Calcium in PDB 8ppz: Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor
Enzymatic activity of Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor
All present enzymatic activity of Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor:
2.7.11.1;
5.2.1.8;
Protein crystallography data
The structure of Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor, PDB code: 8ppz
was solved by
C.Meyners,
R.C.E.Deutscher,
F.Hausch,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.72 /
1.85
|
Space group
|
P 2 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.912,
64.68,
93.349,
90,
90,
90
|
R / Rfree (%)
|
19.2 /
23.8
|
Other elements in 8ppz:
The structure of Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor
(pdb code 8ppz). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor, PDB code: 8ppz:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 8ppz
Go back to
Calcium Binding Sites List in 8ppz
Calcium binding site 1 out
of 4 in the Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca202
b:55.2
occ:1.00
|
HB4
|
A:0AN201
|
3.2
|
22.5
|
1.0
|
HE1
|
A:TYR82
|
3.5
|
25.6
|
1.0
|
HG22
|
A:ILE56
|
3.6
|
26.8
|
1.0
|
HG21
|
A:ILE56
|
3.9
|
26.8
|
1.0
|
NBH
|
A:0AN201
|
3.9
|
23.9
|
1.0
|
HA
|
A:ILE56
|
3.9
|
23.8
|
1.0
|
HA
|
A:VAL55
|
4.1
|
23.0
|
1.0
|
HH
|
A:TYR82
|
4.1
|
24.3
|
0.0
|
HH12
|
B:ARG2109
|
4.1
|
45.6
|
1.0
|
CAX
|
A:0AN201
|
4.2
|
23.5
|
1.0
|
CBG
|
A:0AN201
|
4.2
|
22.7
|
1.0
|
CG2
|
A:ILE56
|
4.2
|
28.1
|
1.0
|
CE1
|
A:TYR82
|
4.2
|
26.2
|
1.0
|
N
|
A:ILE56
|
4.2
|
22.5
|
1.0
|
C
|
A:VAL55
|
4.3
|
22.5
|
1.0
|
H
|
A:ILE56
|
4.3
|
22.8
|
1.0
|
HE2
|
B:TYR2105
|
4.4
|
23.9
|
1.0
|
O
|
B:HOH2315
|
4.4
|
26.4
|
1.0
|
O
|
A:0AN201
|
4.4
|
22.5
|
1.0
|
HD2
|
B:TYR2105
|
4.4
|
23.1
|
1.0
|
O
|
A:GLU54
|
4.5
|
24.9
|
1.0
|
CA
|
A:ILE56
|
4.5
|
23.6
|
1.0
|
O
|
A:VAL55
|
4.6
|
25.2
|
1.0
|
CA
|
A:VAL55
|
4.6
|
22.6
|
1.0
|
CBI
|
A:0AN201
|
4.6
|
24.1
|
1.0
|
OH
|
A:TYR82
|
4.7
|
24.5
|
1.0
|
HH21
|
B:ARG2109
|
4.7
|
53.6
|
1.0
|
C
|
A:GLU54
|
4.8
|
24.0
|
1.0
|
CZ
|
A:TYR82
|
4.8
|
24.5
|
1.0
|
HAX
|
A:0AN201
|
4.8
|
22.5
|
1.0
|
HBI
|
A:0AN201
|
4.9
|
24.1
|
1.0
|
HG23
|
A:ILE56
|
4.9
|
26.8
|
1.0
|
HD1
|
A:TYR82
|
4.9
|
26.0
|
1.0
|
N
|
A:VAL55
|
4.9
|
24.4
|
1.0
|
CD1
|
A:TYR82
|
4.9
|
25.6
|
1.0
|
NH1
|
B:ARG2109
|
5.0
|
44.3
|
1.0
|
|
Calcium binding site 2 out
of 4 in 8ppz
Go back to
Calcium Binding Sites List in 8ppz
Calcium binding site 2 out
of 4 in the Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2202
b:48.0
occ:0.50
|
O
|
B:HOH2345
|
2.3
|
41.4
|
1.0
|
O
|
B:HOH2331
|
2.6
|
36.4
|
0.5
|
O
|
B:HOH2309
|
2.6
|
37.6
|
1.0
|
O
|
B:HOH2329
|
2.7
|
70.9
|
1.0
|
O
|
B:HOH2304
|
3.2
|
53.4
|
1.0
|
OD1
|
B:ASP2077
|
4.2
|
31.6
|
1.0
|
HD23
|
B:LEU2103
|
4.2
|
24.6
|
1.0
|
OE1
|
B:GLU2080
|
4.3
|
31.2
|
1.0
|
CA
|
B:CA2203
|
4.6
|
65.6
|
1.0
|
O
|
B:HOH2338
|
4.8
|
41.9
|
1.0
|
OXT
|
B:ACT2201
|
4.9
|
56.0
|
1.0
|
|
Calcium binding site 3 out
of 4 in 8ppz
Go back to
Calcium Binding Sites List in 8ppz
Calcium binding site 3 out
of 4 in the Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2203
b:65.6
occ:1.00
|
O
|
B:HOH2345
|
3.3
|
41.4
|
1.0
|
O
|
B:HOH2331
|
3.9
|
36.4
|
0.5
|
HH22
|
B:ARG2076
|
4.0
|
27.1
|
1.0
|
HB2
|
B:ARG2076
|
4.2
|
26.7
|
1.0
|
CZ
|
B:ARG2076
|
4.3
|
27.9
|
1.0
|
HH11
|
B:ARG2076
|
4.4
|
28.7
|
1.0
|
HB3
|
B:ARG2076
|
4.4
|
26.7
|
1.0
|
NH2
|
B:ARG2076
|
4.4
|
26.7
|
1.0
|
HD3
|
B:ARG2076
|
4.4
|
26.5
|
1.0
|
OD1
|
B:ASP2077
|
4.4
|
31.6
|
1.0
|
NH1
|
B:ARG2076
|
4.5
|
29.1
|
1.0
|
NE
|
B:ARG2076
|
4.5
|
27.9
|
1.0
|
O
|
B:HOH2309
|
4.5
|
37.6
|
1.0
|
CA
|
B:CA2202
|
4.6
|
48.0
|
0.5
|
HE
|
B:ARG2076
|
4.7
|
27.3
|
1.0
|
CB
|
B:ARG2076
|
4.8
|
26.8
|
1.0
|
O
|
B:ACT2201
|
4.8
|
63.1
|
1.0
|
HH12
|
B:ARG2076
|
4.9
|
28.7
|
1.0
|
CD
|
B:ARG2076
|
5.0
|
25.3
|
1.0
|
O
|
B:HOH2342
|
5.0
|
30.4
|
1.0
|
|
Calcium binding site 4 out
of 4 in 8ppz
Go back to
Calcium Binding Sites List in 8ppz
Calcium binding site 4 out
of 4 in the Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca2204
b:55.3
occ:1.00
|
O
|
A:HOH329
|
2.4
|
27.9
|
1.0
|
O
|
B:HOH2339
|
2.7
|
26.1
|
1.0
|
HG3
|
B:LYS2095
|
2.8
|
42.1
|
1.0
|
O
|
B:HOH2313
|
2.9
|
36.4
|
1.0
|
HE1
|
A:PHE46
|
2.9
|
21.7
|
1.0
|
HG21
|
B:THR2098
|
3.1
|
26.0
|
1.0
|
O
|
A:HOH373
|
3.2
|
30.4
|
1.0
|
HB
|
B:THR2098
|
3.2
|
25.4
|
1.0
|
HG23
|
B:THR2098
|
3.4
|
25.9
|
1.0
|
HA
|
B:LYS2095
|
3.4
|
27.4
|
1.0
|
CE1
|
A:PHE46
|
3.5
|
21.9
|
1.0
|
CG2
|
B:THR2098
|
3.5
|
26.2
|
1.0
|
O
|
A:HOH334
|
3.7
|
31.9
|
1.0
|
CB
|
B:THR2098
|
3.8
|
25.3
|
1.0
|
CG
|
B:LYS2095
|
3.8
|
44.1
|
1.0
|
HZ
|
A:PHE46
|
4.2
|
20.2
|
1.0
|
OG1
|
B:THR2098
|
4.2
|
24.8
|
1.0
|
CZ
|
A:PHE46
|
4.2
|
20.4
|
1.0
|
HG2
|
B:LYS2095
|
4.2
|
42.1
|
1.0
|
HD1
|
A:PHE46
|
4.3
|
21.8
|
1.0
|
CA
|
B:LYS2095
|
4.3
|
27.7
|
1.0
|
CD1
|
A:PHE46
|
4.3
|
22.2
|
1.0
|
O
|
A:HOH360
|
4.3
|
25.8
|
1.0
|
O
|
A:LYS47
|
4.4
|
25.8
|
1.0
|
O
|
B:LYS2095
|
4.4
|
27.4
|
1.0
|
CB
|
B:LYS2095
|
4.4
|
33.4
|
1.0
|
HD2
|
B:LYS2095
|
4.4
|
48.2
|
1.0
|
HB2
|
B:LYS2095
|
4.5
|
34.2
|
1.0
|
HG22
|
B:THR2098
|
4.5
|
25.9
|
1.0
|
O
|
A:HOH379
|
4.5
|
21.1
|
1.0
|
CD
|
B:LYS2095
|
4.6
|
47.8
|
1.0
|
HD3
|
B:LYS2095
|
4.7
|
48.0
|
1.0
|
C
|
B:LYS2095
|
4.8
|
25.1
|
1.0
|
HG1
|
B:THR2098
|
4.8
|
24.7
|
0.0
|
H
|
A:LYS47
|
4.9
|
21.5
|
1.0
|
HG2
|
B:GLN2099
|
5.0
|
35.7
|
1.0
|
|
Reference:
C.Meyners,
R.C.E.Deutscher,
F.Hausch.
Co-Crystal Structure of FKBP12, Compound 7 and the Frb Fragment of Mtor Chemrxiv 2023.
ISSN: ISSN 2573-2293
DOI: 10.26434/CHEMRXIV-2023-4VB0M
Page generated: Fri Jul 19 11:12:28 2024
|