Magnesium in PDB 8a7k: PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol
Enzymatic activity of PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol
All present enzymatic activity of PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol:
2.5.1.1;
Protein crystallography data
The structure of PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol, PDB code: 8a7k
was solved by
F.Ecker,
W.Boland,
M.Groll,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
15.00 /
1.30
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.08,
70.48,
94.9,
90,
91.29,
90
|
|
R / Rfree (%)
|
14.2 /
16.8
|
Other elements in 8a7k:
The structure of PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol
(pdb code 8a7k). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol, PDB code: 8a7k:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 8a7k
Go back to
Magnesium Binding Sites List in 8a7k
Magnesium binding site 1 out
of 6 in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg504
b:17.2
occ:0.50
|
MN
|
A:MN501
|
0.1
|
13.6
|
0.5
|
|
O11
|
A:ZOL510
|
1.9
|
12.4
|
1.0
|
|
O
|
A:HOH656
|
2.0
|
11.4
|
1.0
|
|
O
|
A:HOH734
|
2.1
|
11.6
|
1.0
|
|
OD2
|
A:ASP179
|
2.1
|
11.0
|
1.0
|
|
OD2
|
A:ASP183
|
2.2
|
11.4
|
1.0
|
|
O16
|
A:ZOL510
|
2.3
|
11.9
|
1.0
|
|
CG
|
A:ASP179
|
3.2
|
11.8
|
1.0
|
|
P9
|
A:ZOL510
|
3.2
|
11.4
|
1.0
|
|
P14
|
A:ZOL510
|
3.4
|
11.6
|
1.0
|
|
CG
|
A:ASP183
|
3.4
|
12.3
|
1.0
|
|
MN
|
A:MN502
|
3.5
|
13.3
|
0.5
|
|
MG
|
A:MG505
|
3.6
|
17.4
|
0.5
|
|
OD1
|
A:ASP179
|
3.6
|
11.5
|
1.0
|
|
O
|
A:HOH716
|
3.6
|
13.8
|
1.0
|
|
C8
|
A:ZOL510
|
3.7
|
11.0
|
1.0
|
|
CB
|
A:ASP183
|
3.8
|
12.0
|
1.0
|
|
O10
|
A:ZOL510
|
3.9
|
11.2
|
1.0
|
|
C7
|
A:ZOL510
|
4.0
|
11.5
|
1.0
|
|
O15
|
A:ZOL510
|
4.0
|
11.5
|
1.0
|
|
NH2
|
A:ARG188
|
4.0
|
13.2
|
1.0
|
|
O
|
A:HOH636
|
4.2
|
13.2
|
1.0
|
|
O12
|
A:ZOL510
|
4.3
|
11.6
|
1.0
|
|
OD1
|
A:ASP180
|
4.4
|
13.3
|
1.0
|
|
OG
|
A:SER185
|
4.4
|
13.8
|
1.0
|
|
O
|
A:ASP179
|
4.4
|
11.8
|
1.0
|
|
CB
|
A:ASP179
|
4.5
|
11.2
|
1.0
|
|
O
|
A:HOH664
|
4.5
|
15.8
|
1.0
|
|
O
|
A:HOH687
|
4.5
|
12.2
|
1.0
|
|
OD1
|
A:ASP183
|
4.5
|
12.3
|
1.0
|
|
O
|
A:HOH674
|
4.6
|
13.7
|
1.0
|
|
C
|
A:ASP179
|
4.7
|
10.7
|
1.0
|
|
O17
|
A:ZOL510
|
4.7
|
11.9
|
1.0
|
|
MG
|
A:MG506
|
4.8
|
17.2
|
0.5
|
|
MN
|
A:MN503
|
4.8
|
14.0
|
0.5
|
|
O
|
A:HOH625
|
5.0
|
12.5
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 8a7k
Go back to
Magnesium Binding Sites List in 8a7k
Magnesium binding site 2 out
of 6 in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg505
b:17.4
occ:0.50
|
MN
|
A:MN502
|
0.1
|
13.3
|
0.5
|
|
O
|
A:HOH625
|
1.8
|
12.5
|
1.0
|
|
O
|
A:HOH653
|
2.1
|
11.9
|
1.0
|
|
O
|
A:HOH687
|
2.1
|
12.2
|
1.0
|
|
OD1
|
A:ASP179
|
2.1
|
11.5
|
1.0
|
|
O16
|
A:ZOL510
|
2.2
|
11.9
|
1.0
|
|
OD2
|
A:ASP183
|
2.3
|
11.4
|
1.0
|
|
CG
|
A:ASP183
|
3.1
|
12.3
|
1.0
|
|
OD1
|
A:ASP183
|
3.2
|
12.3
|
1.0
|
|
CG
|
A:ASP179
|
3.2
|
11.8
|
1.0
|
|
OD2
|
A:ASP179
|
3.4
|
11.0
|
1.0
|
|
MN
|
A:MN501
|
3.4
|
13.6
|
0.5
|
|
P14
|
A:ZOL510
|
3.5
|
11.6
|
1.0
|
|
MG
|
A:MG504
|
3.6
|
17.2
|
0.5
|
|
O17
|
A:ZOL510
|
3.6
|
11.9
|
1.0
|
|
OD1
|
A:ASP250
|
3.8
|
14.0
|
1.0
|
|
NE2
|
A:GLN247
|
3.9
|
15.8
|
1.0
|
|
O
|
A:HOH640
|
4.1
|
13.8
|
1.0
|
|
OE1
|
A:GLN247
|
4.2
|
14.6
|
1.0
|
|
NZ
|
A:LYS342
|
4.3
|
16.0
|
1.0
|
|
CD
|
A:GLN247
|
4.3
|
15.2
|
1.0
|
|
O
|
A:HOH734
|
4.4
|
11.6
|
1.0
|
|
O
|
A:HOH676
|
4.4
|
13.8
|
1.0
|
|
CB
|
A:ASP179
|
4.4
|
11.2
|
1.0
|
|
CB
|
A:ASP183
|
4.5
|
12.0
|
1.0
|
|
C19
|
A:ZOL510
|
4.5
|
12.3
|
1.0
|
|
CG
|
A:ASP250
|
4.5
|
13.0
|
1.0
|
|
O15
|
A:ZOL510
|
4.6
|
11.5
|
1.0
|
|
C7
|
A:ZOL510
|
4.7
|
11.5
|
1.0
|
|
O
|
A:ASP179
|
4.7
|
11.8
|
1.0
|
|
C8
|
A:ZOL510
|
4.8
|
11.0
|
1.0
|
|
OD2
|
A:ASP250
|
4.8
|
14.9
|
1.0
|
|
N15
|
A:ZOL510
|
4.8
|
11.6
|
1.0
|
|
CA
|
A:ASP179
|
4.9
|
11.3
|
1.0
|
|
O
|
A:HOH674
|
4.9
|
13.7
|
1.0
|
|
O11
|
A:ZOL510
|
5.0
|
12.4
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 8a7k
Go back to
Magnesium Binding Sites List in 8a7k
Magnesium binding site 3 out
of 6 in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg506
b:17.2
occ:0.50
|
MN
|
A:MN503
|
0.0
|
14.0
|
0.5
|
|
O10
|
A:ZOL510
|
2.0
|
11.2
|
1.0
|
|
O15
|
A:ZOL510
|
2.0
|
11.5
|
1.0
|
|
O
|
A:HOH755
|
2.1
|
12.6
|
1.0
|
|
O
|
A:HOH648
|
2.1
|
12.1
|
1.0
|
|
OD2
|
A:ASP319
|
2.1
|
12.4
|
1.0
|
|
O
|
A:HOH636
|
2.2
|
13.2
|
1.0
|
|
CG
|
A:ASP319
|
3.2
|
11.9
|
1.0
|
|
P9
|
A:ZOL510
|
3.3
|
11.4
|
1.0
|
|
P14
|
A:ZOL510
|
3.4
|
11.6
|
1.0
|
|
O13
|
A:ZOL510
|
3.5
|
12.2
|
1.0
|
|
C8
|
A:ZOL510
|
3.5
|
11.0
|
1.0
|
|
OD1
|
A:ASP319
|
3.6
|
13.1
|
1.0
|
|
O
|
A:HOH774
|
4.0
|
15.8
|
1.0
|
|
O11
|
A:ZOL510
|
4.0
|
12.4
|
1.0
|
|
O
|
A:HOH676
|
4.1
|
13.8
|
1.0
|
|
O
|
A:ASP319
|
4.1
|
11.9
|
1.0
|
|
OD2
|
A:ASP337
|
4.2
|
13.6
|
1.0
|
|
O
|
A:HOH734
|
4.2
|
11.6
|
1.0
|
|
NE2
|
A:GLN316
|
4.3
|
13.2
|
1.0
|
|
OD1
|
A:ASP323
|
4.3
|
17.1
|
1.0
|
|
O16
|
A:ZOL510
|
4.4
|
11.9
|
1.0
|
|
NZ
|
A:LYS333
|
4.4
|
12.1
|
1.0
|
|
CB
|
A:ASP319
|
4.4
|
11.9
|
1.0
|
|
O12
|
A:ZOL510
|
4.4
|
11.6
|
1.0
|
|
OD1
|
A:ASP337
|
4.4
|
12.6
|
1.0
|
|
OD1
|
A:ASP320
|
4.5
|
12.9
|
1.0
|
|
O17
|
A:ZOL510
|
4.5
|
11.9
|
1.0
|
|
C
|
A:ASP319
|
4.5
|
10.5
|
1.0
|
|
CB
|
A:ASP323
|
4.6
|
12.8
|
1.0
|
|
CG
|
A:ASP337
|
4.7
|
12.7
|
1.0
|
|
O
|
A:HOH716
|
4.8
|
13.8
|
1.0
|
|
CE
|
A:LYS333
|
4.8
|
14.6
|
1.0
|
|
MG
|
A:MG504
|
4.8
|
17.2
|
0.5
|
|
MN
|
A:MN501
|
4.8
|
13.6
|
0.5
|
|
CG
|
A:ASP323
|
4.9
|
14.1
|
1.0
|
|
N
|
A:ASP320
|
4.9
|
11.2
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 8a7k
Go back to
Magnesium Binding Sites List in 8a7k
Magnesium binding site 4 out
of 6 in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg504
b:16.2
occ:0.50
|
MN
|
B:MN501
|
0.1
|
13.8
|
0.5
|
|
O
|
B:HOH625
|
1.9
|
13.5
|
1.0
|
|
O
|
B:HOH647
|
2.0
|
12.3
|
1.0
|
|
OD1
|
B:ASP179
|
2.1
|
10.9
|
1.0
|
|
O
|
B:HOH752
|
2.1
|
12.5
|
1.0
|
|
O15
|
B:ZOL509
|
2.2
|
10.8
|
1.0
|
|
OD2
|
B:ASP183
|
2.2
|
11.1
|
1.0
|
|
CG
|
B:ASP183
|
3.1
|
12.4
|
1.0
|
|
CG
|
B:ASP179
|
3.1
|
10.6
|
1.0
|
|
OD1
|
B:ASP183
|
3.2
|
12.6
|
1.0
|
|
MN
|
B:MN503
|
3.4
|
13.3
|
0.5
|
|
OD2
|
B:ASP179
|
3.4
|
10.3
|
1.0
|
|
P14
|
B:ZOL509
|
3.4
|
11.8
|
1.0
|
|
MG
|
B:MG505
|
3.5
|
15.7
|
0.5
|
|
O16
|
B:ZOL509
|
3.5
|
12.6
|
1.0
|
|
NE2
|
B:GLN247
|
3.9
|
12.1
|
0.5
|
|
OD1
|
B:ASP250
|
3.9
|
14.9
|
1.0
|
|
OE1
|
B:GLN247
|
4.1
|
12.4
|
0.5
|
|
NE2
|
B:GLN247
|
4.2
|
14.1
|
0.5
|
|
O
|
B:HOH628
|
4.2
|
15.3
|
1.0
|
|
OE1
|
B:GLN247
|
4.3
|
11.5
|
0.5
|
|
NZ
|
B:LYS342
|
4.3
|
17.3
|
1.0
|
|
CD
|
B:GLN247
|
4.3
|
10.9
|
0.5
|
|
O
|
B:HOH739
|
4.3
|
11.7
|
1.0
|
|
O
|
B:HOH683
|
4.4
|
13.7
|
1.0
|
|
C19
|
B:ZOL509
|
4.4
|
13.5
|
1.0
|
|
CB
|
B:ASP179
|
4.4
|
10.6
|
1.0
|
|
CB
|
B:ASP183
|
4.5
|
11.5
|
1.0
|
|
CG
|
B:ASP250
|
4.5
|
13.2
|
1.0
|
|
O17
|
B:ZOL509
|
4.5
|
11.8
|
1.0
|
|
CD
|
B:GLN247
|
4.7
|
11.4
|
0.5
|
|
O
|
B:ASP179
|
4.7
|
11.6
|
1.0
|
|
C7
|
B:ZOL509
|
4.7
|
11.0
|
1.0
|
|
C8
|
B:ZOL509
|
4.7
|
10.7
|
1.0
|
|
OD2
|
B:ASP250
|
4.7
|
15.5
|
1.0
|
|
N15
|
B:ZOL509
|
4.8
|
11.9
|
1.0
|
|
O12
|
B:ZOL509
|
4.9
|
10.2
|
1.0
|
|
CA
|
B:ASP179
|
4.9
|
11.3
|
1.0
|
|
O
|
B:HOH667
|
5.0
|
11.1
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 8a7k
Go back to
Magnesium Binding Sites List in 8a7k
Magnesium binding site 5 out
of 6 in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg505
b:15.7
occ:0.50
|
MN
|
B:MN503
|
0.1
|
13.3
|
0.5
|
|
O12
|
B:ZOL509
|
1.9
|
10.2
|
1.0
|
|
O
|
B:HOH667
|
2.0
|
11.1
|
1.0
|
|
O
|
B:HOH739
|
2.1
|
11.7
|
1.0
|
|
OD2
|
B:ASP179
|
2.1
|
10.3
|
1.0
|
|
OD2
|
B:ASP183
|
2.2
|
11.1
|
1.0
|
|
O15
|
B:ZOL509
|
2.2
|
10.8
|
1.0
|
|
CG
|
B:ASP179
|
3.2
|
10.6
|
1.0
|
|
P9
|
B:ZOL509
|
3.2
|
11.5
|
1.0
|
|
MN
|
B:MN501
|
3.4
|
13.8
|
0.5
|
|
CG
|
B:ASP183
|
3.4
|
12.4
|
1.0
|
|
P14
|
B:ZOL509
|
3.4
|
11.8
|
1.0
|
|
MG
|
B:MG504
|
3.5
|
16.2
|
0.5
|
|
OD1
|
B:ASP179
|
3.5
|
10.9
|
1.0
|
|
C8
|
B:ZOL509
|
3.7
|
10.7
|
1.0
|
|
O
|
B:HOH743
|
3.7
|
14.1
|
1.0
|
|
CB
|
B:ASP183
|
3.8
|
11.5
|
1.0
|
|
O11
|
B:ZOL509
|
4.0
|
12.3
|
1.0
|
|
O17
|
B:ZOL509
|
4.0
|
11.8
|
1.0
|
|
C7
|
B:ZOL509
|
4.0
|
11.0
|
1.0
|
|
NH2
|
B:ARG188
|
4.1
|
13.2
|
1.0
|
|
O
|
B:HOH621
|
4.3
|
13.4
|
1.0
|
|
O10
|
B:ZOL509
|
4.3
|
11.4
|
1.0
|
|
O
|
B:ASP179
|
4.4
|
11.6
|
1.0
|
|
OD1
|
B:ASP180
|
4.4
|
12.8
|
1.0
|
|
OG
|
B:SER185
|
4.4
|
13.2
|
1.0
|
|
O
|
B:HOH752
|
4.4
|
12.5
|
1.0
|
|
CB
|
B:ASP179
|
4.5
|
10.6
|
1.0
|
|
OD1
|
B:ASP183
|
4.5
|
12.6
|
1.0
|
|
O
|
B:HOH677
|
4.6
|
14.9
|
1.0
|
|
O
|
B:HOH689
|
4.6
|
14.7
|
1.0
|
|
O16
|
B:ZOL509
|
4.7
|
12.6
|
1.0
|
|
C
|
B:ASP179
|
4.7
|
10.5
|
1.0
|
|
MN
|
B:MN502
|
4.8
|
15.0
|
0.5
|
|
MG
|
B:MG506
|
4.8
|
16.1
|
0.5
|
|
O
|
B:HOH625
|
5.0
|
13.5
|
1.0
|
|
O
|
B:HOH647
|
5.0
|
12.3
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 8a7k
Go back to
Magnesium Binding Sites List in 8a7k
Magnesium binding site 6 out
of 6 in the PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of PCIDS1 in Complex with MG2+/MN2+, Ipp, and Zol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg506
b:16.1
occ:0.50
|
MN
|
B:MN502
|
0.0
|
15.0
|
0.5
|
|
O11
|
B:ZOL509
|
2.0
|
12.3
|
1.0
|
|
O17
|
B:ZOL509
|
2.1
|
11.8
|
1.0
|
|
O
|
B:HOH757
|
2.1
|
14.3
|
1.0
|
|
O
|
B:HOH639
|
2.1
|
12.9
|
1.0
|
|
OD2
|
B:ASP319
|
2.1
|
12.2
|
1.0
|
|
O
|
B:HOH621
|
2.1
|
13.4
|
1.0
|
|
CG
|
B:ASP319
|
3.1
|
12.8
|
1.0
|
|
P9
|
B:ZOL509
|
3.3
|
11.5
|
1.0
|
|
P14
|
B:ZOL509
|
3.4
|
11.8
|
1.0
|
|
OD1
|
B:ASP319
|
3.5
|
13.7
|
1.0
|
|
O13
|
B:ZOL509
|
3.6
|
12.3
|
1.0
|
|
C8
|
B:ZOL509
|
3.6
|
10.7
|
1.0
|
|
O12
|
B:ZOL509
|
4.0
|
10.2
|
1.0
|
|
O
|
B:HOH683
|
4.0
|
13.7
|
1.0
|
|
O
|
B:HOH760
|
4.1
|
17.5
|
1.0
|
|
OD1
|
B:ASP323
|
4.2
|
19.2
|
1.0
|
|
O
|
B:ASP319
|
4.2
|
12.4
|
1.0
|
|
O
|
B:HOH739
|
4.2
|
11.7
|
1.0
|
|
OD2
|
B:ASP337
|
4.2
|
12.9
|
1.0
|
|
NE2
|
B:GLN316
|
4.3
|
12.5
|
1.0
|
|
O15
|
B:ZOL509
|
4.3
|
10.8
|
1.0
|
|
OD1
|
B:ASP337
|
4.4
|
13.8
|
1.0
|
|
CB
|
B:ASP319
|
4.4
|
12.5
|
1.0
|
|
OD1
|
B:ASP320
|
4.4
|
13.6
|
1.0
|
|
O10
|
B:ZOL509
|
4.4
|
11.4
|
1.0
|
|
O16
|
B:ZOL509
|
4.5
|
12.6
|
1.0
|
|
C
|
B:ASP319
|
4.5
|
11.4
|
1.0
|
|
NZ
|
B:LYS333
|
4.5
|
12.4
|
1.0
|
|
CB
|
B:ASP323
|
4.6
|
12.6
|
1.0
|
|
CG
|
B:ASP337
|
4.7
|
12.5
|
1.0
|
|
O
|
B:HOH743
|
4.8
|
14.1
|
1.0
|
|
CG
|
B:ASP323
|
4.8
|
16.1
|
1.0
|
|
MG
|
B:MG505
|
4.8
|
15.7
|
0.5
|
|
CE
|
B:LYS333
|
4.8
|
13.5
|
1.0
|
|
MN
|
B:MN503
|
4.9
|
13.3
|
0.5
|
|
N
|
B:ASP320
|
4.9
|
12.0
|
1.0
|
|
Reference:
F.Ecker,
W.Boland,
M.Groll.
Metal-Dependent Enzyme Symmetry Guides the Biosynthetic Flux of Terpene Precursors To Be Published 2023.
DOI: 10.1038/S41557-023-01235-9
Page generated: Thu Oct 3 17:56:32 2024
|
