Calcium in PDB 6vjc: Lmfpps Mutant T164Y in Complex with 476A, Ipp & Ca
Enzymatic activity of Lmfpps Mutant T164Y in Complex with 476A, Ipp & Ca
All present enzymatic activity of Lmfpps Mutant T164Y in Complex with 476A, Ipp & Ca:
2.5.1.1;
2.5.1.10;
Protein crystallography data
The structure of Lmfpps Mutant T164Y in Complex with 476A, Ipp & Ca, PDB code: 6vjc
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)
|
42.98 /
1.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
80.525,
85.889,
107.202,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.8 /
19.9
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Lmfpps Mutant T164Y in Complex with 476A, Ipp & Ca
(pdb code 6vjc). 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 T164Y in Complex with 476A, Ipp & Ca, PDB code: 6vjc:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 6vjc
Go back to
Calcium Binding Sites List in 6vjc
Calcium binding site 1 out
of 6 in the Lmfpps Mutant T164Y 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 T164Y in Complex with 476A, Ipp & Ca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:19.4
occ:1.00
|
O16
|
A:476405
|
2.3
|
20.4
|
1.0
|
OD2
|
A:ASP250
|
2.3
|
17.6
|
1.0
|
O
|
A:HOH593
|
2.3
|
18.9
|
1.0
|
O12
|
A:476405
|
2.4
|
17.9
|
1.0
|
O
|
A:HOH637
|
2.4
|
20.0
|
1.0
|
O
|
A:HOH694
|
2.5
|
19.2
|
1.0
|
CG
|
A:ASP250
|
3.4
|
19.8
|
1.0
|
P9
|
A:476405
|
3.5
|
19.8
|
1.0
|
P10
|
A:476405
|
3.6
|
19.3
|
1.0
|
C8
|
A:476405
|
3.8
|
17.6
|
1.0
|
O
|
A:HOH674
|
3.8
|
18.8
|
1.0
|
OD1
|
A:ASP250
|
3.9
|
17.8
|
1.0
|
O
|
A:HOH641
|
4.0
|
24.2
|
1.0
|
O
|
A:ASP250
|
4.2
|
19.3
|
1.0
|
NE2
|
A:GLN247
|
4.3
|
20.6
|
1.0
|
O
|
A:HOH787
|
4.3
|
23.9
|
1.0
|
O15
|
A:476405
|
4.4
|
18.1
|
1.0
|
OD2
|
A:ASP268
|
4.4
|
22.1
|
1.0
|
NZ
|
A:LYS264
|
4.4
|
20.0
|
1.0
|
OD1
|
A:ASP268
|
4.5
|
22.3
|
1.0
|
O11
|
A:476405
|
4.5
|
17.7
|
1.0
|
O
|
A:HOH784
|
4.6
|
20.8
|
1.0
|
CB
|
A:ASP250
|
4.6
|
18.6
|
1.0
|
C
|
A:ASP250
|
4.6
|
18.0
|
1.0
|
O13
|
A:476405
|
4.6
|
17.5
|
1.0
|
O14
|
A:476405
|
4.7
|
19.8
|
1.0
|
CE
|
A:LYS264
|
4.7
|
20.1
|
1.0
|
CB
|
A:ASP254
|
4.8
|
21.0
|
1.0
|
OD1
|
A:ASP251
|
4.8
|
18.9
|
1.0
|
OD2
|
A:ASP254
|
4.8
|
23.9
|
1.0
|
CG
|
A:ASP268
|
4.8
|
24.9
|
1.0
|
|
Calcium binding site 2 out
of 6 in 6vjc
Go back to
Calcium Binding Sites List in 6vjc
Calcium binding site 2 out
of 6 in the Lmfpps Mutant T164Y 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 T164Y in Complex with 476A, Ipp & Ca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:21.1
occ:1.00
|
OD2
|
A:ASP102
|
2.2
|
20.7
|
1.0
|
O13
|
A:476405
|
2.3
|
17.5
|
1.0
|
O
|
A:HOH784
|
2.3
|
20.8
|
1.0
|
O
|
A:HOH526
|
2.3
|
20.4
|
1.0
|
OD2
|
A:ASP98
|
2.3
|
18.2
|
1.0
|
O15
|
A:476405
|
2.4
|
18.1
|
1.0
|
CG
|
A:ASP102
|
3.4
|
22.8
|
1.0
|
CG
|
A:ASP98
|
3.4
|
19.4
|
1.0
|
P10
|
A:476405
|
3.4
|
19.3
|
1.0
|
CA
|
A:CA403
|
3.5
|
20.1
|
1.0
|
P9
|
A:476405
|
3.6
|
19.8
|
1.0
|
C8
|
A:476405
|
3.9
|
17.6
|
1.0
|
OD1
|
A:ASP98
|
3.9
|
21.3
|
1.0
|
O12
|
A:476405
|
3.9
|
17.9
|
1.0
|
CB
|
A:ASP102
|
3.9
|
19.8
|
1.0
|
C7
|
A:476405
|
4.0
|
19.0
|
1.0
|
O
|
A:HOH789
|
4.2
|
27.3
|
1.0
|
NH2
|
A:ARG107
|
4.3
|
17.9
|
1.0
|
OG
|
A:SER104
|
4.3
|
22.0
|
1.0
|
O16
|
A:476405
|
4.3
|
20.4
|
1.0
|
OD1
|
A:ASP102
|
4.4
|
23.6
|
1.0
|
OD1
|
A:ASP99
|
4.5
|
20.3
|
1.0
|
O
|
A:HOH674
|
4.5
|
18.8
|
1.0
|
O
|
A:ASP98
|
4.6
|
18.7
|
1.0
|
O
|
A:HOH698
|
4.6
|
27.2
|
1.0
|
CB
|
A:ASP98
|
4.7
|
18.9
|
1.0
|
O11
|
A:476405
|
4.7
|
17.7
|
1.0
|
O14
|
A:476405
|
4.8
|
19.8
|
1.0
|
O
|
A:HOH578
|
4.8
|
28.5
|
1.0
|
C
|
A:ASP98
|
4.9
|
18.3
|
1.0
|
O
|
A:HOH752
|
4.9
|
18.1
|
1.0
|
O
|
A:HOH629
|
5.0
|
24.6
|
1.0
|
|
Calcium binding site 3 out
of 6 in 6vjc
Go back to
Calcium Binding Sites List in 6vjc
Calcium binding site 3 out
of 6 in the Lmfpps Mutant T164Y 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 T164Y in Complex with 476A, Ipp & Ca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:20.1
occ:1.00
|
O
|
A:HOH719
|
2.4
|
18.3
|
1.0
|
O
|
A:HOH557
|
2.4
|
21.2
|
1.0
|
OD1
|
A:ASP98
|
2.4
|
21.3
|
1.0
|
O15
|
A:476405
|
2.4
|
18.1
|
1.0
|
OD2
|
A:ASP102
|
2.4
|
20.7
|
1.0
|
O
|
A:HOH752
|
2.5
|
18.1
|
1.0
|
OD1
|
A:ASP102
|
3.0
|
23.6
|
1.0
|
CG
|
A:ASP102
|
3.0
|
22.8
|
1.0
|
CG
|
A:ASP98
|
3.1
|
19.4
|
1.0
|
OD2
|
A:ASP98
|
3.2
|
18.2
|
1.0
|
CA
|
A:CA402
|
3.5
|
21.1
|
1.0
|
P9
|
A:476405
|
3.6
|
19.8
|
1.0
|
O14
|
A:476405
|
3.7
|
19.8
|
1.0
|
NE2
|
A:GLN167
|
4.2
|
18.4
|
1.0
|
OD1
|
A:ASP170
|
4.2
|
23.6
|
1.0
|
O
|
A:HOH553
|
4.3
|
22.4
|
1.0
|
OE1
|
A:GLN167
|
4.4
|
26.6
|
1.0
|
CB
|
A:ASP102
|
4.5
|
19.8
|
1.0
|
O16
|
A:476405
|
4.6
|
20.4
|
1.0
|
OD2
|
A:ASP170
|
4.6
|
25.4
|
1.0
|
CG
|
A:ASP170
|
4.6
|
20.8
|
1.0
|
O
|
A:HOH641
|
4.6
|
24.2
|
1.0
|
CB
|
A:ASP98
|
4.6
|
18.9
|
1.0
|
NZ
|
A:LYS273
|
4.7
|
38.6
|
1.0
|
CD
|
A:GLN167
|
4.7
|
21.0
|
1.0
|
O
|
A:HOH784
|
4.8
|
20.8
|
1.0
|
C7
|
A:476405
|
4.9
|
19.0
|
1.0
|
C8
|
A:476405
|
4.9
|
17.6
|
1.0
|
O
|
A:HOH556
|
4.9
|
35.1
|
1.0
|
O
|
A:ASP98
|
4.9
|
18.7
|
1.0
|
|
Calcium binding site 4 out
of 6 in 6vjc
Go back to
Calcium Binding Sites List in 6vjc
Calcium binding site 4 out
of 6 in the Lmfpps Mutant T164Y 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 T164Y in Complex with 476A, Ipp & Ca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca401
b:19.2
occ:1.00
|
OD2
|
B:ASP250
|
2.3
|
19.6
|
1.0
|
O16
|
B:476405
|
2.3
|
21.7
|
1.0
|
O12
|
B:476405
|
2.3
|
19.7
|
1.0
|
O
|
B:HOH775
|
2.4
|
18.9
|
1.0
|
O
|
B:HOH644
|
2.4
|
16.8
|
1.0
|
O
|
B:HOH711
|
2.5
|
20.5
|
1.0
|
CG
|
B:ASP250
|
3.3
|
21.6
|
1.0
|
P9
|
B:476405
|
3.5
|
19.9
|
1.0
|
P10
|
B:476405
|
3.5
|
18.5
|
1.0
|
C8
|
B:476405
|
3.8
|
17.7
|
1.0
|
O
|
B:HOH760
|
3.8
|
20.3
|
1.0
|
OD1
|
B:ASP250
|
3.8
|
19.3
|
1.0
|
O
|
B:HOH713
|
4.0
|
21.8
|
1.0
|
NE2
|
B:GLN247
|
4.3
|
16.2
|
1.0
|
O
|
B:ASP250
|
4.3
|
20.9
|
1.0
|
NZ
|
B:LYS264
|
4.3
|
20.6
|
1.0
|
O
|
B:HOH872
|
4.3
|
21.6
|
1.0
|
O15
|
B:476405
|
4.4
|
18.2
|
1.0
|
OD2
|
B:ASP268
|
4.4
|
25.5
|
1.0
|
CB
|
B:ASP250
|
4.5
|
20.6
|
1.0
|
O13
|
B:476405
|
4.5
|
16.7
|
1.0
|
O11
|
B:476405
|
4.5
|
18.1
|
1.0
|
C
|
B:ASP250
|
4.6
|
20.7
|
1.0
|
OD1
|
B:ASP268
|
4.6
|
22.4
|
1.0
|
O
|
B:HOH864
|
4.6
|
21.3
|
1.0
|
O14
|
B:476405
|
4.7
|
18.2
|
1.0
|
CE
|
B:LYS264
|
4.7
|
22.1
|
1.0
|
CB
|
B:ASP254
|
4.7
|
24.9
|
1.0
|
OD1
|
B:ASP251
|
4.8
|
19.7
|
1.0
|
OD2
|
B:ASP254
|
4.8
|
24.7
|
1.0
|
CG
|
B:ASP268
|
4.9
|
24.1
|
1.0
|
|
Calcium binding site 5 out
of 6 in 6vjc
Go back to
Calcium Binding Sites List in 6vjc
Calcium binding site 5 out
of 6 in the Lmfpps Mutant T164Y 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 T164Y in Complex with 476A, Ipp & Ca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca402
b:22.1
occ:1.00
|
O13
|
B:476405
|
2.2
|
16.7
|
1.0
|
OD2
|
B:ASP102
|
2.2
|
21.7
|
1.0
|
O
|
B:HOH864
|
2.3
|
21.3
|
1.0
|
OD2
|
B:ASP98
|
2.3
|
17.2
|
1.0
|
O
|
B:HOH634
|
2.3
|
21.6
|
1.0
|
O15
|
B:476405
|
2.4
|
18.2
|
1.0
|
CG
|
B:ASP102
|
3.4
|
22.1
|
1.0
|
P10
|
B:476405
|
3.4
|
18.5
|
1.0
|
CG
|
B:ASP98
|
3.4
|
18.4
|
1.0
|
CA
|
B:CA403
|
3.5
|
19.3
|
1.0
|
P9
|
B:476405
|
3.5
|
19.9
|
1.0
|
C8
|
B:476405
|
3.8
|
17.7
|
1.0
|
OD1
|
B:ASP98
|
3.9
|
21.9
|
1.0
|
C7
|
B:476405
|
3.9
|
18.7
|
1.0
|
CB
|
B:ASP102
|
3.9
|
19.8
|
1.0
|
O12
|
B:476405
|
4.0
|
19.7
|
1.0
|
O
|
B:HOH875
|
4.2
|
24.6
|
1.0
|
NH2
|
B:ARG107
|
4.2
|
19.0
|
1.0
|
O16
|
B:476405
|
4.2
|
21.7
|
1.0
|
OG
|
B:SER104
|
4.3
|
21.5
|
1.0
|
OD1
|
B:ASP102
|
4.4
|
22.4
|
1.0
|
OD1
|
B:ASP99
|
4.5
|
18.8
|
1.0
|
O
|
B:HOH760
|
4.5
|
20.3
|
1.0
|
O11
|
B:476405
|
4.6
|
18.1
|
1.0
|
O
|
B:HOH747
|
4.6
|
26.8
|
1.0
|
CB
|
B:ASP98
|
4.6
|
18.8
|
1.0
|
O
|
B:ASP98
|
4.7
|
17.7
|
1.0
|
O14
|
B:476405
|
4.7
|
18.2
|
1.0
|
O
|
B:HOH851
|
4.8
|
21.1
|
1.0
|
O
|
B:HOH684
|
4.9
|
24.6
|
1.0
|
O
|
B:HOH707
|
4.9
|
31.2
|
1.0
|
C
|
B:ASP98
|
5.0
|
19.1
|
1.0
|
|
Calcium binding site 6 out
of 6 in 6vjc
Go back to
Calcium Binding Sites List in 6vjc
Calcium binding site 6 out
of 6 in the Lmfpps Mutant T164Y 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 T164Y in Complex with 476A, Ipp & Ca within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca403
b:19.3
occ:1.00
|
O
|
B:HOH697
|
2.3
|
19.6
|
1.0
|
OD2
|
B:ASP102
|
2.4
|
21.7
|
1.0
|
OD1
|
B:ASP98
|
2.4
|
21.9
|
1.0
|
O
|
B:HOH624
|
2.4
|
23.6
|
1.0
|
O
|
B:HOH851
|
2.4
|
21.1
|
1.0
|
O15
|
B:476405
|
2.4
|
18.2
|
1.0
|
OD1
|
B:ASP102
|
2.9
|
22.4
|
1.0
|
CG
|
B:ASP102
|
3.0
|
22.1
|
1.0
|
CG
|
B:ASP98
|
3.1
|
18.4
|
1.0
|
OD2
|
B:ASP98
|
3.3
|
17.2
|
1.0
|
CA
|
B:CA402
|
3.5
|
22.1
|
1.0
|
P9
|
B:476405
|
3.6
|
19.9
|
1.0
|
O14
|
B:476405
|
3.7
|
18.2
|
1.0
|
OD1
|
B:ASP170
|
4.1
|
25.4
|
1.0
|
NE2
|
B:GLN167
|
4.2
|
20.9
|
1.0
|
O
|
A:HOH517
|
4.3
|
25.0
|
1.0
|
OE1
|
B:GLN167
|
4.4
|
23.5
|
1.0
|
CB
|
B:ASP102
|
4.5
|
19.8
|
1.0
|
CG
|
B:ASP170
|
4.5
|
20.2
|
1.0
|
OD2
|
B:ASP170
|
4.5
|
25.0
|
1.0
|
CB
|
B:ASP98
|
4.6
|
18.8
|
1.0
|
O16
|
B:476405
|
4.6
|
21.7
|
1.0
|
O
|
B:HOH713
|
4.7
|
21.8
|
1.0
|
NZ
|
B:LYS273
|
4.7
|
40.7
|
1.0
|
CD
|
B:GLN167
|
4.7
|
22.0
|
1.0
|
C7
|
B:476405
|
4.8
|
18.7
|
1.0
|
O
|
B:HOH864
|
4.8
|
21.3
|
1.0
|
C8
|
B:476405
|
4.9
|
17.7
|
1.0
|
O
|
B:HOH604
|
4.9
|
35.4
|
1.0
|
O
|
B:ASP98
|
4.9
|
17.7
|
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 17:12:32 2024
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