Magnesium in PDB 3ryw: Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811
Protein crystallography data
The structure of Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811, PDB code: 3ryw
was solved by
J.H.No,
Y.-L.Liu,
Y.Zhang,
E.Oldfield,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.22 /
2.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
99.744,
106.582,
139.031,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.8 /
26
|
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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811
(pdb code 3ryw). 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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811, PDB code: 3ryw:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 12 in 3ryw
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Magnesium Binding Sites List in 3ryw
Magnesium binding site 1 out
of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811
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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg2002
b:23.5
occ:1.00
|
OAF
|
A:K9H2001
|
2.2
|
29.0
|
1.0
|
OAB
|
A:K9H2001
|
2.3
|
30.5
|
1.0
|
OD1
|
A:ASP287
|
2.5
|
33.1
|
1.0
|
OD1
|
A:ASP305
|
3.5
|
40.0
|
1.0
|
CG
|
A:ASP287
|
3.5
|
32.4
|
1.0
|
OD2
|
A:ASP305
|
3.8
|
44.4
|
1.0
|
PBA
|
A:K9H2001
|
3.8
|
29.8
|
1.0
|
OD2
|
A:ASP291
|
3.8
|
38.4
|
1.0
|
PAZ
|
A:K9H2001
|
3.9
|
33.1
|
1.0
|
OD2
|
A:ASP287
|
4.0
|
30.6
|
1.0
|
CG
|
A:ASP305
|
4.0
|
39.2
|
1.0
|
O
|
A:ASP287
|
4.2
|
27.3
|
1.0
|
OAC
|
A:K9H2001
|
4.3
|
32.0
|
1.0
|
OD2
|
A:ASP288
|
4.3
|
37.3
|
1.0
|
CG
|
A:ASP291
|
4.5
|
41.6
|
1.0
|
NE2
|
A:GLN284
|
4.5
|
31.2
|
1.0
|
CAY
|
A:K9H2001
|
4.5
|
32.1
|
1.0
|
CB
|
A:ASP291
|
4.6
|
39.3
|
1.0
|
C
|
A:ASP287
|
4.6
|
28.8
|
1.0
|
OAD
|
A:K9H2001
|
4.7
|
32.0
|
1.0
|
CB
|
A:ASP287
|
4.7
|
29.6
|
1.0
|
OAG
|
A:K9H2001
|
4.8
|
29.8
|
1.0
|
OAE
|
A:K9H2001
|
4.8
|
36.5
|
1.0
|
MG
|
A:MG2003
|
4.8
|
11.6
|
1.0
|
NZ
|
A:LYS301
|
4.9
|
32.6
|
1.0
|
|
Magnesium binding site 2 out
of 12 in 3ryw
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Magnesium Binding Sites List in 3ryw
Magnesium binding site 2 out
of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811
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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg2003
b:11.6
occ:1.00
|
OD2
|
A:ASP130
|
2.0
|
33.1
|
1.0
|
OD2
|
A:ASP126
|
2.3
|
22.3
|
1.0
|
O
|
A:HOH2108
|
2.5
|
20.6
|
1.0
|
OAC
|
A:K9H2001
|
2.5
|
32.0
|
1.0
|
OAD
|
A:K9H2001
|
2.7
|
32.0
|
1.0
|
CAY
|
A:K9H2001
|
2.9
|
32.1
|
1.0
|
CG
|
A:ASP130
|
3.1
|
33.2
|
1.0
|
CG
|
A:ASP126
|
3.2
|
21.5
|
1.0
|
PBA
|
A:K9H2001
|
3.3
|
29.8
|
1.0
|
PAZ
|
A:K9H2001
|
3.4
|
33.1
|
1.0
|
OD1
|
A:ASP126
|
3.4
|
21.9
|
1.0
|
CB
|
A:ASP130
|
3.5
|
30.6
|
1.0
|
MG
|
A:MG2004
|
3.6
|
16.1
|
1.0
|
OAB
|
A:K9H2001
|
3.8
|
30.5
|
1.0
|
OAF
|
A:K9H2001
|
4.0
|
29.0
|
1.0
|
OD1
|
A:ASP130
|
4.2
|
38.4
|
1.0
|
CAT
|
A:K9H2001
|
4.3
|
36.0
|
1.0
|
OAG
|
A:K9H2001
|
4.6
|
29.8
|
1.0
|
CB
|
A:ASP126
|
4.6
|
21.5
|
1.0
|
O
|
A:ASP126
|
4.6
|
21.7
|
1.0
|
OAE
|
A:K9H2001
|
4.8
|
36.5
|
1.0
|
MG
|
A:MG2002
|
4.8
|
23.5
|
1.0
|
NH1
|
A:ARG135
|
4.9
|
23.5
|
1.0
|
C
|
A:ASP126
|
5.0
|
23.2
|
1.0
|
|
Magnesium binding site 3 out
of 12 in 3ryw
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Magnesium Binding Sites List in 3ryw
Magnesium binding site 3 out
of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811
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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg2004
b:16.1
occ:1.00
|
OAD
|
A:K9H2001
|
2.0
|
32.0
|
1.0
|
OD1
|
A:ASP126
|
2.3
|
21.9
|
1.0
|
OD2
|
A:ASP130
|
2.4
|
33.1
|
1.0
|
OD1
|
A:ASP130
|
2.8
|
38.4
|
1.0
|
CG
|
A:ASP130
|
3.0
|
33.2
|
1.0
|
OE1
|
A:GLN195
|
3.1
|
29.3
|
1.0
|
OD2
|
A:ASP198
|
3.3
|
38.7
|
1.0
|
CG
|
A:ASP126
|
3.3
|
21.5
|
1.0
|
PAZ
|
A:K9H2001
|
3.5
|
33.1
|
1.0
|
MG
|
A:MG2003
|
3.6
|
11.6
|
1.0
|
OD2
|
A:ASP126
|
3.8
|
22.3
|
1.0
|
OAE
|
A:K9H2001
|
3.9
|
36.5
|
1.0
|
CD
|
A:GLN195
|
3.9
|
28.0
|
1.0
|
NE2
|
A:GLN195
|
3.9
|
26.7
|
1.0
|
CG
|
A:ASP198
|
4.2
|
33.8
|
1.0
|
CAY
|
A:K9H2001
|
4.3
|
32.1
|
1.0
|
CE
|
A:LYS310
|
4.4
|
35.2
|
1.0
|
CB
|
A:ASP130
|
4.5
|
30.6
|
1.0
|
OAB
|
A:K9H2001
|
4.6
|
30.5
|
1.0
|
NZ
|
A:LYS310
|
4.6
|
38.0
|
1.0
|
CB
|
A:ASP126
|
4.6
|
21.5
|
1.0
|
NZ
|
A:LYS243
|
4.7
|
29.5
|
1.0
|
OD1
|
A:ASP198
|
4.8
|
36.5
|
1.0
|
CAJ
|
A:K9H2001
|
4.9
|
37.7
|
1.0
|
O
|
A:ASP126
|
5.0
|
21.7
|
1.0
|
|
Magnesium binding site 4 out
of 12 in 3ryw
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Magnesium Binding Sites List in 3ryw
Magnesium binding site 4 out
of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811
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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg2002
b:21.6
occ:1.00
|
OAF
|
B:K9H2001
|
2.2
|
35.1
|
1.0
|
OD1
|
B:ASP287
|
2.3
|
50.1
|
1.0
|
OAB
|
B:K9H2001
|
2.6
|
30.0
|
1.0
|
CG
|
B:ASP287
|
3.3
|
43.2
|
1.0
|
OD1
|
B:ASP305
|
3.7
|
47.3
|
1.0
|
OD2
|
B:ASP287
|
3.7
|
42.8
|
1.0
|
OAD
|
B:K9H2001
|
3.8
|
32.3
|
1.0
|
PBA
|
B:K9H2001
|
3.8
|
32.0
|
1.0
|
PAZ
|
B:K9H2001
|
3.8
|
33.3
|
1.0
|
OD2
|
B:ASP291
|
3.9
|
49.1
|
1.0
|
OD2
|
B:ASP305
|
3.9
|
42.1
|
1.0
|
O
|
B:ASP287
|
4.1
|
33.2
|
1.0
|
CG
|
B:ASP305
|
4.2
|
41.9
|
1.0
|
OD2
|
B:ASP288
|
4.3
|
53.3
|
1.0
|
NE2
|
B:GLN284
|
4.4
|
41.7
|
1.0
|
C
|
B:ASP287
|
4.5
|
34.8
|
1.0
|
CB
|
B:ASP287
|
4.5
|
38.6
|
1.0
|
OAC
|
B:K9H2001
|
4.5
|
32.1
|
1.0
|
CAY
|
B:K9H2001
|
4.5
|
32.3
|
1.0
|
CG
|
B:ASP291
|
4.6
|
47.3
|
1.0
|
CB
|
B:ASP291
|
4.6
|
43.1
|
1.0
|
OAG
|
B:K9H2001
|
4.7
|
33.8
|
1.0
|
MG
|
B:MG2003
|
4.9
|
19.1
|
1.0
|
N
|
B:ASP288
|
4.9
|
35.1
|
1.0
|
NZ
|
B:LYS301
|
5.0
|
42.2
|
1.0
|
|
Magnesium binding site 5 out
of 12 in 3ryw
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Magnesium Binding Sites List in 3ryw
Magnesium binding site 5 out
of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811
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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg2003
b:19.1
occ:1.00
|
OD2
|
B:ASP130
|
2.0
|
27.6
|
1.0
|
OAD
|
B:K9H2001
|
2.1
|
32.3
|
1.0
|
OD2
|
B:ASP126
|
2.3
|
27.6
|
1.0
|
OAC
|
B:K9H2001
|
2.4
|
32.1
|
1.0
|
CG
|
B:ASP130
|
3.1
|
27.4
|
1.0
|
CG
|
B:ASP126
|
3.2
|
26.7
|
1.0
|
CAY
|
B:K9H2001
|
3.4
|
32.3
|
1.0
|
PBA
|
B:K9H2001
|
3.4
|
32.0
|
1.0
|
OD1
|
B:ASP126
|
3.4
|
29.3
|
1.0
|
PAZ
|
B:K9H2001
|
3.4
|
33.3
|
1.0
|
CB
|
B:ASP130
|
3.5
|
27.8
|
1.0
|
MG
|
B:MG2004
|
3.6
|
13.5
|
1.0
|
OAF
|
B:K9H2001
|
3.8
|
35.1
|
1.0
|
OD1
|
B:ASP130
|
4.1
|
29.0
|
1.0
|
OAB
|
B:K9H2001
|
4.4
|
30.0
|
1.0
|
OAE
|
B:K9H2001
|
4.4
|
33.8
|
1.0
|
O
|
B:HOH2104
|
4.5
|
22.0
|
1.0
|
CB
|
B:ASP126
|
4.6
|
24.8
|
1.0
|
O
|
B:ASP126
|
4.7
|
25.3
|
1.0
|
OAG
|
B:K9H2001
|
4.7
|
33.8
|
1.0
|
CAT
|
B:K9H2001
|
4.9
|
31.8
|
1.0
|
MG
|
B:MG2002
|
4.9
|
21.6
|
1.0
|
NH1
|
B:ARG135
|
4.9
|
29.6
|
1.0
|
|
Magnesium binding site 6 out
of 12 in 3ryw
Go back to
Magnesium Binding Sites List in 3ryw
Magnesium binding site 6 out
of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811
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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg2004
b:13.5
occ:1.00
|
OD1
|
B:ASP126
|
2.4
|
29.3
|
1.0
|
OD2
|
B:ASP130
|
2.4
|
27.6
|
1.0
|
OAD
|
B:K9H2001
|
2.7
|
32.3
|
1.0
|
OAE
|
B:K9H2001
|
2.9
|
33.8
|
1.0
|
OD1
|
B:ASP130
|
3.0
|
29.0
|
1.0
|
CG
|
B:ASP130
|
3.1
|
27.4
|
1.0
|
OE1
|
B:GLN195
|
3.2
|
33.8
|
1.0
|
OD2
|
B:ASP198
|
3.3
|
41.1
|
1.0
|
PAZ
|
B:K9H2001
|
3.4
|
33.3
|
1.0
|
CG
|
B:ASP126
|
3.5
|
26.7
|
1.0
|
MG
|
B:MG2003
|
3.6
|
19.1
|
1.0
|
OD2
|
B:ASP126
|
3.8
|
27.6
|
1.0
|
CD
|
B:GLN195
|
4.0
|
29.8
|
1.0
|
NE2
|
B:GLN195
|
4.1
|
29.8
|
1.0
|
CG
|
B:ASP198
|
4.3
|
33.2
|
1.0
|
CE
|
B:LYS310
|
4.4
|
27.6
|
1.0
|
CAY
|
B:K9H2001
|
4.5
|
32.3
|
1.0
|
NZ
|
B:LYS243
|
4.5
|
42.5
|
1.0
|
CB
|
B:ASP130
|
4.6
|
27.8
|
1.0
|
OAB
|
B:K9H2001
|
4.6
|
30.0
|
1.0
|
NZ
|
B:LYS310
|
4.7
|
28.5
|
1.0
|
CB
|
B:ASP126
|
4.8
|
24.8
|
1.0
|
OD1
|
B:ASP198
|
4.8
|
35.6
|
1.0
|
CAJ
|
B:K9H2001
|
4.9
|
31.2
|
1.0
|
|
Magnesium binding site 7 out
of 12 in 3ryw
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Magnesium Binding Sites List in 3ryw
Magnesium binding site 7 out
of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811
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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg2002
b:29.1
occ:1.00
|
OAF
|
C:K9H2001
|
1.9
|
29.5
|
1.0
|
OD1
|
C:ASP287
|
2.4
|
35.0
|
1.0
|
OAB
|
C:K9H2001
|
2.6
|
27.2
|
1.0
|
CG
|
C:ASP287
|
3.3
|
37.1
|
1.0
|
OD2
|
C:ASP287
|
3.6
|
38.9
|
1.0
|
PBA
|
C:K9H2001
|
3.6
|
27.7
|
1.0
|
OD1
|
C:ASP305
|
3.7
|
49.2
|
1.0
|
OD2
|
C:ASP291
|
3.9
|
47.2
|
1.0
|
PAZ
|
C:K9H2001
|
3.9
|
28.5
|
1.0
|
OD2
|
C:ASP305
|
4.0
|
51.9
|
1.0
|
O
|
C:ASP287
|
4.2
|
31.4
|
1.0
|
CG
|
C:ASP305
|
4.3
|
47.7
|
1.0
|
OAC
|
C:K9H2001
|
4.3
|
28.6
|
1.0
|
OAD
|
C:K9H2001
|
4.4
|
27.3
|
1.0
|
OAG
|
C:K9H2001
|
4.5
|
28.6
|
1.0
|
CAY
|
C:K9H2001
|
4.5
|
29.2
|
1.0
|
CB
|
C:ASP287
|
4.6
|
34.3
|
1.0
|
NZ
|
C:LYS301
|
4.6
|
47.2
|
1.0
|
OD2
|
C:ASP288
|
4.6
|
51.0
|
1.0
|
CG
|
C:ASP291
|
4.6
|
45.2
|
1.0
|
C
|
C:ASP287
|
4.6
|
33.1
|
1.0
|
NE2
|
C:GLN284
|
4.6
|
36.4
|
1.0
|
CB
|
C:ASP291
|
4.7
|
43.0
|
1.0
|
CE
|
C:LYS301
|
4.9
|
50.1
|
1.0
|
MG
|
C:MG2003
|
5.0
|
15.5
|
1.0
|
|
Magnesium binding site 8 out
of 12 in 3ryw
Go back to
Magnesium Binding Sites List in 3ryw
Magnesium binding site 8 out
of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811
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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg2003
b:15.5
occ:1.00
|
OD2
|
C:ASP130
|
2.1
|
30.1
|
1.0
|
OAD
|
C:K9H2001
|
2.1
|
27.3
|
1.0
|
OD2
|
C:ASP126
|
2.5
|
27.2
|
1.0
|
OAC
|
C:K9H2001
|
2.5
|
28.6
|
1.0
|
CG
|
C:ASP130
|
3.1
|
28.6
|
1.0
|
CAY
|
C:K9H2001
|
3.4
|
29.2
|
1.0
|
CB
|
C:ASP130
|
3.4
|
27.9
|
1.0
|
PBA
|
C:K9H2001
|
3.4
|
27.7
|
1.0
|
PAZ
|
C:K9H2001
|
3.4
|
28.5
|
1.0
|
CG
|
C:ASP126
|
3.5
|
25.0
|
1.0
|
OD1
|
C:ASP126
|
3.7
|
25.5
|
1.0
|
OAF
|
C:K9H2001
|
3.9
|
29.5
|
1.0
|
MG
|
C:MG2004
|
4.0
|
22.9
|
1.0
|
OAB
|
C:K9H2001
|
4.2
|
27.2
|
1.0
|
OD1
|
C:ASP130
|
4.2
|
31.3
|
1.0
|
OAE
|
C:K9H2001
|
4.6
|
30.7
|
1.0
|
O
|
C:ASP126
|
4.7
|
22.3
|
1.0
|
OAG
|
C:K9H2001
|
4.8
|
28.6
|
1.0
|
NH1
|
C:ARG135
|
4.8
|
27.3
|
1.0
|
CB
|
C:ASP126
|
4.8
|
23.3
|
1.0
|
CAT
|
C:K9H2001
|
4.9
|
32.1
|
1.0
|
CA
|
C:ASP130
|
4.9
|
29.6
|
1.0
|
OD1
|
C:ASP127
|
4.9
|
29.0
|
1.0
|
MG
|
C:MG2002
|
5.0
|
29.1
|
1.0
|
|
Magnesium binding site 9 out
of 12 in 3ryw
Go back to
Magnesium Binding Sites List in 3ryw
Magnesium binding site 9 out
of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811
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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg2004
b:22.9
occ:1.00
|
OD1
|
C:ASP126
|
2.4
|
25.5
|
1.0
|
OAD
|
C:K9H2001
|
2.4
|
27.3
|
1.0
|
OD2
|
C:ASP130
|
2.6
|
30.1
|
1.0
|
OAE
|
C:K9H2001
|
2.9
|
30.7
|
1.0
|
OE1
|
C:GLN195
|
3.1
|
29.5
|
1.0
|
OD2
|
C:ASP198
|
3.1
|
44.4
|
1.0
|
PAZ
|
C:K9H2001
|
3.2
|
28.5
|
1.0
|
OD1
|
C:ASP130
|
3.2
|
31.3
|
1.0
|
CG
|
C:ASP130
|
3.3
|
28.6
|
1.0
|
CG
|
C:ASP126
|
3.5
|
25.0
|
1.0
|
OD2
|
C:ASP126
|
3.9
|
27.2
|
1.0
|
CD
|
C:GLN195
|
4.0
|
28.2
|
1.0
|
MG
|
C:MG2003
|
4.0
|
15.5
|
1.0
|
CG
|
C:ASP198
|
4.0
|
40.6
|
1.0
|
NE2
|
C:GLN195
|
4.1
|
29.1
|
1.0
|
OAB
|
C:K9H2001
|
4.3
|
27.2
|
1.0
|
CAY
|
C:K9H2001
|
4.4
|
29.2
|
1.0
|
CE
|
C:LYS310
|
4.5
|
30.9
|
1.0
|
NZ
|
C:LYS243
|
4.5
|
39.3
|
1.0
|
OD1
|
C:ASP198
|
4.5
|
43.0
|
1.0
|
NZ
|
C:LYS310
|
4.7
|
33.9
|
1.0
|
CB
|
C:ASP130
|
4.8
|
27.9
|
1.0
|
CB
|
C:ASP126
|
4.8
|
23.3
|
1.0
|
CB
|
C:ASP198
|
5.0
|
37.2
|
1.0
|
|
Magnesium binding site 10 out
of 12 in 3ryw
Go back to
Magnesium Binding Sites List in 3ryw
Magnesium binding site 10 out
of 12 in the Crystal Structure of P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811
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 P. Vivax Geranylgeranyl Diphosphate Synthase Complexed with Bph-811 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg2002
b:30.0
occ:1.00
|
OD1
|
D:ASP287
|
2.1
|
53.0
|
1.0
|
OAF
|
D:K9H2001
|
2.2
|
24.9
|
1.0
|
OAB
|
D:K9H2001
|
2.6
|
25.0
|
1.0
|
CG
|
D:ASP287
|
3.0
|
48.1
|
1.0
|
OD2
|
D:ASP287
|
3.4
|
52.9
|
1.0
|
O
|
D:ASP287
|
3.8
|
32.3
|
1.0
|
PBA
|
D:K9H2001
|
3.8
|
24.8
|
1.0
|
OD1
|
D:ASP305
|
3.8
|
54.3
|
1.0
|
OD2
|
D:ASP291
|
3.9
|
59.7
|
1.0
|
OD2
|
D:ASP305
|
4.0
|
58.1
|
1.0
|
PAZ
|
D:K9H2001
|
4.0
|
26.6
|
1.0
|
CB
|
D:ASP287
|
4.2
|
41.7
|
1.0
|
C
|
D:ASP287
|
4.2
|
36.4
|
1.0
|
OD2
|
D:ASP288
|
4.3
|
41.9
|
1.0
|
NE2
|
D:GLN284
|
4.3
|
37.0
|
1.0
|
CG
|
D:ASP305
|
4.3
|
52.4
|
1.0
|
CB
|
D:ASP291
|
4.5
|
46.5
|
1.0
|
OAD
|
D:K9H2001
|
4.6
|
23.4
|
1.0
|
CG
|
D:ASP291
|
4.6
|
51.7
|
1.0
|
CAY
|
D:K9H2001
|
4.6
|
26.7
|
1.0
|
NZ
|
D:LYS301
|
4.6
|
47.6
|
1.0
|
OAC
|
D:K9H2001
|
4.7
|
25.4
|
1.0
|
N
|
D:ASP288
|
4.7
|
36.1
|
1.0
|
OAG
|
D:K9H2001
|
4.7
|
26.5
|
1.0
|
CA
|
D:ASP287
|
4.8
|
37.4
|
1.0
|
CA
|
D:ASP288
|
4.9
|
36.6
|
1.0
|
CE
|
D:LYS301
|
5.0
|
45.1
|
1.0
|
|
Reference:
J.H.No,
F.De Macedo Dossin,
Y.Zhang,
Y.L.Liu,
W.Zhu,
X.Feng,
J.A.Yoo,
E.Lee,
K.Wang,
R.Hui,
L.H.Freitas-Junior,
E.Oldfield.
Lipophilic Analogs of Zoledronate and Risedronate Inhibit Plasmodium Geranylgeranyl Diphosphate Synthase (Ggpps) and Exhibit Potent Antimalarial Activity. Proc.Natl.Acad.Sci.Usa V. 109 4058 2012.
ISSN: ISSN 0027-8424
PubMed: 22392982
DOI: 10.1073/PNAS.1118215109
Page generated: Thu Aug 15 10:43:05 2024
|