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Rubidium in PDB 6bpg: Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions

Enzymatic activity of Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions

All present enzymatic activity of Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions:
1.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions, PDB code: 6bpg was solved by E.F.Lopez-Orduna, R.A.Munoz-Clares, L.Gonzalez-Segura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.22 / 3.09
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 325.954, 130.358, 100.695, 90.00, 94.93, 90.00
R / Rfree (%) 18.1 / 23.4

Rubidium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Rubidium atom in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions (pdb code 6bpg). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 16 binding sites of Rubidium where determined in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions, PDB code: 6bpg:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Rubidium binding site 1 out of 16 in 6bpg

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Rubidium binding site 1 out of 16 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb501

b:70.7
occ:1.00
 O A:ILE27 2.8 55.8 1.0
OD1 A:ASP93 2.9 58.7 1.0
O A:VAL180 2.9 58.4 1.0
O A:ASP93 3.2 60.6 1.0
OG1 A:THR26 3.2 55.0 1.0
N A:ILE27 3.6 56.7 1.0
CG1 A:VAL180 3.7 56.0 1.0
C A:VAL180 3.8 56.1 1.0
C A:ILE27 3.9 57.0 1.0
CG A:ASP93 4.2 59.2 1.0
CG2 A:THR181 4.2 55.6 1.0
C A:ASP93 4.2 58.0 1.0
CA A:ILE27 4.3 57.9 1.0
O A:VAL329 4.3 56.5 1.0
CB A:THR26 4.4 55.8 1.0
C A:THR26 4.5 58.3 1.0
CA A:VAL180 4.5 55.0 1.0
CA A:THR26 4.6 57.5 1.0
CA A:ASP93 4.6 57.4 1.0
N A:THR181 4.7 55.4 1.0
CB A:VAL180 4.7 54.5 1.0
CA A:THR181 4.7 55.0 1.0
CB A:ILE27 4.8 59.0 1.0
CD A:PRO29 4.9 55.3 1.0
CB A:ASP93 5.0 56.3 1.0

Rubidium binding site 2 out of 16 in 6bpg

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Rubidium binding site 2 out of 16 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb502

b:54.4
occ:1.00
 O A:LYS457 2.6 40.7 1.0
O B:LEU246 2.9 41.8 1.0
O A:GLY460 2.9 43.5 1.0
CG2 A:VAL461 3.5 44.5 1.0
OE2 B:GLU248 3.7 46.7 1.0
C A:LYS457 3.8 41.2 1.0
C A:GLY460 3.9 44.9 1.0
CG B:GLU248 4.1 43.7 1.0
C B:LEU246 4.1 41.7 1.0
CD B:GLU248 4.2 48.8 1.0
N A:LYS457 4.3 40.4 1.0
OE1 B:GLU223 4.3 44.8 1.0
CD2 B:LEU246 4.3 43.5 1.0
CA A:LYS457 4.3 41.1 1.0
CA A:VAL461 4.4 43.0 1.0
N A:VAL461 4.5 45.6 1.0
N B:GLU248 4.6 41.4 1.0
CB A:VAL461 4.6 43.6 1.0
CA B:LYS247 4.6 40.2 1.0
C B:LYS247 4.7 39.8 1.0
C A:TYR456 4.7 40.1 1.0
CG B:LEU246 4.8 43.0 1.0
N B:LYS247 4.8 40.8 1.0
N A:GLN458 4.9 41.9 1.0
OE2 B:GLU223 4.9 47.5 1.0
O A:TYR456 4.9 40.6 1.0
CB B:LEU246 4.9 43.0 1.0
CD B:GLU223 4.9 46.0 1.0

Rubidium binding site 3 out of 16 in 6bpg

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Rubidium binding site 3 out of 16 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb501

b:47.0
occ:1.00
 O B:LYS457 2.6 40.4 1.0
O A:LEU246 2.9 40.2 1.0
O B:GLY460 3.0 38.0 1.0
C B:LYS457 3.8 40.5 1.0
CG2 B:VAL461 3.8 38.8 1.0
OE1 A:GLU223 3.9 44.8 1.0
CG A:GLU248 4.0 40.8 1.0
C B:GLY460 4.1 38.2 1.0
C A:LEU246 4.1 40.7 1.0
OE2 A:GLU248 4.3 42.9 1.0
N B:LYS457 4.3 39.1 1.0
CA B:LYS457 4.4 39.7 1.0
N A:GLU248 4.5 41.1 1.0
CD2 A:LEU246 4.6 40.7 1.0
CD A:GLU248 4.6 42.5 1.0
CA A:LYS247 4.6 40.2 1.0
C A:LYS247 4.7 39.7 1.0
C B:TYR456 4.7 39.4 1.0
CG A:LEU246 4.8 40.4 1.0
CA B:VAL461 4.8 38.1 1.0
N B:VAL461 4.8 38.5 1.0
CD A:GLU223 4.8 46.3 1.0
N B:GLN458 4.9 39.6 1.0
OE2 A:GLU223 4.9 45.7 1.0
N A:LYS247 4.9 40.4 1.0
O B:TYR456 4.9 40.1 1.0
CB A:LEU246 5.0 40.5 1.0
N B:GLY460 5.0 38.8 1.0
CB B:VAL461 5.0 38.5 1.0

Rubidium binding site 4 out of 16 in 6bpg

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Rubidium binding site 4 out of 16 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb502

b:50.7
occ:1.00
 O B:ILE27 2.8 36.5 1.0
O B:VAL180 2.8 35.6 1.0
O B:ASP93 2.9 38.4 1.0
OG1 B:THR26 3.2 34.9 1.0
OD1 B:ASP93 3.2 37.8 1.0
N B:ILE27 3.6 37.5 1.0
C B:ILE27 3.8 37.4 1.0
C B:VAL180 3.8 35.5 1.0
CG1 B:VAL180 3.9 36.4 1.0
C B:ASP93 3.9 38.2 1.0
CA B:ILE27 4.2 38.1 1.0
CG B:ASP93 4.3 38.4 1.0
CA B:ASP93 4.3 38.4 1.0
CG2 B:THR181 4.4 36.8 1.0
CB B:THR26 4.4 35.7 1.0
C B:THR26 4.4 37.0 1.0
CA B:VAL180 4.5 35.8 1.0
CA B:THR26 4.6 36.6 1.0
N B:THR181 4.7 36.9 1.0
CD B:PRO29 4.8 37.6 1.0
CA B:THR181 4.8 37.0 1.0
CB B:VAL180 4.9 36.0 1.0
CB B:ASP93 4.9 38.4 1.0
N B:ASN28 4.9 38.5 1.0
CB B:ILE27 4.9 38.7 1.0
O B:VAL329 4.9 40.0 1.0

Rubidium binding site 5 out of 16 in 6bpg

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Rubidium binding site 5 out of 16 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 5 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb501

b:55.9
occ:1.00
 O C:LYS457 2.9 43.6 1.0
O D:LEU246 2.9 41.6 1.0
O C:GLY460 3.1 42.1 1.0
OE2 D:GLU223 3.4 43.8 1.0
OE2 D:GLU248 3.8 50.0 1.0
CG D:GLU248 3.8 43.2 1.0
OE1 D:GLU223 3.8 46.1 1.0
CD D:GLU223 3.8 45.0 1.0
C C:LYS457 4.0 44.1 1.0
C D:LEU246 4.1 41.9 1.0
CD D:GLU248 4.2 49.3 1.0
CG2 C:VAL461 4.3 44.3 1.0
C C:GLY460 4.3 42.0 1.0
N C:LYS457 4.3 43.5 1.0
CA C:LYS457 4.5 44.2 1.0
N D:GLU248 4.5 41.1 1.0
CA D:LYS247 4.7 39.7 1.0
C C:TYR456 4.8 41.4 1.0
C D:LYS247 4.8 39.6 1.0
CA C:VAL461 4.8 42.5 1.0
N D:LYS247 4.9 40.5 1.0
CB D:LEU246 4.9 44.5 1.0
O C:GLY455 4.9 41.6 1.0
N C:VAL461 5.0 42.8 1.0
O D:GLU223 5.0 39.4 1.0

Rubidium binding site 6 out of 16 in 6bpg

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Rubidium binding site 6 out of 16 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 6 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb502

b:77.8
occ:1.00
 O C:ILE27 2.8 67.1 1.0
O C:ASP93 3.0 65.3 1.0
OG1 C:THR26 3.1 62.6 1.0
O C:VAL180 3.1 63.8 1.0
OD1 C:ASP93 3.3 65.0 1.0
N C:ILE27 3.6 65.3 1.0
C C:ILE27 3.8 66.3 1.0
CG1 C:VAL180 4.0 63.4 1.0
C C:ASP93 4.0 63.0 1.0
C C:VAL180 4.1 62.0 1.0
CA C:ILE27 4.3 66.9 1.0
CB C:THR26 4.3 63.5 1.0
CG C:ASP93 4.3 64.2 1.0
CA C:ASP93 4.3 63.5 1.0
O C:VAL329 4.3 62.7 1.0
C C:THR26 4.4 66.7 1.0
CG2 C:THR181 4.5 60.6 1.0
CA C:THR26 4.6 65.9 1.0
CD C:PRO29 4.6 63.4 1.0
CA C:VAL180 4.8 60.2 1.0
N C:ASN28 4.8 67.1 1.0
CB C:ASP93 4.9 63.4 1.0
N C:THR181 4.9 62.3 1.0
CA C:THR181 5.0 61.7 1.0

Rubidium binding site 7 out of 16 in 6bpg

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Rubidium binding site 7 out of 16 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 7 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Rb501

b:53.0
occ:1.00
 O D:LYS457 2.7 39.2 1.0
O C:LEU246 2.9 41.3 1.0
O D:GLY460 3.4 39.2 1.0
OE1 C:GLU223 3.7 39.7 1.0
C D:LYS457 3.8 40.1 1.0
CG2 D:VAL461 3.8 40.6 1.0
C C:LEU246 4.1 41.7 1.0
CD C:GLU248 4.1 47.6 1.0
OE2 C:GLU223 4.2 41.0 1.0
OE2 C:GLU248 4.2 46.5 1.0
N D:LYS457 4.2 39.6 1.0
CA D:LYS457 4.3 41.1 1.0
CG C:GLU248 4.3 44.3 1.0
CD C:GLU223 4.4 40.1 1.0
C D:GLY460 4.4 39.0 1.0
CA C:LYS247 4.6 41.8 1.0
N C:GLU248 4.6 42.1 1.0
OE1 C:GLU248 4.6 48.8 1.0
C C:LYS247 4.8 41.6 1.0
N C:LYS247 4.8 42.3 1.0
C D:TYR456 4.8 36.9 1.0
CG C:LEU246 4.9 42.5 1.0
CB D:VAL461 4.9 40.0 1.0
CA D:VAL461 5.0 39.5 1.0
O C:GLU223 5.0 39.9 1.0
N D:GLN458 5.0 41.6 1.0
CD2 C:LEU246 5.0 43.5 1.0

Rubidium binding site 8 out of 16 in 6bpg

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Rubidium binding site 8 out of 16 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 8 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Rb502

b:58.2
occ:1.00
 O D:ILE27 2.7 42.9 1.0
O D:ASP93 2.8 46.5 1.0
O D:VAL180 3.1 42.5 1.0
OD1 D:ASP93 3.2 46.8 1.0
OG1 D:THR26 3.3 40.6 1.0
N D:ILE27 3.7 41.8 1.0
C D:ILE27 3.8 42.8 1.0
C D:ASP93 3.8 45.8 1.0
CG1 D:VAL180 3.9 43.9 1.0
C D:VAL180 4.2 42.0 1.0
CA D:ASP93 4.2 45.4 1.0
CG D:ASP93 4.3 45.7 1.0
CA D:ILE27 4.3 43.4 1.0
C D:THR26 4.5 42.6 1.0
CB D:THR26 4.5 41.0 1.0
O D:VAL329 4.5 43.8 1.0
CD D:PRO29 4.6 42.0 1.0
CA D:THR26 4.7 41.8 1.0
CG D:PRO29 4.7 41.5 1.0
CB D:ASP93 4.8 44.5 1.0
CG2 D:THR181 4.8 44.5 1.0
N D:ASN28 4.8 42.8 1.0
CA D:VAL180 4.9 42.6 1.0
O D:LEU92 4.9 43.6 1.0

Rubidium binding site 9 out of 16 in 6bpg

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Rubidium binding site 9 out of 16 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 9 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Rb501

b:43.2
occ:1.00
 O E:LYS457 2.8 37.0 1.0
O F:LEU246 2.9 37.6 1.0
O E:GLY460 3.0 35.8 1.0
OE1 F:GLU223 3.4 42.6 1.0
CG2 E:VAL461 4.0 36.2 1.0
C E:LYS457 4.0 36.9 1.0
C F:LEU246 4.1 37.3 1.0
C E:GLY460 4.2 36.0 1.0
CD F:GLU223 4.4 44.2 1.0
N E:LYS457 4.5 35.9 1.0
N F:GLU248 4.5 37.8 1.0
CD2 F:LEU246 4.6 37.4 1.0
CA E:LYS457 4.6 36.5 1.0
CA F:LYS247 4.6 36.8 1.0
OE2 F:GLU223 4.7 43.2 1.0
CA E:VAL461 4.7 35.1 1.0
C F:LYS247 4.8 36.9 1.0
CB F:LEU246 4.8 37.0 1.0
CG F:LEU246 4.8 37.1 1.0
N F:LYS247 4.8 36.4 1.0
N E:VAL461 4.9 35.0 1.0
CB E:VAL461 4.9 36.0 1.0
C E:TYR456 4.9 35.8 1.0

Rubidium binding site 10 out of 16 in 6bpg

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Rubidium binding site 10 out of 16 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 10 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Pseudomonas Aeruginosa with Bound Rubidium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Rb502

b:67.2
occ:1.00
 O E:ASP93 2.7 50.5 1.0
O E:VAL180 3.0 47.4 1.0
O E:ILE27 3.0 47.6 1.0
OG1 E:THR26 3.1 46.2 1.0
OD1 E:ASP93 3.4 50.7 1.0
C E:ASP93 3.8 49.5 1.0
N E:ILE27 3.8 47.2 1.0
C E:ILE27 4.0 47.5 1.0
C E:VAL180 4.0 45.9 1.0
CG1 E:VAL180 4.1 49.7 1.0
O E:VAL329 4.3 48.1 1.0
CG E:ASP93 4.3 49.7 1.0
CA E:ASP93 4.3 48.5 1.0
CB E:THR26 4.4 46.7 1.0
CA E:ILE27 4.5 47.8 1.0
CG2 E:THR181 4.5 48.2 1.0
C E:THR26 4.6 47.9 1.0
CG E:PRO29 4.7 47.5 1.0
CA E:THR26 4.7 47.3 1.0
CA E:VAL180 4.7 46.6 1.0
CD E:PRO29 4.7 48.3 1.0
N E:THR181 4.8 47.3 1.0
CB E:ASP93 4.9 48.0 1.0
CA E:THR181 4.9 47.8 1.0
N E:THR94 4.9 47.9 1.0

Reference:

E.F.Lopez-Orduna, R.A.Munoz-Clares, L.Gonzalez-Segura. Crystallographic Identification of Monovalent Cation-Binding Sites in Two Betaine Aldehyde Dehydrogenases To Be Published.
Page generated: Thu Oct 10 12:09:56 2024

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