Magnesium in PDB 6vyd: Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation
Protein crystallography data
The structure of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation, PDB code: 6vyd
was solved by
C.J.Herbst-Gervasoni,
D.W.Christianson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.17 /
1.46
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.599,
87.260,
163.209,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15 /
18.4
|
Other elements in 6vyd:
The structure of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation
(pdb code 6vyd). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation, PDB code: 6vyd:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 6vyd
Go back to
Magnesium Binding Sites List in 6vyd
Magnesium binding site 1 out
of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg401
b:14.2
occ:1.00
|
O2
|
A:POP406
|
2.0
|
12.9
|
1.0
|
O5
|
A:POP406
|
2.0
|
12.8
|
1.0
|
O
|
A:HOH557
|
2.1
|
14.7
|
1.0
|
OD2
|
A:ASP94
|
2.1
|
15.7
|
1.0
|
OE2
|
A:GLU98
|
2.1
|
14.8
|
1.0
|
O
|
A:HOH565
|
2.2
|
16.2
|
1.0
|
CG
|
A:ASP94
|
3.1
|
16.3
|
1.0
|
CD
|
A:GLU98
|
3.1
|
14.6
|
1.0
|
MG
|
A:MG402
|
3.1
|
14.6
|
1.0
|
P1
|
A:POP406
|
3.2
|
12.6
|
1.0
|
P2
|
A:POP406
|
3.3
|
13.4
|
1.0
|
OD1
|
A:ASP94
|
3.4
|
15.5
|
1.0
|
O
|
A:POP406
|
3.4
|
12.6
|
1.0
|
OE1
|
A:GLU98
|
3.5
|
16.3
|
1.0
|
O1
|
A:POP406
|
3.7
|
14.4
|
1.0
|
NH2
|
A:ARG300
|
3.9
|
15.6
|
1.0
|
NH1
|
A:ARG216
|
3.9
|
17.4
|
1.0
|
O6
|
A:POP406
|
4.1
|
15.3
|
1.0
|
O
|
A:HOH570
|
4.2
|
14.5
|
1.0
|
OE1
|
A:GLU217
|
4.3
|
14.9
|
1.0
|
O4
|
A:POP406
|
4.4
|
13.6
|
1.0
|
CG
|
A:GLU98
|
4.4
|
14.8
|
1.0
|
O
|
A:HOH581
|
4.4
|
14.1
|
1.0
|
NH2
|
A:ARG216
|
4.4
|
18.3
|
1.0
|
CB
|
A:ASP94
|
4.4
|
15.6
|
1.0
|
O3
|
A:POP406
|
4.5
|
13.7
|
1.0
|
O
|
A:HOH729
|
4.5
|
20.7
|
1.0
|
OG
|
A:SER95
|
4.6
|
15.9
|
1.0
|
O
|
A:HOH567
|
4.6
|
14.9
|
1.0
|
CZ
|
A:ARG216
|
4.6
|
19.0
|
1.0
|
MG
|
A:MG403
|
4.7
|
13.7
|
1.0
|
O
|
A:HOH721
|
4.8
|
20.4
|
1.0
|
C
|
A:ASP94
|
4.9
|
13.7
|
1.0
|
O
|
A:ASP94
|
4.9
|
15.3
|
1.0
|
N
|
A:SER95
|
4.9
|
15.8
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 6vyd
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Magnesium Binding Sites List in 6vyd
Magnesium binding site 2 out
of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:14.6
occ:1.00
|
O
|
A:HOH570
|
2.0
|
14.5
|
1.0
|
O
|
A:HOH567
|
2.1
|
14.9
|
1.0
|
OD1
|
A:ASP94
|
2.1
|
15.5
|
1.0
|
OE2
|
A:GLU98
|
2.1
|
14.8
|
1.0
|
O
|
A:HOH562
|
2.1
|
15.8
|
1.0
|
O2
|
A:POP406
|
2.1
|
12.9
|
1.0
|
CD
|
A:GLU98
|
3.1
|
14.6
|
1.0
|
CG
|
A:ASP94
|
3.1
|
16.3
|
1.0
|
MG
|
A:MG401
|
3.1
|
14.2
|
1.0
|
P1
|
A:POP406
|
3.3
|
12.6
|
1.0
|
OD2
|
A:ASP94
|
3.4
|
15.7
|
1.0
|
CG
|
A:GLU98
|
3.6
|
14.8
|
1.0
|
O3
|
A:POP406
|
3.6
|
13.7
|
1.0
|
O
|
A:HOH624
|
3.8
|
19.7
|
1.0
|
OD1
|
A:ASP168
|
4.0
|
14.8
|
1.0
|
OE1
|
A:GLU98
|
4.1
|
16.3
|
1.0
|
OD2
|
A:ASP168
|
4.1
|
15.1
|
1.0
|
O
|
A:HOH581
|
4.1
|
14.1
|
1.0
|
O1
|
A:POP406
|
4.2
|
14.4
|
1.0
|
O
|
A:HOH557
|
4.3
|
14.7
|
1.0
|
CG
|
A:ASP168
|
4.4
|
13.5
|
1.0
|
NH1
|
A:ARG165
|
4.4
|
13.4
|
1.0
|
CB
|
A:ASP94
|
4.4
|
15.6
|
1.0
|
O
|
A:POP406
|
4.5
|
12.6
|
1.0
|
O
|
A:ASP168
|
4.5
|
16.6
|
1.0
|
O
|
A:ASP94
|
4.6
|
15.3
|
1.0
|
O5
|
A:POP406
|
4.8
|
12.8
|
1.0
|
O
|
A:HOH565
|
4.9
|
16.2
|
1.0
|
C
|
A:ASP94
|
5.0
|
13.7
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 6vyd
Go back to
Magnesium Binding Sites List in 6vyd
Magnesium binding site 3 out
of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:13.7
occ:1.00
|
O1
|
A:POP406
|
2.0
|
14.4
|
1.0
|
O6
|
A:POP406
|
2.1
|
15.3
|
1.0
|
OE1
|
A:GLU217
|
2.1
|
14.9
|
1.0
|
OD1
|
A:ASN209
|
2.1
|
13.1
|
1.0
|
O
|
A:HOH591
|
2.1
|
13.0
|
1.0
|
OG
|
A:SER213
|
2.3
|
14.2
|
1.0
|
CG
|
A:ASN209
|
3.1
|
13.4
|
1.0
|
CD
|
A:GLU217
|
3.1
|
15.5
|
1.0
|
P2
|
A:POP406
|
3.2
|
13.4
|
1.0
|
CB
|
A:SER213
|
3.3
|
13.2
|
1.0
|
P1
|
A:POP406
|
3.3
|
12.6
|
1.0
|
O
|
A:POP406
|
3.4
|
12.6
|
1.0
|
ND2
|
A:ASN209
|
3.5
|
13.2
|
1.0
|
OE2
|
A:GLU217
|
3.6
|
14.5
|
1.0
|
O
|
A:HOH581
|
3.8
|
14.1
|
1.0
|
NH2
|
A:ARG165
|
3.8
|
13.5
|
1.0
|
O5
|
A:POP406
|
3.9
|
12.8
|
1.0
|
O
|
A:HOH557
|
3.9
|
14.7
|
1.0
|
O
|
A:ASN209
|
4.1
|
13.7
|
1.0
|
O2
|
A:POP406
|
4.2
|
12.9
|
1.0
|
O3
|
A:POP406
|
4.3
|
13.7
|
1.0
|
CG
|
A:GLU217
|
4.3
|
16.0
|
1.0
|
C
|
A:ASN209
|
4.4
|
11.4
|
1.0
|
CB
|
A:ASN209
|
4.4
|
13.0
|
1.0
|
O4
|
A:POP406
|
4.5
|
13.6
|
1.0
|
NH1
|
A:ARG216
|
4.5
|
17.4
|
1.0
|
CA
|
A:SER213
|
4.6
|
12.8
|
1.0
|
OD2
|
A:ASP210
|
4.7
|
15.1
|
1.0
|
N
|
A:ASP210
|
4.7
|
12.7
|
1.0
|
MG
|
A:MG401
|
4.7
|
14.2
|
1.0
|
CA
|
A:ASP210
|
4.8
|
12.1
|
1.0
|
CZ
|
A:ARG165
|
4.8
|
12.5
|
1.0
|
ND2
|
A:ASN228
|
5.0
|
16.8
|
1.0
|
C
|
A:SER213
|
5.0
|
13.5
|
1.0
|
OH
|
A:TYR301
|
5.0
|
15.1
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 6vyd
Go back to
Magnesium Binding Sites List in 6vyd
Magnesium binding site 4 out
of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg401
b:27.4
occ:1.00
|
OD2
|
B:ASP94
|
2.0
|
23.6
|
1.0
|
O3
|
B:POP408
|
2.0
|
24.5
|
1.0
|
O
|
B:HOH566
|
2.1
|
20.3
|
1.0
|
O5
|
B:POP408
|
2.1
|
21.9
|
1.0
|
O
|
B:HOH574
|
2.1
|
21.4
|
1.0
|
OE2
|
B:GLU98
|
2.2
|
23.4
|
1.0
|
CG
|
B:ASP94
|
3.0
|
24.7
|
1.0
|
CD
|
B:GLU98
|
3.2
|
29.0
|
1.0
|
MG
|
B:MG402
|
3.2
|
22.7
|
1.0
|
P2
|
B:POP408
|
3.2
|
22.3
|
1.0
|
P1
|
B:POP408
|
3.3
|
23.1
|
1.0
|
OD1
|
B:ASP94
|
3.4
|
24.0
|
1.0
|
O
|
B:POP408
|
3.4
|
21.1
|
1.0
|
OE1
|
B:GLU98
|
3.4
|
30.8
|
1.0
|
O6
|
B:POP408
|
3.7
|
21.8
|
1.0
|
NH1
|
B:ARG300
|
4.0
|
23.5
|
1.0
|
NH2
|
B:ARG216
|
4.0
|
34.2
|
1.0
|
O2
|
B:POP408
|
4.1
|
23.8
|
1.0
|
OE2
|
B:GLU217
|
4.3
|
27.1
|
1.0
|
NH1
|
B:ARG216
|
4.4
|
36.8
|
1.0
|
CB
|
B:ASP94
|
4.4
|
24.9
|
1.0
|
O
|
B:HOH540
|
4.4
|
20.5
|
1.0
|
O1
|
B:POP408
|
4.4
|
23.4
|
1.0
|
O
|
B:HOH669
|
4.5
|
33.9
|
1.0
|
CG
|
B:GLU98
|
4.5
|
30.6
|
1.0
|
O4
|
B:POP408
|
4.5
|
24.1
|
1.0
|
O
|
B:HOH558
|
4.5
|
22.3
|
1.0
|
CZ
|
B:ARG216
|
4.6
|
36.5
|
1.0
|
O
|
B:HOH538
|
4.6
|
19.5
|
1.0
|
OG
|
B:SER95
|
4.7
|
32.2
|
1.0
|
MG
|
B:MG403
|
4.8
|
25.7
|
1.0
|
C
|
B:ASP94
|
4.9
|
27.2
|
1.0
|
N
|
B:SER95
|
4.9
|
27.1
|
1.0
|
O
|
B:ASP94
|
5.0
|
28.1
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 6vyd
Go back to
Magnesium Binding Sites List in 6vyd
Magnesium binding site 5 out
of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg402
b:22.7
occ:1.00
|
O
|
B:HOH583
|
2.1
|
24.0
|
1.0
|
OD1
|
B:ASP94
|
2.1
|
24.0
|
1.0
|
O
|
B:HOH540
|
2.1
|
20.5
|
1.0
|
O
|
B:HOH538
|
2.1
|
19.5
|
1.0
|
O5
|
B:POP408
|
2.1
|
21.9
|
1.0
|
OE2
|
B:GLU98
|
2.1
|
23.4
|
1.0
|
CG
|
B:ASP94
|
3.1
|
24.7
|
1.0
|
CD
|
B:GLU98
|
3.1
|
29.0
|
1.0
|
MG
|
B:MG401
|
3.2
|
27.4
|
1.0
|
P2
|
B:POP408
|
3.3
|
22.3
|
1.0
|
OD2
|
B:ASP94
|
3.4
|
23.6
|
1.0
|
O4
|
B:POP408
|
3.6
|
24.1
|
1.0
|
CG
|
B:GLU98
|
3.6
|
30.6
|
1.0
|
O
|
B:HOH648
|
3.8
|
29.8
|
1.0
|
OD2
|
B:ASP168
|
4.0
|
23.6
|
1.0
|
OE1
|
B:GLU98
|
4.1
|
30.8
|
1.0
|
OD1
|
B:ASP168
|
4.1
|
24.6
|
1.0
|
O
|
B:HOH558
|
4.1
|
22.3
|
1.0
|
O6
|
B:POP408
|
4.1
|
21.8
|
1.0
|
O
|
B:HOH566
|
4.3
|
20.3
|
1.0
|
CG
|
B:ASP168
|
4.4
|
23.5
|
1.0
|
NH1
|
B:ARG165
|
4.4
|
21.7
|
1.0
|
CB
|
B:ASP94
|
4.4
|
24.9
|
1.0
|
O
|
B:POP408
|
4.5
|
21.1
|
1.0
|
O
|
B:HOH502
|
4.5
|
39.8
|
1.0
|
O
|
B:ASP168
|
4.5
|
24.2
|
1.0
|
O
|
B:ASP94
|
4.6
|
28.1
|
1.0
|
O
|
B:HOH574
|
4.8
|
21.4
|
1.0
|
O3
|
B:POP408
|
4.8
|
24.5
|
1.0
|
C
|
B:ASP94
|
5.0
|
27.2
|
1.0
|
CA
|
B:ASP94
|
5.0
|
24.8
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 6vyd
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Magnesium Binding Sites List in 6vyd
Magnesium binding site 6 out
of 6 in the Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation
Mono view
Stereo pair view
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A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg403
b:25.7
occ:1.00
|
OE2
|
B:GLU217
|
2.0
|
27.1
|
1.0
|
O6
|
B:POP408
|
2.1
|
21.8
|
1.0
|
OD1
|
B:ASN209
|
2.1
|
20.7
|
1.0
|
O2
|
B:POP408
|
2.2
|
23.8
|
1.0
|
O
|
B:HOH541
|
2.2
|
21.9
|
1.0
|
OG
|
B:SER213
|
2.2
|
23.7
|
1.0
|
CD
|
B:GLU217
|
3.0
|
26.4
|
1.0
|
CG
|
B:ASN209
|
3.1
|
21.6
|
1.0
|
CB
|
B:SER213
|
3.3
|
24.8
|
1.0
|
P1
|
B:POP408
|
3.4
|
23.1
|
1.0
|
P2
|
B:POP408
|
3.4
|
22.3
|
1.0
|
OE1
|
B:GLU217
|
3.5
|
24.4
|
1.0
|
O
|
B:POP408
|
3.6
|
21.1
|
1.0
|
ND2
|
B:ASN209
|
3.6
|
22.3
|
1.0
|
NH2
|
B:ARG165
|
3.7
|
23.8
|
1.0
|
O
|
B:HOH558
|
3.9
|
22.3
|
1.0
|
O
|
B:HOH566
|
4.0
|
20.3
|
1.0
|
O
|
B:ASN209
|
4.0
|
21.2
|
1.0
|
O3
|
B:POP408
|
4.1
|
24.5
|
1.0
|
O5
|
B:POP408
|
4.3
|
21.9
|
1.0
|
CG
|
B:GLU217
|
4.3
|
26.5
|
1.0
|
C
|
B:ASN209
|
4.3
|
19.9
|
1.0
|
O4
|
B:POP408
|
4.4
|
24.1
|
1.0
|
CB
|
B:ASN209
|
4.5
|
20.2
|
1.0
|
OD1
|
B:ASP210
|
4.5
|
22.5
|
1.0
|
O1
|
B:POP408
|
4.6
|
23.4
|
1.0
|
N
|
B:ASP210
|
4.6
|
22.4
|
1.0
|
NH2
|
B:ARG216
|
4.6
|
34.2
|
1.0
|
CA
|
B:SER213
|
4.7
|
25.5
|
1.0
|
CA
|
B:ASP210
|
4.7
|
22.6
|
1.0
|
CZ
|
B:ARG165
|
4.8
|
21.3
|
1.0
|
MG
|
B:MG401
|
4.8
|
27.4
|
1.0
|
ND2
|
B:ASN228
|
4.9
|
25.6
|
1.0
|
C
|
B:SER213
|
5.0
|
29.3
|
1.0
|
O
|
B:ILE227
|
5.0
|
27.3
|
1.0
|
|
Reference:
C.J.Herbst-Gervasoni,
D.W.Christianson.
Terpenoid Cyclase Fggs in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium Cation To Be Published.
Page generated: Tue Oct 1 22:16:51 2024
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