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Rubidium in PDB 6arl: Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions

Enzymatic activity of Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions

All present enzymatic activity of Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions:
2.3.1.9;

Protein crystallography data

The structure of Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions, PDB code: 6arl was solved by A.C.Marshall, C.S.Bond, J.B.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.72 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.250, 105.440, 110.280, 90.00, 108.78, 90.00
R / Rfree (%) 20.1 / 24.1

Other elements in 6arl:

The structure of Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Rubidium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Rubidium atom in the Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions (pdb code 6arl). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 13 binding sites of Rubidium where determined in the Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions, PDB code: 6arl:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Rubidium binding site 1 out of 13 in 6arl

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Rubidium binding site 1 out of 13 in the Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb401

b:76.4
occ:0.98
 O A:VAL44 2.7 54.1 1.0
O A:LEU47 2.8 49.0 1.0
O A:LEU41 3.0 49.2 1.0
C A:VAL44 3.9 54.5 1.0
C A:LEU47 4.0 49.2 1.0
C A:LEU41 4.1 48.2 1.0
O A:ALA42 4.2 52.6 1.0
CA A:ALA42 4.3 49.2 1.0
C A:ALA42 4.4 50.6 1.0
N A:LEU47 4.5 52.0 1.0
N A:VAL44 4.5 51.7 1.0
CA A:VAL44 4.6 52.7 1.0
N A:ALA42 4.6 47.3 1.0
CA A:LEU47 4.7 49.9 1.0
CD A:PRO49 4.8 54.3 1.0
CB A:VAL44 4.8 51.2 1.0
N A:ASP45 4.9 66.5 1.0
CB A:LEU47 4.9 48.4 1.0
CA A:LYS48 4.9 56.9 1.0
N A:GLY46 5.0 55.8 1.0
CA A:ASP45 5.0 68.4 1.0
N A:LYS48 5.0 57.5 1.0

Rubidium binding site 2 out of 13 in 6arl

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Rubidium binding site 2 out of 13 in the Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb402

b:67.2
occ:1.00
 O A:ASP200 2.9 63.8 1.0
O A:GLU201 2.9 60.3 1.0
O A:ILE203 3.2 47.7 1.0
O A:HOH626 3.3 45.4 1.0
C A:GLU201 3.6 60.3 1.0
CA A:GLU201 4.0 62.1 1.0
C A:ASP200 4.0 64.6 1.0
C A:ILE203 4.1 46.4 1.0
N A:GLU201 4.5 61.3 1.0
N A:ILE203 4.7 47.1 1.0
N A:GLU202 4.7 50.5 1.0
N A:ALA204 4.8 45.8 1.0
CE A:LYS43 4.8 46.3 1.0
CA A:ALA204 4.8 46.5 1.0
OE1 A:GLU201 4.9 66.1 1.0
O A:HOH590 4.9 41.2 1.0
C A:GLU202 4.9 47.6 1.0

Rubidium binding site 3 out of 13 in 6arl

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Rubidium binding site 3 out of 13 in the Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb403

b:48.6
occ:0.99
 O A:SER252 2.7 46.7 1.0
OH A:TYR187 2.8 46.8 1.0
O A:PRO250 2.8 53.2 1.0
O A:VAL350 3.0 44.0 1.0
O A:ALA249 3.1 51.3 1.0
C A:PRO250 3.5 53.5 1.0
CA A:PRO250 3.7 53.5 1.0
CZ A:TYR187 3.8 48.2 1.0
C A:SER252 3.9 47.0 1.0
OE2 A:GLU224 3.9 48.9 1.0
CG A:PRO254 4.0 42.0 1.0
O A:HOH578 4.1 41.8 1.0
C A:VAL350 4.1 44.1 1.0
CE2 A:TYR187 4.1 49.2 1.0
C A:ALA249 4.1 52.2 1.0
CG1 A:VAL350 4.2 46.9 1.0
CD A:PRO254 4.3 42.2 1.0
N A:SER252 4.4 49.1 1.0
N A:PRO250 4.5 53.2 1.0
CD A:GLU224 4.6 47.0 1.0
O A:HOH619 4.6 48.1 1.0
N A:ASN251 4.6 52.9 1.0
CA A:VAL350 4.6 43.5 1.0
N A:PRO254 4.6 43.2 1.0
CA A:SER253 4.7 42.0 1.0
C A:SER253 4.7 41.0 1.0
CA A:SER252 4.8 48.6 1.0
N A:SER253 4.8 43.6 1.0
CG A:GLU224 4.9 46.4 1.0
CB A:VAL350 5.0 45.4 1.0

Rubidium binding site 4 out of 13 in 6arl

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Rubidium binding site 4 out of 13 in the Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 of Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb401

b:39.1
occ:0.96
 O B:SER252 2.7 35.6 1.0
O B:PRO250 2.8 39.6 1.0
OH B:TYR187 2.9 38.4 1.0
O B:VAL350 3.0 34.2 1.0
O B:ALA249 3.3 36.9 1.0
C B:PRO250 3.4 40.9 1.0
CA B:PRO250 3.7 41.2 1.0
OE1 B:GLU224 3.9 36.2 1.0
C B:SER252 3.9 35.7 1.0
CZ B:TYR187 4.0 39.4 1.0
CG B:PRO254 4.0 33.6 1.0
C B:VAL350 4.1 33.8 1.0
CG1 B:VAL350 4.1 36.5 1.0
O B:HOH525 4.1 41.0 1.0
CD B:PRO254 4.1 33.3 1.0
CE2 B:TYR187 4.3 40.6 1.0
C B:ALA249 4.3 38.6 1.0
O B:HOH630 4.3 41.5 1.0
N B:SER252 4.4 40.2 1.0
N B:ASN251 4.5 42.6 1.0
N B:PRO250 4.5 41.4 1.0
N B:PRO254 4.5 33.2 1.0
CA B:VAL350 4.5 33.3 1.0
CD B:GLU224 4.6 34.7 1.0
C B:SER253 4.7 30.4 1.0
CA B:SER253 4.7 31.1 1.0
CA B:SER252 4.8 38.5 1.0
N B:SER253 4.8 33.0 1.0
CG B:GLU224 4.9 34.1 1.0
CA B:ASN251 4.9 43.2 1.0
C B:ASN251 4.9 42.3 1.0
CB B:VAL350 4.9 34.9 1.0
CB B:PRO250 5.0 43.6 1.0

Rubidium binding site 5 out of 13 in 6arl

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Rubidium binding site 5 out of 13 in the Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 5 of Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb402

b:45.7
occ:0.88
 O B:ILE203 2.9 35.1 1.0
O B:ASP200 2.9 42.0 1.0
O B:GLU201 2.9 46.3 1.0
O B:HOH677 3.2 40.4 1.0
C B:GLU201 3.7 46.4 1.0
O B:HOH620 3.7 40.2 1.0
O B:HOH583 3.8 43.0 1.0
CA B:GLU201 4.0 47.9 1.0
C B:ASP200 4.0 42.1 1.0
C B:ILE203 4.0 34.0 1.0
O B:HOH687 4.0 31.5 1.0
OE1 B:GLU201 4.3 49.1 1.0
N B:GLU201 4.5 48.1 1.0
N B:ILE203 4.7 33.5 1.0
CA B:ALA204 4.8 37.0 1.0
CE B:LYS43 4.8 38.6 1.0
N B:GLU202 4.8 36.5 1.0
N B:ALA204 4.8 36.1 1.0
C B:GLU202 4.9 34.5 1.0
CD B:PRO205 4.9 36.6 1.0
CA B:ILE203 5.0 33.3 1.0

Rubidium binding site 6 out of 13 in 6arl

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Rubidium binding site 6 out of 13 in the Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 6 of Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb403

b:77.1
occ:0.98
 O B:HOH665 2.9 42.3 1.0
O B:VAL44 3.0 45.4 1.0
O B:LEU47 3.1 45.1 1.0
O B:LEU41 3.1 39.9 1.0
O B:HOH659 3.1 58.9 1.0
CA B:ALA42 3.9 41.4 1.0
C B:LEU41 4.0 39.1 1.0
C B:VAL44 4.1 44.9 1.0
O B:ALA42 4.2 41.6 1.0
C B:ALA42 4.2 40.5 1.0
C B:LEU47 4.3 44.9 1.0
N B:ALA42 4.4 39.8 1.0
N B:VAL44 4.6 43.0 1.0
CA B:VAL44 4.8 43.2 1.0
N B:LEU47 4.9 45.7 1.0

Rubidium binding site 7 out of 13 in 6arl

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Rubidium binding site 7 out of 13 in the Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 7 of Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb401

b:17.0
occ:0.94
 O C:SER252 2.7 19.4 1.0
O C:HOH820 2.9 31.1 1.0
OH C:TYR187 2.9 16.9 1.0
O C:PRO250 3.0 21.4 1.0
O C:VAL350 3.0 15.3 1.0
O C:ALA249 3.2 22.0 1.0
C C:PRO250 3.6 22.4 1.0
CA C:PRO250 3.8 22.8 1.0
O C:HOH847 3.9 24.3 1.0
CZ C:TYR187 3.9 17.0 1.0
C C:SER252 4.0 20.2 1.0
C C:VAL350 4.0 15.0 1.0
CE2 C:TYR187 4.1 17.5 1.0
CG1 C:VAL350 4.1 16.5 1.0
OE1 C:GLU224 4.1 18.1 1.0
C C:ALA249 4.2 22.8 1.0
O C:HOH617 4.2 19.4 1.0
CD C:PRO254 4.4 16.8 1.0
CG C:PRO254 4.4 16.3 1.0
N C:SER252 4.4 21.4 1.0
N C:PRO250 4.5 23.9 1.0
CA C:VAL350 4.5 14.8 1.0
O C:HOH533 4.5 23.8 1.0
N C:PRO254 4.6 17.8 1.0
N C:ASN251 4.6 22.3 1.0
CD C:GLU224 4.7 17.5 1.0
C C:SER253 4.8 17.8 1.0
O C:HOH954 4.8 35.8 1.0
CA C:SER252 4.8 21.2 1.0
CA C:SER253 4.9 17.9 0.6
CA C:SER253 4.9 17.9 0.4
N C:SER253 4.9 19.0 1.0
CB C:VAL350 4.9 15.6 1.0
CB C:PRO254 5.0 17.2 1.0

Rubidium binding site 8 out of 13 in 6arl

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Rubidium binding site 8 out of 13 in the Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 8 of Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb402

b:18.2
occ:0.83
 O C:HOH874 2.6 30.0 1.0
O C:ILE203 2.8 13.2 1.0
O C:HOH892 2.9 41.1 1.0
O C:HOH881 2.9 18.2 1.0
O C:ASP200 3.0 15.1 1.0
O C:GLU201 3.0 15.4 1.0
O C:HOH658 3.4 35.2 1.0
C C:GLU201 3.7 15.3 1.0
O C:HOH639 3.8 12.4 1.0
CA C:GLU201 3.9 16.3 0.5
CA C:GLU201 3.9 16.3 0.6
C C:ILE203 4.0 12.6 1.0
C C:ASP200 4.0 15.5 1.0
O C:HOH746 4.2 16.8 1.0
O C:HOH926 4.3 31.6 1.0
N C:GLU201 4.5 16.1 1.0
N C:ILE203 4.6 12.5 1.0
N C:ALA204 4.7 12.6 1.0
N C:GLU202 4.7 14.1 1.0
CA C:ALA204 4.8 13.1 1.0
CD C:PRO205 4.8 14.2 1.0
CE C:LYS43 4.8 14.2 1.0
O C:HOH903 4.9 40.9 1.0
C C:GLU202 4.9 13.6 1.0
NZ C:LYS43 4.9 13.2 1.0
CA C:ILE203 4.9 12.2 1.0
O C:HOH1001 4.9 30.0 1.0

Rubidium binding site 9 out of 13 in 6arl

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Rubidium binding site 9 out of 13 in the Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 9 of Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb403

b:19.1
occ:0.72
 O C:LEU47 2.7 15.1 1.0
O C:LEU41 2.9 14.8 1.0
O C:VAL44 2.9 17.9 1.0
O C:HOH845 3.0 36.4 1.0
O C:HOH870 3.3 21.7 1.0
O C:HOH807 3.6 42.8 1.0
O C:HOH686 3.7 32.7 1.0
C C:LEU41 3.9 14.1 1.0
C C:LEU47 4.0 15.3 1.0
C C:VAL44 4.0 18.0 1.0
CA C:ALA42 4.0 14.9 1.0
O C:ALA42 4.1 16.4 1.0
C C:ALA42 4.2 16.0 1.0
N C:VAL44 4.3 17.0 1.0
N C:ALA42 4.4 14.4 1.0
CA C:VAL44 4.6 17.6 1.0
N C:LEU47 4.7 16.3 1.0
CB C:VAL44 4.8 17.8 1.0
CA C:LYS48 4.8 18.3 1.0
CD C:PRO49 4.9 13.6 1.0
CA C:LEU47 4.9 15.8 1.0
N C:LYS48 4.9 19.1 1.0
N C:LYS43 4.9 15.7 1.0

Rubidium binding site 10 out of 13 in 6arl

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Rubidium binding site 10 out of 13 in the Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 10 of Aspergillus Fumigatus Cytosolic Thiolase: Apo Enzyme in Complex with Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Rb401

b:14.1
occ:0.95
 O D:SER252 2.7 15.4 1.0
O D:PRO250 2.8 15.6 1.0
OH D:TYR187 2.9 14.1 1.0
O D:HOH653 2.9 30.0 0.6
O D:VAL350 2.9 14.0 1.0
O D:HOH653 2.9 30.0 0.4
O D:ALA249 3.2 15.4 1.0
C D:PRO250 3.6 16.1 1.0
CA D:PRO250 3.9 16.6 1.0
CZ D:TYR187 3.9 14.2 1.0
C D:SER252 3.9 15.0 1.0
OE1 D:GLU224 4.0 18.7 1.0
C D:VAL350 4.0 13.3 1.0
CG1 D:VAL350 4.1 13.3 1.0
CE2 D:TYR187 4.2 14.4 1.0
O D:HOH865 4.2 25.9 1.0
C D:ALA249 4.2 15.8 1.0
CG D:PRO254 4.3 15.2 1.0
O D:HOH687 4.3 22.6 1.0
O D:HOH577 4.3 22.4 1.0
CD D:PRO254 4.4 14.7 1.0
N D:SER252 4.5 15.2 1.0
CA D:VAL350 4.5 12.8 1.0
N D:PRO254 4.6 14.8 1.0
N D:PRO250 4.6 17.1 1.0
N D:ASN251 4.6 15.2 1.0
CD D:GLU224 4.6 18.4 1.0
CA D:SER253 4.7 15.2 1.0
C D:SER253 4.7 16.0 1.0
N D:SER253 4.8 15.0 1.0
CA D:SER252 4.8 14.9 1.0
CB D:VAL350 4.9 12.9 1.0
CG D:GLU224 4.9 17.4 1.0

Reference:

A.C.Marshall, C.S.Bond, J.B.Bruning. Structure of Aspergillus Fumigatus Cytosolic Thiolase: Trapped Tetrahedral Reaction Intermediates and Activation By Monovalent Cations Acs Catalysis V.8(3) 1973 2018.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.7B02873
Page generated: Thu Oct 10 12:08:47 2024

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