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Calcium in PDB 6tz8: Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506

Enzymatic activity of Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506

All present enzymatic activity of Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506:
3.1.3.16; 5.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506, PDB code: 6tz8 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.57 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.720, 120.700, 134.960, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 24.3

Other elements in 6tz8:

The structure of Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506 also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506 (pdb code 6tz8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506, PDB code: 6tz8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6tz8

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Calcium binding site 1 out of 8 in the Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca300

b:67.5
occ:1.00
 OE2 B:GLU45 2.3 85.1 1.0
OD1 B:ASP36 2.4 68.8 1.0
OG B:SER38 2.4 69.6 1.0
O B:SER40 2.5 68.0 1.0
OD1 B:ASP34 2.6 68.2 1.0
OE1 B:GLU45 2.7 64.3 1.0
CD B:GLU45 2.9 78.9 1.0
CG B:ASP36 3.2 69.2 1.0
OD2 B:ASP36 3.3 64.1 1.0
CB B:SER38 3.5 61.1 1.0
C B:SER40 3.5 68.6 1.0
CG B:ASP34 3.7 75.5 1.0
N B:SER38 4.1 52.6 1.0
CA B:ILE41 4.2 60.8 1.0
N B:ILE41 4.2 67.5 1.0
OD2 B:ASP34 4.2 78.7 1.0
N B:ASP42 4.3 79.4 1.0
CA B:SER38 4.3 66.0 1.0
CG B:GLU45 4.4 77.0 1.0
OG B:SER40 4.4 61.5 1.0
N B:SER40 4.4 62.1 1.0
CA B:SER40 4.5 61.1 1.0
C B:ILE41 4.6 71.5 1.0
CB B:ASP36 4.6 77.4 1.0
CB B:ASP34 4.8 65.7 1.0
CA B:ASP34 4.8 75.0 1.0
C B:SER38 4.8 69.3 1.0
N B:ASP36 4.9 71.1 1.0
CB B:ASP42 5.0 73.0 1.0

Calcium binding site 2 out of 8 in 6tz8

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Calcium binding site 2 out of 8 in the Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:49.4
occ:1.00
 OG B:SER70 2.4 52.0 1.0
O B:THR72 2.4 43.3 1.0
OE1 B:GLU77 2.6 49.0 1.0
OD1 B:ASP66 2.7 56.6 1.0
OD1 B:ASP68 2.9 50.0 1.0
OD2 B:ASP68 2.9 57.0 1.0
OE2 B:GLU77 3.0 46.2 1.0
CD B:GLU77 3.1 51.2 1.0
CG B:ASP68 3.3 47.2 1.0
C B:THR72 3.5 49.0 1.0
OG1 B:THR72 3.6 62.0 1.0
CB B:SER70 3.7 68.7 1.0
CG B:ASP66 3.7 50.9 1.0
OD2 B:ASP74 3.8 40.3 1.0
OD2 B:ASP66 4.1 52.4 1.0
N B:SER70 4.2 55.6 1.0
N B:THR72 4.2 62.4 1.0
CA B:THR72 4.3 53.8 1.0
CA B:SER70 4.4 56.4 1.0
N B:VAL73 4.4 45.1 1.0
CB B:THR72 4.5 61.2 1.0
CG B:GLU77 4.6 56.8 1.0
N B:ASP74 4.6 49.3 1.0
CA B:VAL73 4.6 48.6 1.0
CG B:ASP74 4.6 57.3 1.0
C B:SER70 4.8 62.4 1.0
CB B:ASP68 4.8 53.7 1.0
CB B:ASP66 4.9 41.9 1.0
N B:GLY69 4.9 60.6 1.0
CA B:ASP66 4.9 42.3 1.0

Calcium binding site 3 out of 8 in 6tz8

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Calcium binding site 3 out of 8 in the Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:38.5
occ:1.00
 OD1 B:ASP107 2.3 47.9 1.0
OD1 B:ASP105 2.3 39.7 1.0
O B:TYR109 2.4 31.5 1.0
OE1 B:GLU114 2.4 47.2 1.0
OE2 B:GLU114 2.5 40.4 1.0
OD1 B:ASP103 2.7 28.6 1.0
CD B:GLU114 2.7 41.0 1.0
OD2 B:ASP105 2.9 34.0 1.0
CG B:ASP105 2.9 37.9 1.0
CG B:ASP107 3.0 40.9 1.0
OD2 B:ASP107 3.4 29.7 1.0
C B:TYR109 3.5 32.2 1.0
CG B:ASP103 3.8 39.7 1.0
CG B:GLU114 4.2 35.2 1.0
CB B:ASP107 4.3 41.9 1.0
N B:TYR109 4.3 41.6 1.0
CA B:TYR109 4.3 28.3 1.0
CB B:ASP105 4.4 31.4 1.0
N B:ILE110 4.4 41.0 1.0
OD2 B:ASP103 4.4 35.6 1.0
N B:ASP107 4.4 30.3 1.0
CA B:ILE110 4.5 40.1 1.0
N B:ASP105 4.6 38.4 1.0
CB B:TYR109 4.7 27.3 1.0
N B:SER111 4.7 31.1 1.0
CA B:ASP107 4.8 36.0 1.0
CA B:ASP103 4.8 36.1 1.0
CB B:ASP103 4.9 42.5 1.0
OG B:SER111 4.9 43.3 1.0
CA B:ASP105 4.9 36.0 1.0
N B:ARG106 4.9 36.3 1.0
C B:ASP107 5.0 33.2 1.0

Calcium binding site 4 out of 8 in 6tz8

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Calcium binding site 4 out of 8 in the Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:40.7
occ:1.00
 OD1 B:ASP148 2.3 50.7 1.0
O B:LYS150 2.3 40.3 1.0
OE1 B:GLU155 2.4 40.3 1.0
OD1 B:ASP146 2.5 42.6 1.0
OD2 B:ASP148 2.6 56.7 1.0
OE2 B:GLU155 2.7 33.6 1.0
CG B:ASP148 2.8 46.4 1.0
OD1 B:ASP144 2.8 47.8 1.0
CD B:GLU155 2.9 36.9 1.0
CG B:ASP146 3.5 45.9 1.0
C B:LYS150 3.5 44.8 1.0
CG B:ASP144 3.6 48.4 1.0
OD2 B:ASP146 3.7 37.6 1.0
OD2 B:ASP144 4.2 52.4 1.0
CB B:ASP148 4.2 31.9 1.0
CA B:ASP144 4.3 30.4 1.0
N B:LYS150 4.3 40.0 1.0
CG B:GLU155 4.3 38.9 1.0
CA B:LEU151 4.3 34.2 1.0
N B:LEU151 4.3 43.8 1.0
CB B:ASP144 4.3 37.5 1.0
N B:SER152 4.4 37.6 1.0
CA B:LYS150 4.5 31.6 1.0
N B:LYS145 4.5 39.4 1.0
N B:ASP148 4.6 37.2 1.0
N B:ASP146 4.6 38.7 1.0
C B:LEU151 4.8 34.7 1.0
CB B:ASP146 4.8 49.7 1.0
CA B:ASP148 4.9 35.2 1.0
CD2 B:LEU151 4.9 30.6 1.0
C B:ASP144 5.0 38.0 1.0
N B:GLY149 5.0 38.5 1.0
OG B:SER152 5.0 30.4 1.0

Calcium binding site 5 out of 8 in 6tz8

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Calcium binding site 5 out of 8 in the Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca300

b:81.3
occ:1.00
 O E:SER40 2.3 63.1 1.0
OD1 E:ASP36 2.3 90.2 1.0
OD1 E:ASP34 2.4 90.1 1.0
OE1 E:GLU45 2.6 0.1 1.0
OE2 E:GLU45 2.7 89.7 1.0
CD E:GLU45 2.9 95.4 1.0
OG E:SER38 3.0 66.4 1.0
CG E:ASP34 3.0 85.2 1.0
C E:SER40 3.4 67.3 1.0
CG E:ASP36 3.5 90.2 1.0
OD2 E:ASP34 3.5 80.7 1.0
CA E:ILE41 3.9 78.2 1.0
OD2 E:ASP36 3.9 72.3 1.0
CA E:ASP34 3.9 89.1 1.0
CB E:ASP34 4.0 82.8 1.0
N E:ILE41 4.1 73.6 1.0
N E:SER38 4.1 47.2 1.0
CB E:SER38 4.2 73.7 1.0
CG E:GLU45 4.2 91.3 1.0
C E:ASP34 4.4 93.8 1.0
N E:ASP42 4.5 89.8 1.0
N E:LYS35 4.5 0.0 1.0
N E:ASP36 4.5 86.7 1.0
N E:SER40 4.5 79.5 1.0
N E:GLY37 4.5 79.6 1.0
C E:ILE41 4.6 88.2 1.0
CA E:SER40 4.6 62.6 1.0
CA E:SER38 4.7 67.4 1.0
CB E:ASP36 4.7 0.3 1.0
CB E:GLU45 4.8 88.9 1.0
CB E:ILE41 4.9 73.7 1.0
CA E:ASP36 5.0 97.7 1.0
C E:ASP36 5.0 96.2 1.0

Calcium binding site 6 out of 8 in 6tz8

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Calcium binding site 6 out of 8 in the Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:54.8
occ:1.00
 O E:THR72 2.2 41.7 1.0
OG E:SER70 2.3 56.4 1.0
OD1 E:ASP66 2.5 57.8 1.0
OE1 E:GLU77 2.5 49.2 1.0
OE2 E:GLU77 2.7 55.1 1.0
CD E:GLU77 2.9 57.7 1.0
OD1 E:ASP68 3.1 68.6 1.0
C E:THR72 3.5 50.4 1.0
OD2 E:ASP68 3.5 78.4 1.0
CB E:SER70 3.7 74.1 1.0
CG E:ASP68 3.7 80.8 1.0
CG E:ASP66 3.7 58.9 1.0
OD2 E:ASP74 3.8 55.6 1.0
OG1 E:THR72 3.9 58.4 1.0
N E:SER70 4.0 71.3 1.0
N E:THR72 4.1 68.6 1.0
CA E:THR72 4.3 60.8 1.0
CA E:SER70 4.3 71.2 1.0
CG E:GLU77 4.4 56.6 1.0
N E:VAL73 4.5 51.9 1.0
OD2 E:ASP66 4.5 61.6 1.0
C E:SER70 4.5 67.6 1.0
N E:ASP74 4.6 58.1 1.0
CA E:ASP66 4.6 54.9 1.0
CA E:VAL73 4.6 61.5 1.0
CB E:ASP66 4.6 55.4 1.0
CB E:THR72 4.6 63.1 1.0
CG E:ASP74 4.8 54.7 1.0
N E:GLY71 4.8 70.7 1.0
N E:GLY69 4.9 69.2 1.0
O E:SER70 5.0 58.6 1.0

Calcium binding site 7 out of 8 in 6tz8

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Calcium binding site 7 out of 8 in the Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:29.6
occ:1.00
 OD1 E:ASP107 2.3 44.0 1.0
OE1 E:GLU114 2.4 34.3 1.0
O E:TYR109 2.4 28.6 1.0
OD1 E:ASP105 2.5 36.1 1.0
OD1 E:ASP103 2.5 25.9 1.0
OE2 E:GLU114 2.8 37.7 1.0
CD E:GLU114 2.8 33.2 1.0
CG E:ASP107 3.1 42.4 1.0
CG E:ASP105 3.2 43.8 1.0
OD2 E:ASP105 3.3 47.9 1.0
OD2 E:ASP107 3.5 32.7 1.0
C E:TYR109 3.5 29.6 1.0
CG E:ASP103 3.7 32.0 1.0
CG E:GLU114 4.2 29.4 1.0
CB E:ASP107 4.3 41.5 1.0
OD2 E:ASP103 4.3 35.1 1.0
N E:TYR109 4.4 39.1 1.0
N E:ILE110 4.4 30.6 1.0
CA E:TYR109 4.4 30.9 1.0
CA E:ILE110 4.4 34.5 1.0
OG E:SER111 4.5 49.0 1.0
N E:ASP107 4.5 28.1 1.0
CA E:ASP103 4.6 31.9 1.0
CB E:ASP103 4.6 33.9 1.0
CB E:ASP105 4.7 35.9 1.0
CB E:TYR109 4.7 30.4 1.0
N E:ASP105 4.7 34.5 1.0
N E:SER111 4.7 27.4 1.0
N E:MET104 4.9 30.4 1.0
CA E:ASP107 4.9 31.8 1.0
C E:ILE110 4.9 31.0 1.0
CB E:GLU114 4.9 31.6 1.0
C E:ASP103 5.0 31.8 1.0

Calcium binding site 8 out of 8 in 6tz8

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Calcium binding site 8 out of 8 in the Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Cryptococcus Neoformans Calceineurin A, Calcineurin B, and FKBP12 with Fk-506 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca303

b:38.1
occ:1.00
 OD1 E:ASP148 2.3 41.3 1.0
O E:LYS150 2.3 37.4 1.0
OE1 E:GLU155 2.4 37.7 1.0
OE2 E:GLU155 2.5 40.5 1.0
OD1 E:ASP146 2.5 34.1 1.0
CD E:GLU155 2.8 42.8 1.0
OD1 E:ASP144 2.8 41.9 1.0
CG E:ASP148 2.9 37.2 1.0
OD2 E:ASP148 2.9 36.3 1.0
CG E:ASP146 3.5 39.4 1.0
C E:LYS150 3.5 35.2 1.0
CG E:ASP144 3.6 40.5 1.0
OD2 E:ASP146 3.8 31.7 1.0
CA E:ASP144 4.2 33.4 1.0
CA E:LEU151 4.2 29.1 1.0
N E:SER152 4.2 36.4 1.0
OD2 E:ASP144 4.2 30.8 1.0
CG E:GLU155 4.3 40.9 1.0
N E:LEU151 4.3 29.7 1.0
CB E:ASP144 4.3 35.8 1.0
N E:LYS145 4.3 36.4 1.0
CB E:ASP148 4.4 30.9 1.0
N E:LYS150 4.4 32.1 1.0
N E:ASP146 4.5 35.2 1.0
CA E:LYS150 4.5 27.9 1.0
N E:ASP148 4.6 35.5 1.0
C E:LEU151 4.7 34.7 1.0
CD2 E:LEU151 4.7 27.4 1.0
C E:ASP144 4.8 40.8 1.0
CB E:ASP146 4.8 41.9 1.0
OG E:SER152 4.9 34.0 1.0
N E:GLY149 5.0 33.3 1.0
CA E:ASP148 5.0 35.1 1.0

Reference:

P.R.Juvvadi, D.Fox 3Rd, B.G.Bobay, M.J.Hoy, S.M.C.Gobeil, R.A.Venters, Z.Chang, J.J.Lin, A.F.Averette, D.C.Cole, B.C.Barrington, J.D.Wheaton, M.Ciofani, M.Trzoss, X.Li, S.C.Lee, Y.L.Chen, M.Mutz, L.D.Spicer, M.A.Schumacher, J.Heitman, W.J.Steinbach. Harnessing Calcineurin-FK506-FKBP12 Crystal Structures From Invasive Fungal Pathogens to Develop Antifungal Agents. Nat Commun V. 10 4275 2019.
ISSN: ESSN 2041-1723
PubMed: 31537789
DOI: 10.1038/S41467-019-12199-1
Page generated: Tue Jul 16 15:39:41 2024

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