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Rubidium in PDB 7ae5: Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form

Enzymatic activity of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form

All present enzymatic activity of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form:
4.1.1.61; 4.1.1.63;

Protein crystallography data

The structure of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, PDB code: 7ae5 was solved by S.A.Marshall, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.14 / 2.19
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 98.23, 108.3, 111.42, 117.72, 101.32, 91.8
R / Rfree (%) 22.3 / 26.3

Other elements in 7ae5:

The structure of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Rubidium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Rubidium atom in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form (pdb code 7ae5). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 12 binding sites of Rubidium where determined in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form, PDB code: 7ae5:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Rubidium binding site 1 out of 12 in 7ae5

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Rubidium binding site 1 out of 12 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb501

b:45.0
occ:1.00
 O B:HOH665 2.5 45.2 1.0
OD2 B:ASP413 2.5 47.7 1.0
O B:ASP441 2.5 50.6 1.0
O B:ARG407 2.5 45.3 1.0
OD1 B:ASP413 2.5 46.2 1.0
O B:THR443 2.5 42.4 1.0
CG B:ASP413 2.7 46.4 1.0
C B:ASP441 3.6 49.5 1.0
C B:THR443 3.6 43.1 1.0
C B:ARG407 3.7 45.7 1.0
N B:THR443 3.7 37.5 1.0
CG B:ASP441 3.9 48.2 1.0
OD2 B:ASP441 3.9 50.3 1.0
NZ B:LYS412 4.0 44.5 1.0
OD1 B:ASP441 4.0 48.6 1.0
CB B:ASP413 4.1 45.3 1.0
CA B:THR443 4.2 39.9 1.0
C B:ALA442 4.3 39.9 1.0
CB B:ASP441 4.3 45.2 1.0
CA B:ALA442 4.4 37.5 1.0
N B:ALA442 4.4 34.6 1.0
OG1 B:THR443 4.5 36.7 1.0
CB B:ARG407 4.5 45.3 1.0
N B:VAL408 4.6 35.2 1.0
CA B:VAL408 4.6 34.5 1.0
CA B:ARG407 4.6 46.4 1.0
CA B:ASP441 4.6 46.4 1.0
N B:THR444 4.7 40.8 1.0
O B:HOH611 4.8 47.5 1.0
CD B:PRO445 4.9 39.3 1.0

Rubidium binding site 2 out of 12 in 7ae5

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Rubidium binding site 2 out of 12 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb502

b:75.7
occ:1.00
 O B:HOH667 2.5 59.3 1.0
OH B:TYR223 2.5 54.9 1.0
OE2 B:GLU227 2.5 59.8 1.0
O B:VAL164 2.5 47.9 1.0
O B:MET216 2.5 49.9 1.0
O B:THR219 2.5 42.9 1.0
CD B:GLU227 3.6 61.0 1.0
C B:MET216 3.6 48.9 1.0
C B:THR219 3.6 41.7 1.0
C B:VAL164 3.7 43.3 1.0
SD B:MET216 3.7 51.6 1.0
CZ B:TYR223 3.8 55.1 1.0
O B:HOH693 3.8 62.9 1.0
OE1 B:GLU227 4.0 61.9 1.0
CA B:ALA217 4.0 48.5 1.0
O B:ALA217 4.1 49.5 1.0
C B:ALA217 4.2 48.4 1.0
N B:ALA217 4.2 47.8 1.0
CG B:MET216 4.3 50.6 1.0
CE1 B:TYR223 4.3 53.4 1.0
N B:THR219 4.4 39.6 1.0
CA B:THR219 4.4 40.1 1.0
CA B:GLY165 4.6 51.3 1.0
N B:GLY165 4.6 52.6 1.0
N B:PRO220 4.6 58.3 1.0
CA B:PRO220 4.6 60.6 1.0
CA B:VAL164 4.7 44.2 1.0
CB B:THR219 4.7 40.0 1.0
N B:VAL164 4.7 47.5 1.0
CA B:MET216 4.7 48.6 1.0
CG B:GLU227 4.8 61.1 1.0
CE2 B:TYR223 4.8 56.8 1.0
CB B:VAL164 4.9 44.5 1.0
O B:PRO220 5.0 64.3 1.0

Rubidium binding site 3 out of 12 in 7ae5

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Rubidium binding site 3 out of 12 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb501

b:44.8
occ:1.00
 O C:HOH613 2.5 46.9 1.0
O C:HOH666 2.5 36.4 1.0
OD2 C:ASP413 2.5 45.9 1.0
O C:ARG407 2.5 45.9 1.0
OD1 C:ASP413 2.5 45.7 1.0
O C:ASP441 2.5 41.6 1.0
O C:THR443 2.5 35.7 1.0
CG C:ASP413 2.7 45.3 1.0
OD1 C:ASP441 3.5 42.4 1.0
C C:ASP441 3.6 41.6 1.0
C C:THR443 3.6 36.6 1.0
N C:THR443 3.7 33.7 1.0
C C:ARG407 3.7 45.6 1.0
CG C:ASP441 3.8 40.6 1.0
CB C:ASP413 4.0 44.3 1.0
OD2 C:ASP441 4.2 40.0 1.0
CA C:THR443 4.2 35.5 1.0
CB C:ASP441 4.3 39.1 1.0
C C:ALA442 4.3 34.6 1.0
OG1 C:THR443 4.4 35.0 1.0
CA C:ALA442 4.4 33.7 1.0
N C:ALA442 4.4 33.1 1.0
CB C:ARG407 4.4 45.5 1.0
CA C:ARG407 4.5 45.6 1.0
CA C:ASP441 4.6 40.4 1.0
N C:VAL408 4.6 37.0 1.0
CA C:VAL408 4.6 36.8 1.0
N C:THR444 4.8 29.1 1.0
CD C:PRO445 5.0 38.1 1.0
O C:HOH651 5.0 37.5 1.0
CB C:THR443 5.0 36.1 1.0

Rubidium binding site 4 out of 12 in 7ae5

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Rubidium binding site 4 out of 12 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb502

b:60.6
occ:1.00
 OH C:TYR223 2.4 48.1 1.0
O C:THR219 2.5 38.6 1.0
O C:VAL164 2.5 45.9 1.0
O C:MET216 2.5 38.7 1.0
OE2 C:GLU227 2.9 53.4 1.0
SD C:MET216 3.5 40.0 1.0
C C:MET216 3.5 37.9 1.0
C C:THR219 3.6 37.6 1.0
CZ C:TYR223 3.7 49.3 1.0
C C:VAL164 3.7 44.0 1.0
CA C:ALA217 3.8 35.0 1.0
O C:ALA217 3.9 34.5 1.0
CD C:GLU227 4.0 54.6 1.0
C C:ALA217 4.1 34.4 1.0
N C:ALA217 4.1 35.4 1.0
CE1 C:TYR223 4.2 49.0 1.0
CG C:MET216 4.3 40.6 1.0
N C:THR219 4.4 36.1 1.0
OE1 C:GLU227 4.4 55.7 1.0
CA C:THR219 4.5 37.0 1.0
CA C:GLY165 4.5 48.2 1.0
CA C:PRO220 4.5 51.3 1.0
N C:PRO220 4.5 50.8 1.0
N C:GLY165 4.6 50.3 1.0
CA C:VAL164 4.7 44.6 1.0
CA C:MET216 4.7 38.1 1.0
N C:VAL164 4.7 49.5 1.0
CB C:THR219 4.8 38.6 1.0
CE2 C:TYR223 4.8 50.7 1.0
CB C:VAL164 4.9 43.5 1.0

Rubidium binding site 5 out of 12 in 7ae5

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Rubidium binding site 5 out of 12 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 5 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Rb501

b:48.6
occ:1.00
 O D:ARG407 2.5 39.6 0.4
O D:HOH630 2.5 33.8 1.0
O D:ARG407 2.5 39.7 0.6
O D:ASP441 2.5 43.4 1.0
OD2 D:ASP413 2.5 45.7 1.0
OD1 D:ASP413 2.5 47.2 1.0
O D:THR443 2.5 38.6 1.0
CG D:ASP413 2.7 45.9 1.0
N D:THR443 3.6 37.1 1.0
C D:THR443 3.6 39.5 1.0
C D:ASP441 3.6 43.7 1.0
C D:ARG407 3.7 39.0 0.6
C D:ARG407 3.7 39.0 0.4
OD2 D:ASP441 3.7 40.8 1.0
CG D:ASP441 3.7 40.9 1.0
OD1 D:ASP441 3.9 42.3 1.0
CB D:ASP413 4.1 44.8 1.0
CA D:THR443 4.2 38.3 1.0
C D:ALA442 4.2 37.0 1.0
CB D:ASP441 4.4 39.9 1.0
CB D:ARG407 4.4 39.6 0.6
CA D:ALA442 4.4 36.9 1.0
OG1 D:THR443 4.4 36.2 1.0
CB D:ARG407 4.4 39.6 0.4
N D:ALA442 4.4 35.0 1.0
CA D:ARG407 4.5 39.3 0.6
CA D:ARG407 4.5 39.3 0.4
N D:VAL408 4.6 35.0 1.0
CA D:ASP441 4.6 42.0 1.0
CA D:VAL408 4.6 34.8 1.0
N D:THR444 4.7 31.1 1.0
O D:HOH605 4.8 48.5 1.0
CD D:PRO445 4.9 35.2 1.0
CB D:THR443 4.9 37.5 1.0
O D:HOH620 5.0 36.3 1.0

Rubidium binding site 6 out of 12 in 7ae5

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Rubidium binding site 6 out of 12 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 6 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Rb502

b:367.4
occ:1.00
 OH D:TYR223 2.4 63.0 1.0
O D:MET216 2.5 50.8 1.0
O D:VAL164 2.5 56.7 1.0
O D:THR219 2.5 60.5 1.0
OE1 D:GLU227 2.8 56.2 1.0
SD D:MET216 2.9 51.5 1.0
C D:MET216 3.4 49.8 1.0
CZ D:TYR223 3.6 63.5 1.0
C D:THR219 3.7 60.0 1.0
C D:VAL164 3.7 54.0 1.0
CA D:ALA217 3.8 45.8 1.0
CG D:MET216 3.8 51.2 1.0
CD D:GLU227 3.9 57.9 1.0
O D:ALA217 4.0 44.7 1.0
N D:ALA217 4.0 46.5 1.0
CE2 D:TYR223 4.0 63.2 1.0
C D:ALA217 4.1 44.4 1.0
OE2 D:GLU227 4.4 59.3 1.0
CE D:MET216 4.4 50.6 1.0
N D:THR219 4.4 58.0 1.0
CA D:THR219 4.5 59.0 1.0
CA D:MET216 4.5 49.4 1.0
CA D:VAL164 4.6 55.1 1.0
N D:GLY165 4.6 62.6 1.0
N D:VAL164 4.6 59.3 1.0
CA D:GLY165 4.6 58.9 1.0
N D:PRO220 4.7 72.9 1.0
CB D:THR219 4.7 59.3 1.0
CB D:MET216 4.7 49.8 1.0
CA D:PRO220 4.8 73.7 1.0
CE1 D:TYR223 4.8 64.3 1.0
CB D:VAL164 4.8 57.2 1.0

Rubidium binding site 7 out of 12 in 7ae5

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Rubidium binding site 7 out of 12 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 7 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Rb501

b:47.5
occ:1.00
 O E:HOH676 2.5 36.2 1.0
OD2 E:ASP413 2.5 48.2 1.0
O E:ASP441 2.5 38.2 1.0
O E:ARG407 2.5 45.4 1.0
OD1 E:ASP413 2.5 48.6 1.0
O E:THR443 2.5 40.4 1.0
CG E:ASP413 2.7 47.4 1.0
C E:ASP441 3.6 37.4 1.0
C E:THR443 3.6 40.8 1.0
N E:THR443 3.6 36.9 1.0
C E:ARG407 3.7 44.9 1.0
OD1 E:ASP441 3.7 41.5 1.0
CG E:ASP441 3.7 41.0 1.0
O E:HOH701 3.8 50.9 1.0
OD2 E:ASP441 3.9 42.5 1.0
CB E:ASP413 4.0 45.4 1.0
CA E:THR443 4.2 39.2 1.0
C E:ALA442 4.3 37.5 1.0
CB E:ASP441 4.3 38.8 1.0
CA E:ALA442 4.3 35.6 1.0
N E:ALA442 4.4 35.4 1.0
OG1 E:THR443 4.4 41.6 1.0
CB E:ARG407 4.4 46.5 1.0
N E:VAL408 4.6 31.8 1.0
CA E:VAL408 4.6 30.5 1.0
CA E:ARG407 4.6 46.3 1.0
CA E:ASP441 4.6 37.3 1.0
N E:THR444 4.7 39.6 1.0
CB E:THR443 5.0 40.7 1.0

Rubidium binding site 8 out of 12 in 7ae5

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Rubidium binding site 8 out of 12 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 8 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Rb502

b:47.7
occ:1.00
 O E:HOH606 2.4 69.1 1.0
OH E:TYR223 2.5 42.5 1.0
OE2 E:GLU227 2.5 56.5 1.0
O E:THR219 2.5 42.9 1.0
O E:MET216 2.5 47.0 1.0
O E:VAL164 2.5 47.0 1.0
C E:MET216 3.5 46.0 1.0
CD E:GLU227 3.6 57.5 1.0
C E:THR219 3.6 41.6 1.0
SD E:MET216 3.6 49.0 1.0
C E:VAL164 3.7 45.5 1.0
CZ E:TYR223 3.7 42.1 1.0
CA E:ALA217 3.9 39.6 1.0
O E:ALA217 3.9 40.3 1.0
C E:ALA217 4.1 39.1 1.0
OE1 E:GLU227 4.1 58.0 1.0
N E:ALA217 4.1 38.3 1.0
CE1 E:TYR223 4.3 40.7 1.0
N E:THR219 4.3 39.1 1.0
CG E:MET216 4.4 47.4 1.0
CA E:THR219 4.5 39.4 1.0
CA E:GLY165 4.5 50.8 1.0
N E:GLY165 4.5 52.1 1.0
N E:PRO220 4.5 50.0 1.0
CA E:PRO220 4.6 52.4 1.0
CA E:VAL164 4.7 45.0 1.0
CA E:MET216 4.7 44.7 1.0
N E:VAL164 4.7 46.7 1.0
CB E:THR219 4.8 38.8 1.0
CG E:GLU227 4.8 58.1 1.0
CE2 E:TYR223 4.9 43.2 1.0
CB E:VAL164 5.0 44.5 1.0

Rubidium binding site 9 out of 12 in 7ae5

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Rubidium binding site 9 out of 12 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 9 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Rb501

b:63.0
occ:1.00
 O F:HOH607 2.5 51.2 1.0
O F:HOH660 2.5 36.1 1.0
OD2 F:ASP413 2.5 48.5 1.0
O F:ASP441 2.5 40.7 1.0
O F:ARG407 2.5 51.0 1.0
OD1 F:ASP413 2.5 47.5 1.0
O F:THR443 2.5 41.8 1.0
CG F:ASP413 2.7 47.0 1.0
C F:ASP441 3.6 40.1 1.0
C F:THR443 3.6 42.5 1.0
N F:THR443 3.7 38.8 1.0
C F:ARG407 3.7 51.6 1.0
OD1 F:ASP441 3.7 43.0 1.0
CG F:ASP441 3.8 42.8 1.0
CB F:ASP413 4.0 45.0 1.0
OD2 F:ASP441 4.1 44.2 1.0
CA F:THR443 4.2 40.9 1.0
C F:ALA442 4.2 34.3 1.0
CA F:ALA442 4.3 32.9 1.0
CB F:ASP441 4.4 41.0 1.0
N F:ALA442 4.4 32.4 1.0
OG1 F:THR443 4.4 42.2 1.0
CB F:ARG407 4.5 53.4 1.0
CA F:VAL408 4.5 28.4 1.0
N F:VAL408 4.5 30.7 1.0
CA F:ARG407 4.6 54.4 1.0
CA F:ASP441 4.6 39.9 1.0
N F:THR444 4.7 41.0 1.0
CB F:THR443 5.0 41.8 1.0

Rubidium binding site 10 out of 12 in 7ae5

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Rubidium binding site 10 out of 12 in the Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 10 of Structure of Sedimentibacter Hydroxybenzoicus Vanillic Acid Decarboxylase (Shvdccd) in Open Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Rb502

b:75.0
occ:1.00
 OH F:TYR223 2.5 52.3 1.0
O F:THR219 2.5 49.2 1.0
OE2 F:GLU227 2.5 58.0 1.0
O F:VAL164 2.5 49.4 1.0
O F:MET216 2.5 45.9 1.0
C F:MET216 3.6 44.3 1.0
CD F:GLU227 3.6 57.9 1.0
C F:THR219 3.6 49.3 1.0
C F:VAL164 3.7 47.7 1.0
CZ F:TYR223 3.7 52.2 1.0
SD F:MET216 3.8 49.2 1.0
CA F:ALA217 3.9 44.9 1.0
O F:ALA217 3.9 44.2 1.0
OE1 F:GLU227 4.1 57.7 1.0
C F:ALA217 4.1 43.7 1.0
N F:ALA217 4.2 44.7 1.0
CE2 F:TYR223 4.3 52.2 1.0
N F:THR219 4.4 49.4 1.0
CG F:MET216 4.4 49.3 1.0
CA F:GLY165 4.5 54.7 1.0
CA F:THR219 4.5 49.3 1.0
N F:GLY165 4.5 56.8 1.0
N F:PRO220 4.5 67.1 1.0
CA F:PRO220 4.6 67.3 1.0
CA F:VAL164 4.7 49.9 1.0
N F:VAL164 4.7 55.5 1.0
CA F:MET216 4.7 43.6 1.0
CB F:THR219 4.8 49.3 1.0
CE1 F:TYR223 4.8 52.0 1.0
CG F:GLU227 4.9 58.0 1.0
CB F:VAL164 5.0 48.9 1.0
N F:SER218 5.0 52.2 1.0

Reference:

S.A.Marshall, K.A.P.Payne, D.Leys. Domain Mobility and Allosteric Activation of Ubid Decarboxylases To Be Published.
Page generated: Fri Sep 24 16:37:19 2021

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