZOL397
|
3.4
|
30.7
|
1.0
|
P9
|
A:ZOL397
|
3.5
|
30.7
|
1.0
|
O
|
A:HOH1117
|
3.5
|
17.6
|
1.0
|
OD2
|
A:ASP287
|
3.6
|
31.3
|
1.0
|
O13
|
A:ZOL397
|
3.7
|
20.3
|
1.0
|
C8
|
A:ZOL397
|
3.8
|
15.1
|
1.0
|
OD1
|
A:ASP305
|
3.9
|
34.6
|
1.0
|
O
|
A:HOH1164
|
3.9
|
27.4
|
1.0
|
OD2
|
A:ASP305
|
4.0
|
39.2
|
1.0
|
O
|
A:HOH1246
|
4.1
|
42.4
|
1.0
|
O17
|
A:ZOL397
|
4.2
|
43.9
|
1.0
|
O12
|
A:ZOL397
|
4.3
|
20.3
|
1.0
|
O
|
A:ASP287
|
4.4
|
32.0
|
1.0
|
CG
|
A:ASP305
|
4.4
|
34.6
|
1.0
|
OD2
|
A:ASP288
|
4.4
|
29.5
|
1.0
|
NE2
|
A:GLN284
|
4.4
|
28.9
|
1.0
|
OD2
|
A:ASP291
|
4.4
|
42.6
|
1.0
|
O10
|
A:ZOL397
|
4.4
|
37.5
|
1.0
|
O15
|
A:ZOL397
|
4.5
|
17.1
|
1.0
|
CB
|
A:ASP287
|
4.5
|
27.4
|
1.0
|
C
|
A:ASP287
|
4.5
|
31.4
|
1.0
|
CB
|
A:ASP291
|
4.6
|
29.6
|
1.0
|
NZ
|
A:LYS301
|
4.8
|
28.7
|
1.0
|
CG
|
A:ASP291
|
4.9
|
36.9
|
1.0
|
N
|
A:ASP288
|
4.9
|
26.3
|
1.0
|
CE
|
A:LYS301
|
4.9
|
28.6
|
1.0
|
|
Magnesium binding site 4 out
of 12 in 3ldw
Go back to
Magnesium Binding Sites List in 3ldw
Magnesium binding site 4 out
of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound
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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1102
b:21.8
occ:1.00
|
O
|
B:HOH1144
|
1.9
|
16.6
|
1.0
|
OD2
|
B:ASP130
|
2.1
|
28.1
|
1.0
|
O
|
B:HOH1145
|
2.1
|
15.8
|
1.0
|
O12
|
B:ZOL397
|
2.2
|
24.6
|
1.0
|
OD2
|
B:ASP126
|
2.3
|
25.8
|
1.0
|
O
|
B:HOH1186
|
2.3
|
23.8
|
1.0
|
CG
|
B:ASP130
|
2.8
|
22.1
|
1.0
|
OD1
|
B:ASP130
|
2.8
|
18.1
|
1.0
|
CG
|
B:ASP126
|
3.2
|
22.6
|
1.0
|
MG
|
B:MG1104
|
3.4
|
15.9
|
1.0
|
P9
|
B:ZOL397
|
3.4
|
23.4
|
1.0
|
O10
|
B:ZOL397
|
3.5
|
31.4
|
1.0
|
OD1
|
B:ASP126
|
3.5
|
20.6
|
1.0
|
OD2
|
B:ASP198
|
3.6
|
41.9
|
1.0
|
O
|
B:HOH1187
|
4.1
|
19.9
|
1.0
|
OD1
|
B:ASP198
|
4.1
|
34.5
|
1.0
|
CG
|
B:ASP198
|
4.2
|
34.9
|
1.0
|
CB
|
B:ASP130
|
4.2
|
21.1
|
1.0
|
OE1
|
B:GLN195
|
4.4
|
26.0
|
1.0
|
NZ
|
B:LYS310
|
4.4
|
24.8
|
1.0
|
NE2
|
B:GLN195
|
4.4
|
14.4
|
1.0
|
O11
|
B:ZOL397
|
4.4
|
11.2
|
1.0
|
CB
|
B:ASP126
|
4.5
|
20.3
|
1.0
|
O
|
B:HOH1261
|
4.6
|
20.0
|
1.0
|
CE
|
B:LYS310
|
4.6
|
16.0
|
1.0
|
O
|
B:ASP126
|
4.7
|
26.2
|
1.0
|
C19
|
B:ZOL397
|
4.8
|
29.8
|
1.0
|
O17
|
B:ZOL397
|
4.8
|
27.1
|
1.0
|
C8
|
B:ZOL397
|
4.8
|
11.1
|
1.0
|
CD
|
B:GLN195
|
4.8
|
25.7
|
1.0
|
C7
|
B:ZOL397
|
4.9
|
27.8
|
1.0
|
N15
|
B:ZOL397
|
4.9
|
22.2
|
1.0
|
NZ
|
B:LYS243
|
5.0
|
23.6
|
1.0
|
CA
|
B:ASP126
|
5.0
|
19.4
|
1.0
|
|
Magnesium binding site 5 out
of 12 in 3ldw
Go back to
Magnesium Binding Sites List in 3ldw
Magnesium binding site 5 out
of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound
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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1103
b:16.4
occ:1.00
|
O16
|
B:ZOL397
|
1.9
|
18.7
|
1.0
|
O
|
B:HOH1149
|
2.0
|
27.6
|
1.0
|
O
|
B:HOH1135
|
2.1
|
34.3
|
1.0
|
O11
|
B:ZOL397
|
2.2
|
11.2
|
1.0
|
OD1
|
B:ASP287
|
2.2
|
24.2
|
1.0
|
O
|
B:HOH1164
|
2.3
|
21.7
|
1.0
|
CG
|
B:ASP287
|
3.1
|
26.2
|
1.0
|
P14
|
B:ZOL397
|
3.4
|
24.9
|
1.0
|
OD2
|
B:ASP287
|
3.4
|
30.9
|
1.0
|
P9
|
B:ZOL397
|
3.6
|
23.4
|
1.0
|
O13
|
B:ZOL397
|
3.6
|
50.1
|
1.0
|
O
|
B:HOH1261
|
3.7
|
20.0
|
1.0
|
C8
|
B:ZOL397
|
3.7
|
11.1
|
1.0
|
C1
|
B:EDO1106
|
3.9
|
38.8
|
1.0
|
OD2
|
B:ASP305
|
4.1
|
27.9
|
1.0
|
O
|
B:ASP287
|
4.1
|
20.7
|
1.0
|
O2
|
B:EDO1106
|
4.2
|
38.2
|
1.0
|
O17
|
B:ZOL397
|
4.3
|
27.1
|
1.0
|
OD2
|
B:ASP291
|
4.3
|
43.2
|
1.0
|
C
|
B:ASP287
|
4.3
|
22.9
|
1.0
|
CB
|
B:ASP287
|
4.4
|
20.9
|
1.0
|
NE2
|
B:GLN284
|
4.4
|
15.3
|
1.0
|
O12
|
B:ZOL397
|
4.4
|
24.6
|
1.0
|
O
|
B:HOH1187
|
4.4
|
19.9
|
1.0
|
CB
|
B:ASP291
|
4.4
|
29.8
|
1.0
|
OD1
|
B:ASP305
|
4.5
|
30.6
|
1.0
|
O15
|
B:ZOL397
|
4.5
|
24.1
|
1.0
|
O10
|
B:ZOL397
|
4.6
|
31.4
|
1.0
|
OD2
|
B:ASP288
|
4.6
|
26.2
|
1.0
|
C2
|
B:EDO1106
|
4.6
|
37.3
|
1.0
|
CG
|
B:ASP305
|
4.7
|
27.7
|
1.0
|
N
|
B:ASP288
|
4.7
|
20.6
|
1.0
|
NZ
|
B:LYS301
|
4.7
|
23.7
|
1.0
|
CG
|
B:ASP291
|
4.7
|
35.1
|
1.0
|
O1
|
B:EDO1106
|
4.8
|
39.1
|
1.0
|
CE
|
B:LYS301
|
4.9
|
23.0
|
1.0
|
CA
|
B:ASP287
|
4.9
|
20.2
|
1.0
|
CA
|
B:ASP288
|
5.0
|
20.5
|
1.0
|
|
Magnesium binding site 6 out
of 12 in 3ldw
Go back to
Magnesium Binding Sites List in 3ldw
Magnesium binding site 6 out
of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound
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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1104
b:15.9
occ:1.00
|
OD2
|
B:ASP130
|
2.0
|
28.1
|
1.0
|
O17
|
B:ZOL397
|
2.0
|
27.1
|
1.0
|
O
|
B:HOH1187
|
2.0
|
19.9
|
1.0
|
OD1
|
B:ASP126
|
2.2
|
20.6
|
1.0
|
O12
|
B:ZOL397
|
2.2
|
24.6
|
1.0
|
O
|
B:HOH1162
|
2.4
|
15.4
|
1.0
|
CG
|
B:ASP130
|
3.0
|
22.1
|
1.0
|
CG
|
B:ASP126
|
3.2
|
22.6
|
1.0
|
P14
|
B:ZOL397
|
3.3
|
24.9
|
1.0
|
MG
|
B:MG1102
|
3.4
|
21.8
|
1.0
|
CB
|
B:ASP130
|
3.4
|
21.1
|
1.0
|
OD2
|
B:ASP126
|
3.5
|
25.8
|
1.0
|
P9
|
B:ZOL397
|
3.6
|
23.4
|
1.0
|
C8
|
B:ZOL397
|
4.0
|
11.1
|
1.0
|
O
|
B:HOH1138
|
4.0
|
25.9
|
1.0
|
O1
|
B:EDO1106
|
4.0
|
39.1
|
1.0
|
O11
|
B:ZOL397
|
4.0
|
11.2
|
1.0
|
O16
|
B:ZOL397
|
4.0
|
18.7
|
1.0
|
OD1
|
B:ASP130
|
4.2
|
18.1
|
1.0
|
NH2
|
B:ARG135
|
4.2
|
15.8
|
1.0
|
O
|
B:HOH1164
|
4.3
|
21.7
|
1.0
|
C7
|
B:ZOL397
|
4.3
|
27.8
|
1.0
|
C1
|
B:EDO1106
|
4.4
|
38.8
|
1.0
|
O
|
B:ASP126
|
4.4
|
26.2
|
1.0
|
O
|
B:HOH1186
|
4.4
|
23.8
|
1.0
|
OD1
|
B:ASP127
|
4.5
|
25.5
|
1.0
|
CB
|
B:ASP126
|
4.5
|
20.3
|
1.0
|
O15
|
B:ZOL397
|
4.5
|
24.1
|
1.0
|
O
|
B:HOH1219
|
4.5
|
16.0
|
1.0
|
C
|
B:ASP126
|
4.7
|
24.6
|
1.0
|
O10
|
B:ZOL397
|
4.8
|
31.4
|
1.0
|
O
|
B:HOH1144
|
4.8
|
16.6
|
1.0
|
CA
|
B:ASP130
|
4.9
|
20.4
|
1.0
|
O
|
B:HOH1188
|
4.9
|
21.0
|
1.0
|
|
Magnesium binding site 7 out
of 12 in 3ldw
Go back to
Magnesium Binding Sites List in 3ldw
Magnesium binding site 7 out
of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound
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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1102
b:23.4
occ:1.00
|
O17
|
C:ZOL397
|
1.9
|
45.8
|
1.0
|
O
|
C:HOH1192
|
2.1
|
25.7
|
1.0
|
OD1
|
C:ASP126
|
2.2
|
18.9
|
1.0
|
O12
|
C:ZOL397
|
2.2
|
27.1
|
1.0
|
O
|
C:HOH1118
|
2.3
|
30.6
|
1.0
|
OD2
|
C:ASP130
|
2.5
|
36.7
|
1.0
|
P14
|
C:ZOL397
|
3.1
|
26.7
|
1.0
|
CG
|
C:ASP126
|
3.2
|
21.5
|
1.0
|
MG
|
C:MG1103
|
3.4
|
27.2
|
1.0
|
CG
|
C:ASP130
|
3.4
|
28.4
|
1.0
|
OD2
|
C:ASP126
|
3.5
|
28.6
|
1.0
|
P9
|
C:ZOL397
|
3.5
|
23.7
|
1.0
|
CB
|
C:ASP130
|
3.6
|
20.3
|
1.0
|
O16
|
C:ZOL397
|
3.8
|
17.0
|
1.0
|
C8
|
C:ZOL397
|
3.9
|
14.8
|
1.0
|
O
|
C:HOH1212
|
3.9
|
38.7
|
1.0
|
O11
|
C:ZOL397
|
4.0
|
12.0
|
1.0
|
C7
|
C:ZOL397
|
4.2
|
20.6
|
1.0
|
O
|
C:HOH1110
|
4.3
|
19.3
|
1.0
|
O
|
C:HOH1120
|
4.3
|
4.3
|
0.5
|
OD1
|
C:ASP127
|
4.4
|
21.8
|
1.0
|
O
|
C:ASP126
|
4.4
|
25.3
|
1.0
|
NH1
|
C:ARG135
|
4.4
|
20.8
|
1.0
|
O15
|
C:ZOL397
|
4.4
|
21.6
|
1.0
|
CB
|
C:ASP126
|
4.5
|
19.5
|
1.0
|
O
|
C:HOH1238
|
4.5
|
22.6
|
1.0
|
O
|
C:HOH1142
|
4.5
|
36.3
|
1.0
|
OD1
|
C:ASP130
|
4.6
|
27.2
|
1.0
|
C
|
C:ASP126
|
4.7
|
24.1
|
1.0
|
O10
|
C:ZOL397
|
4.7
|
38.8
|
1.0
|
|
Magnesium binding site 8 out
of 12 in 3ldw
Go back to
Magnesium Binding Sites List in 3ldw
Magnesium binding site 8 out
of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound
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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1103
b:27.2
occ:1.00
|
OD2
|
C:ASP130
|
1.9
|
36.7
|
1.0
|
O
|
C:HOH1120
|
2.0
|
4.3
|
0.5
|
O
|
C:HOH1175
|
2.1
|
13.4
|
1.0
|
O12
|
C:ZOL397
|
2.1
|
27.1
|
1.0
|
OD2
|
C:ASP126
|
2.2
|
28.6
|
1.0
|
O
|
C:HOH1122
|
2.2
|
29.6
|
1.0
|
CG
|
C:ASP130
|
2.9
|
28.4
|
1.0
|
CG
|
C:ASP126
|
3.1
|
21.5
|
1.0
|
OD1
|
C:ASP130
|
3.2
|
27.2
|
1.0
|
P9
|
C:ZOL397
|
3.3
|
23.7
|
1.0
|
O10
|
C:ZOL397
|
3.4
|
38.8
|
1.0
|
MG
|
C:MG1102
|
3.4
|
23.4
|
1.0
|
OD1
|
C:ASP126
|
3.5
|
18.9
|
1.0
|
OD2
|
C:ASP198
|
3.7
|
41.5
|
1.0
|
NE2
|
C:GLN195
|
4.2
|
27.4
|
1.0
|
O
|
C:HOH1192
|
4.2
|
25.7
|
1.0
|
CG
|
C:ASP198
|
4.2
|
33.2
|
1.0
|
OE1
|
C:GLN195
|
4.2
|
24.2
|
1.0
|
CB
|
C:ASP130
|
4.2
|
20.3
|
1.0
|
OD1
|
C:ASP198
|
4.3
|
31.2
|
1.0
|
O11
|
C:ZOL397
|
4.4
|
12.0
|
1.0
|
CB
|
C:ASP126
|
4.5
|
19.5
|
1.0
|
NZ
|
C:LYS310
|
4.5
|
34.8
|
1.0
|
O
|
C:HOH1176
|
4.6
|
20.4
|
1.0
|
C7
|
C:ZOL397
|
4.6
|
20.6
|
1.0
|
C19
|
C:ZOL397
|
4.6
|
7.1
|
1.0
|
C8
|
C:ZOL397
|
4.6
|
14.8
|
1.0
|
CD
|
C:GLN195
|
4.6
|
28.2
|
1.0
|
O17
|
C:ZOL397
|
4.7
|
45.8
|
1.0
|
O
|
C:ASP126
|
4.7
|
25.3
|
1.0
|
N15
|
C:ZOL397
|
4.7
|
25.6
|
1.0
|
CE
|
C:LYS310
|
4.8
|
27.1
|
1.0
|
NZ
|
C:LYS243
|
4.9
|
29.4
|
1.0
|
CA
|
C:ASP126
|
5.0
|
18.7
|
1.0
|
|
Magnesium binding site 9 out
of 12 in 3ldw
Go back to
Magnesium Binding Sites List in 3ldw
Magnesium binding site 9 out
of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound
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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1104
b:27.3
occ:1.00
|
O
|
C:HOH1191
|
1.9
|
30.4
|
1.0
|
O
|
C:HOH1167
|
2.0
|
54.3
|
1.0
|
O16
|
C:ZOL397
|
2.1
|
17.0
|
1.0
|
O11
|
C:ZOL397
|
2.2
|
12.0
|
1.0
|
OD1
|
C:ASP287
|
2.3
|
32.3
|
1.0
|
O
|
C:HOH1110
|
2.3
|
19.3
|
1.0
|
CG
|
C:ASP287
|
3.2
|
32.4
|
1.0
|
OD2
|
C:ASP287
|
3.4
|
29.4
|
1.0
|
P14
|
C:ZOL397
|
3.6
|
26.7
|
1.0
|
P9
|
C:ZOL397
|
3.6
|
23.7
|
1.0
|
O
|
C:HOH1176
|
3.7
|
20.4
|
1.0
|
O13
|
C:ZOL397
|
3.8
|
32.5
|
1.0
|
C8
|
C:ZOL397
|
3.9
|
14.8
|
1.0
|
OD2
|
C:ASP305
|
4.0
|
38.3
|
1.0
|
O
|
C:ASP287
|
4.1
|
25.5
|
1.0
|
O
|
C:HOH1192
|
4.2
|
25.7
|
1.0
|
OD1
|
C:ASP305
|
4.2
|
34.7
|
1.0
|
OD2
|
C:ASP291
|
4.2
|
46.8
|
1.0
|
C
|
C:ASP287
|
4.3
|
28.2
|
1.0
|
CB
|
C:ASP291
|
4.4
|
30.2
|
1.0
|
CB
|
C:ASP287
|
4.4
|
24.9
|
1.0
|
NE2
|
C:GLN284
|
4.4
|
27.8
|
1.0
|
O12
|
C:ZOL397
|
4.4
|
27.1
|
1.0
|
O15
|
C:ZOL397
|
4.5
|
21.6
|
1.0
|
CG
|
C:ASP305
|
4.5
|
33.5
|
1.0
|
OD2
|
C:ASP288
|
4.5
|
37.9
|
1.0
|
O17
|
C:ZOL397
|
4.5
|
45.8
|
1.0
|
N
|
C:ASP288
|
4.6
|
26.5
|
1.0
|
CG
|
C:ASP291
|
4.7
|
36.2
|
1.0
|
O10
|
C:ZOL397
|
4.7
|
38.8
|
1.0
|
NZ
|
C:LYS301
|
4.7
|
17.3
|
1.0
|
CE
|
C:LYS301
|
4.8
|
20.1
|
1.0
|
CA
|
C:ASP288
|
4.9
|
26.0
|
1.0
|
CA
|
C:ASP287
|
4.9
|
23.9
|
1.0
|
|
Magnesium binding site 10 out
of 12 in 3ldw
Go back to
Magnesium Binding Sites List in 3ldw
Magnesium binding site 10 out
of 12 in the Crystal Structure of Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound
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 Plasmodium Vivax Geranylgeranylpyrophosphate Synthase PVX_092040 with Zoledronate and Ipp Bound within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1102
b:17.3
occ:1.00
|
OD2
|
D:ASP130
|
2.0
|
29.4
|
1.0
|
O11
|
D:ZOL397
|
2.1
|
17.6
|
1.0
|
O
|
D:HOH1200
|
2.1
|
13.1
|
1.0
|
OD2
|
D:ASP126
|
2.1
|
17.7
|
1.0
|
O
|
D:HOH1157
|
2.2
|
22.2
|
1.0
|
O
|
D:HOH1160
|
2.4
|
26.7
|
1.0
|
CG
|
D:ASP130
|
2.7
|
25.2
|
1.0
|
OD1
|
D:ASP130
|
2.8
|
24.1
|
1.0
|
MG
|
D:MG1103
|
3.0
|
18.1
|
1.0
|
CG
|
D:ASP126
|
3.1
|
19.9
|
1.0
|
OD1
|
D:ASP126
|
3.4
|
17.4
|
1.0
|
P9
|
D:ZOL397
|
3.4
|
24.0
|
1.0
|
O12
|
D:ZOL397
|
3.6
|
26.4
|
1.0
|
OD2
|
D:ASP198
|
3.8
|
35.2
|
1.0
|
O
|
D:HOH1158
|
4.1
|
30.6
|
1.0
|
CB
|
D:ASP130
|
4.2
|
22.6
|
1.0
|
NE2
|
D:GLN195
|
4.3
|
20.0
|
1.0
|
OD1
|
D:ASP198
|
4.3
|
27.6
|
1.0
|
CG
|
D:ASP198
|
4.3
|
27.7
|
1.0
|
O10
|
D:ZOL397
|
4.3
|
24.5
|
1.0
|
OE1
|
D:GLN195
|
4.4
|
19.7
|
1.0
|
CB
|
D:ASP126
|
4.4
|
20.1
|
1.0
|
O
|
D:ASP126
|
4.5
|
18.2
|
1.0
|
O
|
D:HOH1159
|
4.5
|
26.3
|
1.0
|
NZ
|
D:LYS310
|
4.6
|
16.2
|
1.0
|
O16
|
D:ZOL397
|
4.7
|
21.1
|
1.0
|
C8
|
D:ZOL397
|
4.7
|
10.9
|
1.0
|
C19
|
D:ZOL397
|
4.7
|
29.2
|
1.0
|
CE
|
D:LYS310
|
4.7
|
18.9
|
1.0
|
CD
|
D:GLN195
|
4.8
|
27.9
|
1.0
|
C7
|
D:ZOL397
|
4.8
|
17.4
|
1.0
|
N15
|
D:ZOL397
|
4.9
|
24.1
|
1.0
|
NZ
|
D:LYS243
|
4.9
|
19.2
|
1.0
|
CA
|
D:ASP126
|
4.9
|
19.0
|
1.0
|
|
Reference:
J.D.Artz,
A.K.Wernimont,
J.E.Dunford,
M.Schapira,
A.Dong,
Y.Zhao,
J.Lew,
R.G.Russell,
F.H.Ebetino,
U.Oppermann,
R.Hui.
Molecular Characterization of A Novel Geranylgeranyl Pyrophosphate Synthase From Plasmodium Parasites. J.Biol.Chem. V. 286 3315 2011.
ISSN: ISSN 0021-9258
PubMed: 21084289
DOI: 10.1074/JBC.M109.027235
Page generated: Wed Aug 14 18:31:06 2024
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