Manganese in PDB 8a7j: PCIDS1 in Complex with MN2+, Ipp, and Zol
Enzymatic activity of PCIDS1 in Complex with MN2+, Ipp, and Zol
All present enzymatic activity of PCIDS1 in Complex with MN2+, Ipp, and Zol:
2.5.1.1;
Protein crystallography data
The structure of PCIDS1 in Complex with MN2+, Ipp, and Zol, PDB code: 8a7j
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 /
1.20
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.83,
70.63,
94.09,
90,
91.43,
90
|
|
R / Rfree (%)
|
13.3 /
15.2
|
Manganese Binding Sites:
The binding sites of Manganese atom in the PCIDS1 in Complex with MN2+, Ipp, and Zol
(pdb code 8a7j). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the
PCIDS1 in Complex with MN2+, Ipp, and Zol, PDB code: 8a7j:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
Manganese binding site 1 out
of 6 in 8a7j
Go back to
Manganese Binding Sites List in 8a7j
Manganese binding site 1 out
of 6 in the PCIDS1 in Complex with MN2+, Ipp, and Zol
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of PCIDS1 in Complex with MN2+, Ipp, and Zol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn501
b:14.8
occ:1.00
|
O11
|
A:ZOL506
|
2.0
|
10.5
|
1.0
|
|
OD2
|
A:ASP179
|
2.0
|
10.5
|
1.0
|
|
O
|
A:HOH677
|
2.1
|
10.7
|
1.0
|
|
O
|
A:HOH817
|
2.1
|
11.1
|
1.0
|
|
O16
|
A:ZOL506
|
2.1
|
10.4
|
1.0
|
|
OD2
|
A:ASP183
|
2.2
|
10.6
|
1.0
|
|
CG
|
A:ASP179
|
3.0
|
10.1
|
1.0
|
|
MN
|
A:MN502
|
3.2
|
14.3
|
1.0
|
|
CG
|
A:ASP183
|
3.3
|
10.1
|
1.0
|
|
P9
|
A:ZOL506
|
3.3
|
10.5
|
1.0
|
|
P14
|
A:ZOL506
|
3.4
|
10.5
|
1.0
|
|
OD1
|
A:ASP179
|
3.4
|
10.9
|
1.0
|
|
CB
|
A:ASP183
|
3.7
|
10.8
|
1.0
|
|
C8
|
A:ZOL506
|
3.7
|
10.3
|
1.0
|
|
O
|
A:HOH787
|
3.8
|
12.5
|
1.0
|
|
O15
|
A:ZOL506
|
4.0
|
10.4
|
1.0
|
|
C7
|
A:ZOL506
|
4.0
|
10.4
|
1.0
|
|
O10
|
A:ZOL506
|
4.1
|
10.7
|
1.0
|
|
NH2
|
A:ARG188
|
4.2
|
10.8
|
1.0
|
|
O
|
A:ASP179
|
4.3
|
10.4
|
1.0
|
|
O
|
A:HOH631
|
4.3
|
11.6
|
1.0
|
|
O
|
A:HOH695
|
4.3
|
11.3
|
1.0
|
|
OD1
|
A:ASP183
|
4.4
|
11.5
|
1.0
|
|
CB
|
A:ASP179
|
4.4
|
9.8
|
1.0
|
|
OG
|
A:SER185
|
4.5
|
12.2
|
1.0
|
|
O12
|
A:ZOL506
|
4.5
|
10.9
|
1.0
|
|
OD1
|
A:ASP180
|
4.5
|
12.3
|
1.0
|
|
O
|
A:HOH699
|
4.5
|
12.8
|
1.0
|
|
C
|
A:ASP179
|
4.6
|
9.7
|
1.0
|
|
O17
|
A:ZOL506
|
4.6
|
10.6
|
1.0
|
|
O
|
A:HOH720
|
4.7
|
13.3
|
1.0
|
|
O
|
A:HOH621
|
4.8
|
12.3
|
1.0
|
|
O
|
A:HOH636
|
4.9
|
10.9
|
1.0
|
|
MN
|
A:MN503
|
4.9
|
15.7
|
1.0
|
|
Manganese binding site 2 out
of 6 in 8a7j
Go back to
Manganese Binding Sites List in 8a7j
Manganese binding site 2 out
of 6 in the PCIDS1 in Complex with MN2+, Ipp, and Zol
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of PCIDS1 in Complex with MN2+, Ipp, and Zol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn502
b:14.3
occ:1.00
|
O
|
A:HOH636
|
2.1
|
10.9
|
1.0
|
|
OD1
|
A:ASP179
|
2.1
|
10.9
|
1.0
|
|
O
|
A:HOH621
|
2.1
|
12.3
|
1.0
|
|
O
|
A:HOH695
|
2.1
|
11.3
|
1.0
|
|
O16
|
A:ZOL506
|
2.1
|
10.4
|
1.0
|
|
OD2
|
A:ASP183
|
2.2
|
10.6
|
1.0
|
|
CG
|
A:ASP179
|
3.0
|
10.1
|
1.0
|
|
CG
|
A:ASP183
|
3.1
|
10.1
|
1.0
|
|
MN
|
A:MN501
|
3.2
|
14.8
|
1.0
|
|
OD1
|
A:ASP183
|
3.3
|
11.5
|
1.0
|
|
P14
|
A:ZOL506
|
3.3
|
10.5
|
1.0
|
|
OD2
|
A:ASP179
|
3.4
|
10.5
|
1.0
|
|
O17
|
A:ZOL506
|
3.4
|
10.6
|
1.0
|
|
OD1
|
A:ASP250
|
3.9
|
12.7
|
1.0
|
|
NE2
|
A:GLN247
|
4.0
|
14.1
|
1.0
|
|
O
|
A:HOH817
|
4.2
|
11.1
|
1.0
|
|
O
|
A:HOH668
|
4.3
|
12.2
|
1.0
|
|
OE1
|
A:GLN247
|
4.3
|
14.5
|
1.0
|
|
NZ
|
A:LYS342
|
4.3
|
14.4
|
1.0
|
|
O
|
A:HOH632
|
4.3
|
13.1
|
1.0
|
|
O15
|
A:ZOL506
|
4.4
|
10.4
|
1.0
|
|
CB
|
A:ASP179
|
4.4
|
9.8
|
1.0
|
|
C19
|
A:ZOL506
|
4.4
|
11.6
|
1.0
|
|
CD
|
A:GLN247
|
4.5
|
14.7
|
1.0
|
|
CB
|
A:ASP183
|
4.5
|
10.8
|
1.0
|
|
C7
|
A:ZOL506
|
4.5
|
10.4
|
1.0
|
|
C8
|
A:ZOL506
|
4.6
|
10.3
|
1.0
|
|
CG
|
A:ASP250
|
4.6
|
11.6
|
1.0
|
|
N15
|
A:ZOL506
|
4.7
|
10.3
|
1.0
|
|
O
|
A:ASP179
|
4.7
|
10.4
|
1.0
|
|
O11
|
A:ZOL506
|
4.7
|
10.5
|
1.0
|
|
OD2
|
A:ASP250
|
4.8
|
13.1
|
1.0
|
|
O
|
A:HOH677
|
4.9
|
10.7
|
1.0
|
|
O
|
A:HOH699
|
4.9
|
12.8
|
1.0
|
|
CA
|
A:ASP179
|
4.9
|
10.0
|
1.0
|
|
Manganese binding site 3 out
of 6 in 8a7j
Go back to
Manganese Binding Sites List in 8a7j
Manganese binding site 3 out
of 6 in the PCIDS1 in Complex with MN2+, Ipp, and Zol
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of PCIDS1 in Complex with MN2+, Ipp, and Zol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn503
b:15.7
occ:1.00
|
O10
|
A:ZOL506
|
2.0
|
10.7
|
1.0
|
|
O15
|
A:ZOL506
|
2.1
|
10.4
|
1.0
|
|
O
|
A:HOH671
|
2.1
|
11.5
|
1.0
|
|
OD2
|
A:ASP319
|
2.1
|
11.2
|
1.0
|
|
O
|
A:HOH777
|
2.1
|
11.7
|
1.0
|
|
O
|
A:HOH631
|
2.2
|
11.6
|
1.0
|
|
CG
|
A:ASP319
|
3.2
|
10.8
|
1.0
|
|
P9
|
A:ZOL506
|
3.3
|
10.5
|
1.0
|
|
P14
|
A:ZOL506
|
3.4
|
10.5
|
1.0
|
|
O13
|
A:ZOL506
|
3.5
|
10.8
|
1.0
|
|
C8
|
A:ZOL506
|
3.6
|
10.3
|
1.0
|
|
OD1
|
A:ASP319
|
3.6
|
11.7
|
1.0
|
|
O
|
A:HOH789
|
4.0
|
14.6
|
1.0
|
|
O11
|
A:ZOL506
|
4.0
|
10.5
|
1.0
|
|
O
|
A:HOH668
|
4.1
|
12.2
|
1.0
|
|
O
|
A:ASP319
|
4.2
|
11.0
|
1.0
|
|
O16
|
A:ZOL506
|
4.2
|
10.4
|
1.0
|
|
OD2
|
A:ASP337
|
4.2
|
11.6
|
1.0
|
|
O
|
A:HOH817
|
4.3
|
11.1
|
1.0
|
|
NE2
|
A:GLN316
|
4.3
|
11.9
|
1.0
|
|
OD1
|
A:ASP323
|
4.3
|
14.6
|
1.0
|
|
OD1
|
A:ASP337
|
4.4
|
11.9
|
1.0
|
|
CB
|
A:ASP319
|
4.4
|
10.7
|
1.0
|
|
NZ
|
A:LYS333
|
4.4
|
11.0
|
1.0
|
|
O12
|
A:ZOL506
|
4.4
|
10.9
|
1.0
|
|
OD1
|
A:ASP320
|
4.5
|
11.3
|
1.0
|
|
O17
|
A:ZOL506
|
4.5
|
10.6
|
1.0
|
|
C
|
A:ASP319
|
4.5
|
10.6
|
1.0
|
|
CB
|
A:ASP323
|
4.6
|
11.2
|
1.0
|
|
CG
|
A:ASP337
|
4.7
|
11.2
|
1.0
|
|
O
|
A:HOH787
|
4.8
|
12.5
|
1.0
|
|
CE
|
A:LYS333
|
4.8
|
12.1
|
1.0
|
|
CG
|
A:ASP323
|
4.9
|
12.6
|
1.0
|
|
N
|
A:ASP320
|
4.9
|
10.5
|
1.0
|
|
MN
|
A:MN501
|
4.9
|
14.8
|
1.0
|
|
Manganese binding site 4 out
of 6 in 8a7j
Go back to
Manganese Binding Sites List in 8a7j
Manganese binding site 4 out
of 6 in the PCIDS1 in Complex with MN2+, Ipp, and Zol
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of PCIDS1 in Complex with MN2+, Ipp, and Zol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn501
b:14.3
occ:1.00
|
OD1
|
B:ASP179
|
2.1
|
10.6
|
1.0
|
|
O
|
B:HOH625
|
2.1
|
11.9
|
1.0
|
|
O
|
B:HOH624
|
2.1
|
11.1
|
1.0
|
|
O
|
B:HOH752
|
2.1
|
11.7
|
1.0
|
|
O15
|
B:ZOL506
|
2.1
|
10.4
|
1.0
|
|
OD2
|
B:ASP183
|
2.1
|
10.5
|
1.0
|
|
CG
|
B:ASP183
|
3.0
|
10.1
|
1.0
|
|
CG
|
B:ASP179
|
3.0
|
9.3
|
1.0
|
|
MN
|
B:MN503
|
3.2
|
14.4
|
1.0
|
|
OD1
|
B:ASP183
|
3.3
|
11.2
|
1.0
|
|
P14
|
B:ZOL506
|
3.3
|
10.3
|
1.0
|
|
OD2
|
B:ASP179
|
3.3
|
10.2
|
1.0
|
|
O16
|
B:ZOL506
|
3.5
|
10.8
|
1.0
|
|
OD1
|
B:ASP250
|
4.0
|
12.3
|
1.0
|
|
NE2
|
B:GLN247
|
4.0
|
10.8
|
0.5
|
|
O
|
B:HOH837
|
4.2
|
11.1
|
1.0
|
|
NE2
|
B:GLN247
|
4.2
|
12.6
|
0.5
|
|
OE1
|
B:GLN247
|
4.3
|
10.9
|
0.5
|
|
O
|
B:HOH668
|
4.3
|
12.2
|
1.0
|
|
OE1
|
B:GLN247
|
4.3
|
11.0
|
0.5
|
|
O
|
B:HOH623
|
4.3
|
12.7
|
1.0
|
|
O17
|
B:ZOL506
|
4.4
|
10.7
|
1.0
|
|
NZ
|
B:LYS342
|
4.4
|
13.8
|
1.0
|
|
CB
|
B:ASP179
|
4.4
|
9.7
|
1.0
|
|
C19
|
B:ZOL506
|
4.4
|
11.2
|
1.0
|
|
CB
|
B:ASP183
|
4.5
|
9.8
|
1.0
|
|
CD
|
B:GLN247
|
4.5
|
10.5
|
0.5
|
|
C8
|
B:ZOL506
|
4.6
|
10.3
|
1.0
|
|
C7
|
B:ZOL506
|
4.6
|
10.6
|
1.0
|
|
CG
|
B:ASP250
|
4.6
|
11.1
|
1.0
|
|
O
|
B:ASP179
|
4.7
|
10.1
|
1.0
|
|
CD
|
B:GLN247
|
4.7
|
11.2
|
0.5
|
|
N15
|
B:ZOL506
|
4.7
|
10.8
|
1.0
|
|
O12
|
B:ZOL506
|
4.7
|
9.8
|
1.0
|
|
OD2
|
B:ASP250
|
4.8
|
13.2
|
1.0
|
|
O
|
B:HOH690
|
4.9
|
10.6
|
1.0
|
|
CA
|
B:ASP179
|
4.9
|
9.3
|
1.0
|
|
O
|
B:HOH685
|
4.9
|
12.7
|
1.0
|
|
Manganese binding site 5 out
of 6 in 8a7j
Go back to
Manganese Binding Sites List in 8a7j
Manganese binding site 5 out
of 6 in the PCIDS1 in Complex with MN2+, Ipp, and Zol
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of PCIDS1 in Complex with MN2+, Ipp, and Zol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn502
b:16.0
occ:1.00
|
O11
|
B:ZOL506
|
2.0
|
11.2
|
1.0
|
|
O
|
B:HOH651
|
2.1
|
11.9
|
1.0
|
|
O17
|
B:ZOL506
|
2.1
|
10.7
|
1.0
|
|
OD2
|
B:ASP319
|
2.1
|
11.0
|
1.0
|
|
O
|
B:HOH816
|
2.1
|
12.1
|
1.0
|
|
O
|
B:HOH627
|
2.2
|
11.9
|
1.0
|
|
CG
|
B:ASP319
|
3.1
|
10.9
|
1.0
|
|
P9
|
B:ZOL506
|
3.3
|
10.4
|
1.0
|
|
P14
|
B:ZOL506
|
3.4
|
10.3
|
1.0
|
|
OD1
|
B:ASP319
|
3.6
|
12.7
|
1.0
|
|
C8
|
B:ZOL506
|
3.6
|
10.3
|
1.0
|
|
O13
|
B:ZOL506
|
3.6
|
11.0
|
1.0
|
|
O
|
B:HOH668
|
4.0
|
12.2
|
1.0
|
|
O12
|
B:ZOL506
|
4.0
|
9.8
|
1.0
|
|
O
|
B:HOH801
|
4.1
|
15.1
|
1.0
|
|
O
|
B:HOH837
|
4.2
|
11.1
|
1.0
|
|
OD1
|
B:ASP323
|
4.2
|
16.2
|
1.0
|
|
O
|
B:ASP319
|
4.2
|
11.0
|
1.0
|
|
OD2
|
B:ASP337
|
4.2
|
11.6
|
1.0
|
|
O15
|
B:ZOL506
|
4.2
|
10.4
|
1.0
|
|
NE2
|
B:GLN316
|
4.2
|
11.3
|
1.0
|
|
OD1
|
B:ASP337
|
4.3
|
11.7
|
1.0
|
|
CB
|
B:ASP319
|
4.4
|
10.3
|
1.0
|
|
O10
|
B:ZOL506
|
4.4
|
10.6
|
1.0
|
|
OD1
|
B:ASP320
|
4.4
|
10.6
|
1.0
|
|
O16
|
B:ZOL506
|
4.5
|
10.8
|
1.0
|
|
C
|
B:ASP319
|
4.5
|
10.3
|
1.0
|
|
NZ
|
B:LYS333
|
4.6
|
11.2
|
1.0
|
|
CB
|
B:ASP323
|
4.6
|
11.9
|
1.0
|
|
CG
|
B:ASP337
|
4.7
|
11.4
|
1.0
|
|
O
|
B:HOH787
|
4.8
|
12.0
|
1.0
|
|
CE
|
B:LYS333
|
4.8
|
11.8
|
1.0
|
|
CG
|
B:ASP323
|
4.8
|
13.6
|
1.0
|
|
N
|
B:ASP320
|
4.9
|
10.3
|
1.0
|
|
MN
|
B:MN503
|
4.9
|
14.4
|
1.0
|
|
Manganese binding site 6 out
of 6 in 8a7j
Go back to
Manganese Binding Sites List in 8a7j
Manganese binding site 6 out
of 6 in the PCIDS1 in Complex with MN2+, Ipp, and Zol
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of PCIDS1 in Complex with MN2+, Ipp, and Zol within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn503
b:14.4
occ:1.00
|
O12
|
B:ZOL506
|
2.0
|
9.8
|
1.0
|
|
OD2
|
B:ASP179
|
2.0
|
10.2
|
1.0
|
|
O
|
B:HOH690
|
2.1
|
10.6
|
1.0
|
|
O
|
B:HOH837
|
2.1
|
11.1
|
1.0
|
|
O15
|
B:ZOL506
|
2.1
|
10.4
|
1.0
|
|
OD2
|
B:ASP183
|
2.2
|
10.5
|
1.0
|
|
CG
|
B:ASP179
|
3.0
|
9.3
|
1.0
|
|
MN
|
B:MN501
|
3.2
|
14.3
|
1.0
|
|
CG
|
B:ASP183
|
3.2
|
10.1
|
1.0
|
|
P9
|
B:ZOL506
|
3.3
|
10.4
|
1.0
|
|
P14
|
B:ZOL506
|
3.4
|
10.3
|
1.0
|
|
OD1
|
B:ASP179
|
3.4
|
10.6
|
1.0
|
|
CB
|
B:ASP183
|
3.7
|
9.8
|
1.0
|
|
C8
|
B:ZOL506
|
3.7
|
10.3
|
1.0
|
|
O
|
B:HOH787
|
3.8
|
12.0
|
1.0
|
|
O17
|
B:ZOL506
|
4.0
|
10.7
|
1.0
|
|
C7
|
B:ZOL506
|
4.1
|
10.6
|
1.0
|
|
O11
|
B:ZOL506
|
4.1
|
11.2
|
1.0
|
|
NH2
|
B:ARG188
|
4.2
|
10.7
|
1.0
|
|
O
|
B:ASP179
|
4.3
|
10.1
|
1.0
|
|
O
|
B:HOH752
|
4.3
|
11.7
|
1.0
|
|
O
|
B:HOH627
|
4.4
|
11.9
|
1.0
|
|
OD1
|
B:ASP183
|
4.4
|
11.2
|
1.0
|
|
CB
|
B:ASP179
|
4.4
|
9.7
|
1.0
|
|
OG
|
B:SER185
|
4.4
|
11.8
|
1.0
|
|
O10
|
B:ZOL506
|
4.5
|
10.6
|
1.0
|
|
OD1
|
B:ASP180
|
4.5
|
11.4
|
1.0
|
|
O
|
B:HOH685
|
4.6
|
12.7
|
1.0
|
|
C
|
B:ASP179
|
4.6
|
9.4
|
1.0
|
|
O16
|
B:ZOL506
|
4.6
|
10.8
|
1.0
|
|
O
|
B:HOH692
|
4.7
|
12.5
|
1.0
|
|
O
|
B:HOH625
|
4.8
|
11.9
|
1.0
|
|
O
|
B:HOH624
|
4.9
|
11.1
|
1.0
|
|
MN
|
B:MN502
|
4.9
|
16.0
|
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: Sun Oct 6 11:17:21 2024
|
