Calcium in PDB 6w7i: Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca
Enzymatic activity of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca
All present enzymatic activity of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca:
2.5.1.1;
2.5.1.10;
Protein crystallography data
The structure of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca, PDB code: 6w7i
was solved by
S.Maheshwari,
Y.S.Kim,
S.Aripirala,
S.B.Gabelli,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
77.85 /
2.10
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.932,
79.977,
81.175,
90.00,
106.39,
90.00
|
R / Rfree (%)
|
18.4 /
23.9
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca
(pdb code 6w7i). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca, PDB code: 6w7i:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 6w7i
Go back to
Calcium Binding Sites List in 6w7i
Calcium binding site 1 out
of 6 in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:12.7
occ:1.00
|
O11
|
A:476406
|
2.2
|
12.1
|
1.0
|
OD2
|
A:ASP250
|
2.2
|
13.0
|
1.0
|
O14
|
A:476406
|
2.3
|
13.6
|
1.0
|
O
|
A:HOH540
|
2.4
|
12.7
|
1.0
|
O
|
A:HOH504
|
2.5
|
15.1
|
1.0
|
O
|
A:HOH599
|
2.5
|
13.8
|
1.0
|
CG
|
A:ASP250
|
3.3
|
13.0
|
1.0
|
P10
|
A:476406
|
3.5
|
12.3
|
1.0
|
P9
|
A:476406
|
3.5
|
15.4
|
1.0
|
C8
|
A:476406
|
3.8
|
13.7
|
1.0
|
OD1
|
A:ASP250
|
3.8
|
11.8
|
1.0
|
C3
|
A:PEG407
|
3.9
|
21.6
|
1.0
|
O4
|
A:PEG407
|
4.1
|
21.5
|
1.0
|
O
|
A:ASP250
|
4.1
|
13.6
|
1.0
|
O
|
A:HOH553
|
4.2
|
9.9
|
1.0
|
NE2
|
A:GLN247
|
4.3
|
7.2
|
1.0
|
OD2
|
A:ASP268
|
4.3
|
16.7
|
1.0
|
C4
|
A:PEG407
|
4.3
|
25.2
|
1.0
|
O15
|
A:476406
|
4.4
|
14.8
|
1.0
|
NZ
|
A:LYS264
|
4.4
|
16.5
|
1.0
|
CB
|
A:ASP250
|
4.4
|
13.0
|
1.0
|
C
|
A:ASP250
|
4.5
|
13.2
|
1.0
|
O13
|
A:476406
|
4.5
|
10.9
|
1.0
|
O12
|
A:476406
|
4.5
|
10.9
|
1.0
|
OD1
|
A:ASP268
|
4.6
|
15.9
|
1.0
|
CB
|
A:ASP254
|
4.6
|
16.4
|
1.0
|
O16
|
A:476406
|
4.6
|
14.6
|
1.0
|
OD1
|
A:ASP251
|
4.7
|
11.8
|
1.0
|
O
|
A:HOH669
|
4.8
|
16.6
|
1.0
|
CG
|
A:ASP268
|
4.8
|
17.9
|
1.0
|
CE
|
A:LYS264
|
4.8
|
16.9
|
1.0
|
OD2
|
A:ASP254
|
4.8
|
17.2
|
1.0
|
N
|
A:ASP251
|
4.9
|
13.5
|
1.0
|
|
Calcium binding site 2 out
of 6 in 6w7i
Go back to
Calcium Binding Sites List in 6w7i
Calcium binding site 2 out
of 6 in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:18.0
occ:1.00
|
O
|
A:HOH531
|
2.2
|
12.6
|
1.0
|
O12
|
A:476406
|
2.2
|
10.9
|
1.0
|
OD2
|
A:ASP102
|
2.3
|
30.0
|
1.0
|
OD2
|
A:ASP98
|
2.4
|
11.4
|
1.0
|
O
|
A:HOH669
|
2.4
|
16.6
|
1.0
|
O15
|
A:476406
|
2.5
|
14.8
|
1.0
|
CG
|
A:ASP102
|
3.4
|
30.0
|
1.0
|
P10
|
A:476406
|
3.4
|
12.3
|
1.0
|
CG
|
A:ASP98
|
3.5
|
12.3
|
1.0
|
CA
|
A:CA403
|
3.6
|
13.6
|
1.0
|
P9
|
A:476406
|
3.6
|
15.4
|
1.0
|
C2
|
A:PEG407
|
3.7
|
24.7
|
1.0
|
C8
|
A:476406
|
3.8
|
13.7
|
1.0
|
C7
|
A:476406
|
3.9
|
14.1
|
1.0
|
CB
|
A:ASP102
|
3.9
|
30.0
|
1.0
|
OD1
|
A:ASP98
|
4.0
|
12.6
|
1.0
|
O11
|
A:476406
|
4.1
|
12.1
|
1.0
|
OG
|
A:SER104
|
4.2
|
17.3
|
1.0
|
NH2
|
A:ARG107
|
4.3
|
11.3
|
1.0
|
OD1
|
A:ASP99
|
4.4
|
13.2
|
1.0
|
O14
|
A:476406
|
4.4
|
13.6
|
1.0
|
O2
|
A:PEG407
|
4.4
|
26.4
|
1.0
|
C1
|
A:PEG407
|
4.4
|
24.6
|
1.0
|
OD1
|
A:ASP102
|
4.4
|
30.0
|
1.0
|
C3
|
A:PEG407
|
4.6
|
21.6
|
1.0
|
O
|
A:ASP98
|
4.6
|
12.3
|
1.0
|
O
|
A:HOH568
|
4.6
|
19.7
|
1.0
|
O13
|
A:476406
|
4.6
|
10.9
|
1.0
|
O
|
A:HOH545
|
4.7
|
23.1
|
1.0
|
CB
|
A:ASP98
|
4.7
|
12.5
|
1.0
|
O16
|
A:476406
|
4.8
|
14.6
|
1.0
|
O1
|
A:PEG407
|
4.9
|
20.8
|
1.0
|
C
|
A:ASP98
|
4.9
|
12.8
|
1.0
|
O
|
A:HOH665
|
4.9
|
8.6
|
1.0
|
|
Calcium binding site 3 out
of 6 in 6w7i
Go back to
Calcium Binding Sites List in 6w7i
Calcium binding site 3 out
of 6 in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:13.6
occ:1.00
|
OD2
|
A:ASP102
|
2.3
|
30.0
|
1.0
|
O15
|
A:476406
|
2.4
|
14.8
|
1.0
|
O
|
A:HOH536
|
2.4
|
11.6
|
1.0
|
O
|
A:HOH665
|
2.4
|
8.6
|
1.0
|
OD1
|
A:ASP98
|
2.5
|
12.6
|
1.0
|
O
|
A:HOH526
|
2.5
|
12.3
|
1.0
|
OD1
|
A:ASP102
|
3.0
|
30.0
|
1.0
|
CG
|
A:ASP102
|
3.0
|
30.0
|
1.0
|
CG
|
A:ASP98
|
3.3
|
12.3
|
1.0
|
OD2
|
A:ASP98
|
3.3
|
11.4
|
1.0
|
CA
|
A:CA402
|
3.6
|
18.0
|
1.0
|
P9
|
A:476406
|
3.6
|
15.4
|
1.0
|
O16
|
A:476406
|
3.7
|
14.6
|
1.0
|
OD1
|
A:ASP170
|
4.0
|
16.0
|
1.0
|
O
|
A:HOH509
|
4.2
|
19.9
|
1.0
|
NE2
|
A:GLN167
|
4.2
|
13.2
|
1.0
|
OE1
|
A:GLN167
|
4.4
|
15.2
|
1.0
|
CG
|
A:ASP170
|
4.5
|
14.8
|
1.0
|
O
|
A:HOH553
|
4.5
|
9.9
|
1.0
|
CB
|
A:ASP102
|
4.5
|
30.0
|
1.0
|
OD2
|
A:ASP170
|
4.6
|
14.2
|
1.0
|
O14
|
A:476406
|
4.6
|
13.6
|
1.0
|
C7
|
A:476406
|
4.6
|
14.1
|
1.0
|
CB
|
A:ASP98
|
4.7
|
12.5
|
1.0
|
CD
|
A:GLN167
|
4.7
|
14.3
|
1.0
|
NZ
|
A:LYS273
|
4.8
|
26.0
|
1.0
|
C8
|
A:476406
|
4.8
|
13.7
|
1.0
|
O
|
A:HOH669
|
4.9
|
16.6
|
1.0
|
C1
|
A:476406
|
5.0
|
14.7
|
1.0
|
O
|
A:HOH505
|
5.0
|
29.2
|
1.0
|
O
|
A:ASP98
|
5.0
|
12.3
|
1.0
|
N2
|
A:476406
|
5.0
|
14.4
|
1.0
|
|
Calcium binding site 4 out
of 6 in 6w7i
Go back to
Calcium Binding Sites List in 6w7i
Calcium binding site 4 out
of 6 in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca401
b:15.6
occ:1.00
|
O16
|
B:476405
|
2.2
|
16.3
|
1.0
|
OD2
|
B:ASP250
|
2.3
|
16.2
|
1.0
|
O12
|
B:476405
|
2.3
|
16.5
|
1.0
|
O
|
B:HOH595
|
2.3
|
13.1
|
1.0
|
O
|
B:HOH527
|
2.5
|
12.8
|
1.0
|
O
|
B:HOH573
|
2.6
|
13.4
|
1.0
|
CG
|
B:ASP250
|
3.3
|
15.8
|
1.0
|
P9
|
B:476405
|
3.5
|
15.8
|
1.0
|
P10
|
B:476405
|
3.5
|
14.3
|
1.0
|
C8
|
B:476405
|
3.8
|
15.9
|
1.0
|
OD1
|
B:ASP250
|
3.8
|
16.1
|
1.0
|
O
|
B:HOH600
|
3.9
|
15.5
|
1.0
|
O
|
B:HOH569
|
4.1
|
12.4
|
1.0
|
O
|
B:HOH695
|
4.2
|
23.3
|
1.0
|
O
|
B:ASP250
|
4.2
|
15.1
|
1.0
|
OD2
|
B:ASP268
|
4.3
|
16.7
|
1.0
|
O14
|
B:476405
|
4.3
|
16.6
|
1.0
|
NE2
|
B:GLN247
|
4.4
|
11.2
|
1.0
|
OD1
|
B:ASP268
|
4.4
|
16.5
|
1.0
|
CB
|
B:ASP250
|
4.5
|
15.1
|
1.0
|
NZ
|
B:LYS264
|
4.5
|
15.2
|
1.0
|
O13
|
B:476405
|
4.5
|
15.4
|
1.0
|
O11
|
B:476405
|
4.5
|
14.8
|
1.0
|
O
|
B:HOH682
|
4.5
|
21.0
|
1.0
|
O15
|
B:476405
|
4.5
|
15.8
|
1.0
|
C
|
B:ASP250
|
4.6
|
15.5
|
1.0
|
CE
|
B:LYS264
|
4.6
|
17.6
|
1.0
|
CB
|
B:ASP254
|
4.7
|
19.4
|
1.0
|
OD1
|
B:ASP251
|
4.7
|
16.3
|
1.0
|
OD2
|
B:ASP254
|
4.8
|
19.8
|
1.0
|
CG
|
B:ASP268
|
4.8
|
18.4
|
1.0
|
|
Calcium binding site 5 out
of 6 in 6w7i
Go back to
Calcium Binding Sites List in 6w7i
Calcium binding site 5 out
of 6 in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca402
b:18.0
occ:1.00
|
O11
|
B:476405
|
2.1
|
14.8
|
1.0
|
O
|
B:HOH550
|
2.2
|
15.7
|
1.0
|
OD2
|
B:ASP102
|
2.3
|
17.2
|
1.0
|
OD2
|
B:ASP98
|
2.3
|
16.1
|
1.0
|
O
|
B:HOH682
|
2.4
|
21.0
|
1.0
|
O14
|
B:476405
|
2.5
|
16.6
|
1.0
|
CG
|
B:ASP102
|
3.4
|
18.3
|
1.0
|
P10
|
B:476405
|
3.4
|
14.3
|
1.0
|
CG
|
B:ASP98
|
3.4
|
12.5
|
1.0
|
CA
|
B:CA403
|
3.6
|
17.5
|
1.0
|
P9
|
B:476405
|
3.7
|
15.8
|
1.0
|
OD1
|
B:ASP98
|
3.7
|
13.0
|
1.0
|
C8
|
B:476405
|
3.8
|
15.9
|
1.0
|
CB
|
B:ASP102
|
3.9
|
18.6
|
1.0
|
O12
|
B:476405
|
4.0
|
16.5
|
1.0
|
O
|
B:HOH690
|
4.0
|
20.6
|
1.0
|
C7
|
B:476405
|
4.0
|
14.4
|
1.0
|
NH2
|
B:ARG107
|
4.2
|
12.8
|
1.0
|
OG
|
B:SER104
|
4.3
|
20.1
|
1.0
|
O16
|
B:476405
|
4.4
|
16.3
|
1.0
|
OD1
|
B:ASP102
|
4.4
|
19.8
|
1.0
|
O
|
B:HOH621
|
4.4
|
21.7
|
1.0
|
OD1
|
B:ASP99
|
4.4
|
13.7
|
1.0
|
O
|
B:HOH600
|
4.4
|
15.5
|
1.0
|
O
|
B:ASP98
|
4.6
|
12.3
|
1.0
|
O13
|
B:476405
|
4.6
|
15.4
|
1.0
|
O
|
B:HOH506
|
4.6
|
24.2
|
1.0
|
CB
|
B:ASP98
|
4.7
|
13.2
|
1.0
|
O
|
B:HOH583
|
4.8
|
17.8
|
1.0
|
C
|
B:ASP98
|
4.9
|
13.0
|
1.0
|
O15
|
B:476405
|
4.9
|
15.8
|
1.0
|
O
|
B:HOH647
|
4.9
|
14.8
|
1.0
|
|
Calcium binding site 6 out
of 6 in 6w7i
Go back to
Calcium Binding Sites List in 6w7i
Calcium binding site 6 out
of 6 in the Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Lmfpps Mutant T164W in Complex with 476A, Ipp & Ca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca403
b:17.5
occ:1.00
|
O
|
B:HOH588
|
2.4
|
14.1
|
1.0
|
O
|
B:HOH647
|
2.4
|
14.8
|
1.0
|
OD1
|
B:ASP98
|
2.4
|
13.0
|
1.0
|
OD2
|
B:ASP102
|
2.4
|
17.2
|
1.0
|
O14
|
B:476405
|
2.5
|
16.6
|
1.0
|
O
|
B:HOH517
|
2.5
|
9.2
|
1.0
|
OD1
|
B:ASP102
|
2.8
|
19.8
|
1.0
|
CG
|
B:ASP102
|
3.0
|
18.3
|
1.0
|
CG
|
B:ASP98
|
3.4
|
12.5
|
1.0
|
OD2
|
B:ASP98
|
3.6
|
16.1
|
1.0
|
CA
|
B:CA402
|
3.6
|
18.0
|
1.0
|
P9
|
B:476405
|
3.7
|
15.8
|
1.0
|
O15
|
B:476405
|
3.8
|
15.8
|
1.0
|
OD1
|
B:ASP170
|
3.8
|
16.1
|
1.0
|
NE2
|
B:GLN167
|
4.2
|
12.5
|
1.0
|
O
|
B:HOH510
|
4.2
|
22.6
|
1.0
|
OE1
|
B:GLN167
|
4.4
|
14.8
|
1.0
|
O
|
B:HOH569
|
4.4
|
12.4
|
1.0
|
CB
|
B:ASP102
|
4.4
|
18.6
|
1.0
|
CG
|
B:ASP170
|
4.5
|
15.9
|
1.0
|
O16
|
B:476405
|
4.6
|
16.3
|
1.0
|
OD2
|
B:ASP170
|
4.7
|
15.8
|
1.0
|
CD
|
B:GLN167
|
4.7
|
13.4
|
1.0
|
CB
|
B:ASP98
|
4.8
|
13.2
|
1.0
|
NZ
|
B:LYS273
|
4.8
|
27.4
|
1.0
|
C7
|
B:476405
|
4.8
|
14.4
|
1.0
|
C8
|
B:476405
|
4.9
|
15.9
|
1.0
|
O
|
B:HOH682
|
4.9
|
21.0
|
1.0
|
O
|
B:ASP98
|
5.0
|
12.3
|
1.0
|
|
Reference:
S.Maheshwari,
Y.S.Kim,
S.Aripirala,
M.Murphy,
L.M.Amzel,
S.B.Gabelli.
Identifying Structural Determinants of Product Specificity in Leishmania Major Farnesyl Diphosphate Synthase. Biochemistry V. 59 2751 2020.
ISSN: ISSN 0006-2960
PubMed: 32584028
DOI: 10.1021/ACS.BIOCHEM.0C00432
Page generated: Tue Jul 16 17:21:45 2024
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