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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:

Chlorine (Cl) 3 atoms

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

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