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Rubidium in PDB 7o5l: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations

Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations

All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations:
3.3.1.1;

Protein crystallography data

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations, PDB code: 7o5l was solved by P.H.Malecki, B.Imiolczyk, J.Barciszewski, J.Czyrko-Horczak, K.Brzezinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.63 / 1.74
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 120.77, 196.07, 82.052, 90, 90, 90
R / Rfree (%) 18.8 / 21.4

Other elements in 7o5l:

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Rubidium Binding Sites:

The binding sites of Rubidium atom in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations (pdb code 7o5l). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 6 binding sites of Rubidium where determined in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations, PDB code: 7o5l:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5; 6;

Rubidium binding site 1 out of 6 in 7o5l

Go back to Rubidium Binding Sites List in 7o5l
Rubidium binding site 1 out of 6 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations


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 S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb502

b:32.4
occ:0.80
 O A:SER420 2.9 49.0 1.0
O A:TYR417 2.9 31.5 1.0
O A:HOH821 2.9 31.1 1.0
O A:HOH736 3.3 34.9 1.0
O A:SER423 3.4 56.2 1.0
CZ A:TYR417 3.5 33.1 1.0
CE1 A:TYR417 3.5 35.0 1.0
OG A:SER423 3.5 68.5 1.0
CE2 A:TYR417 3.6 23.4 1.0
CD1 A:TYR417 3.7 26.6 1.0
CD2 A:TYR417 3.8 28.5 1.0
CG A:TYR417 3.8 26.8 1.0
C A:SER420 3.9 37.6 1.0
C A:TYR417 3.9 28.3 1.0
OH A:TYR417 4.0 35.7 1.0
C A:SER423 4.5 63.4 1.0
CA A:TYR417 4.5 30.7 1.0
CB A:SER420 4.6 42.9 1.0
CA A:SER420 4.6 36.7 1.0
N A:SER420 4.7 35.9 1.0
CB A:SER423 4.7 72.2 1.0
CB A:TYR417 4.8 28.4 1.0
N A:TRP421 4.8 32.5 1.0
N A:SER423 4.9 51.7 1.0
OG A:SER420 4.9 51.3 1.0
CA A:TRP421 4.9 31.9 1.0
CA A:SER423 4.9 65.2 1.0
N A:ILE418 5.0 27.7 1.0

Rubidium binding site 2 out of 6 in 7o5l

Go back to Rubidium Binding Sites List in 7o5l
Rubidium binding site 2 out of 6 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations


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 S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb503

b:65.0
occ:0.80
 O A:ALA316 2.8 35.3 1.0
O A:LYS313 3.0 33.0 1.0
O A:GLU314 3.1 35.6 1.0
C A:GLU314 3.6 34.1 1.0
O A:HOH879 3.7 52.0 1.0
CA A:GLU314 3.9 34.3 1.0
C A:ALA316 3.9 34.6 1.0
O A:HOH905 4.1 38.5 0.5
O A:HOH905 4.1 29.4 0.5
C A:LYS313 4.1 35.6 1.0
N A:ALA316 4.3 29.5 1.0
O A:HOH770 4.4 37.2 0.6
C A:GLN315 4.5 36.6 1.0
N A:GLU314 4.5 31.2 1.0
N A:GLN315 4.5 32.0 1.0
CA A:ALA316 4.7 34.6 1.0
O A:GLN315 4.7 34.7 1.0
N A:LYS317 5.0 32.0 1.0

Rubidium binding site 3 out of 6 in 7o5l

Go back to Rubidium Binding Sites List in 7o5l
Rubidium binding site 3 out of 6 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations


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 S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb504

b:33.3
occ:0.40
 RB A:RB504 0.0 33.3 0.4
RB A:RB504 2.1 41.9 0.4
O A:LEU85 2.9 23.3 1.0
O A:THR87 3.1 21.2 1.0
O A:HOH734 3.3 22.4 1.0
O A:LEU348 3.4 23.6 1.0
O A:SER86 3.4 21.7 1.0
C A:SER86 3.5 21.6 1.0
O A:HOH889 3.6 35.7 1.0
O A:HOH805 3.6 20.4 0.5
CD A:LYS107 3.6 27.8 1.0
O A:HOH673 3.7 41.6 1.0
CA A:SER86 3.8 22.0 1.0
C A:THR87 3.9 22.6 1.0
C A:LEU85 3.9 21.8 1.0
N A:THR87 4.0 22.1 1.0
CG A:LYS107 4.2 27.2 1.0
O A:HOH865 4.2 44.5 1.0
N A:SER86 4.3 19.8 1.0
O A:ALA349 4.3 26.7 1.0
O A:HOH780 4.4 30.2 0.5
CG A:GLN88 4.5 21.1 1.0
CA A:THR87 4.6 18.8 1.0
O A:ALA351 4.6 26.6 1.0
C A:LEU348 4.6 24.5 1.0
N A:GLN88 4.6 21.1 1.0
CA A:ALA349 4.8 24.2 1.0
C A:ALA349 4.9 22.4 1.0
CA A:GLN88 4.9 20.1 1.0
CE A:LYS107 5.0 38.0 1.0

Rubidium binding site 4 out of 6 in 7o5l

Go back to Rubidium Binding Sites List in 7o5l
Rubidium binding site 4 out of 6 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations


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 S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb504

b:41.9
occ:0.40
 RB A:RB504 0.0 41.9 0.4
O A:HOH805 1.9 20.4 0.5
RB A:RB504 2.1 33.3 0.4
O A:ALA351 2.6 26.6 1.0
O A:LEU348 2.9 23.6 1.0
O A:HOH865 3.1 44.5 1.0
O A:HOH734 3.3 22.4 1.0
O A:ALA349 3.5 26.7 1.0
O A:HOH889 3.7 35.7 1.0
C A:ALA351 3.9 24.4 1.0
C A:ALA349 4.0 22.4 1.0
C A:LEU348 4.0 24.5 1.0
O A:HOH780 4.1 30.2 0.5
O A:HOH673 4.3 41.6 1.0
O A:LEU85 4.3 23.3 1.0
N A:ALA351 4.3 23.1 1.0
CA A:ALA349 4.5 24.2 1.0
CA A:ALA351 4.6 19.2 1.0
N A:ALA350 4.6 18.4 1.0
N A:ALA349 4.7 20.9 1.0
C A:ALA350 4.7 23.6 1.0
O A:SER86 4.8 21.7 1.0
N A:GLU352 4.8 21.3 1.0
CA A:GLU352 4.9 21.2 1.0
O A:THR87 5.0 21.2 1.0

Rubidium binding site 5 out of 6 in 7o5l

Go back to Rubidium Binding Sites List in 7o5l
Rubidium binding site 5 out of 6 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations


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 S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb502

b:54.5
occ:0.50
 O C:HOH777 2.2 29.1 0.5
O C:HOH613 2.3 33.2 0.5
O C:ALA351 2.7 28.5 1.0
O C:LEU348 2.9 30.1 1.0
O C:HOH737 3.1 29.5 1.0
O C:ALA349 3.7 29.3 1.0
C C:ALA351 3.9 25.5 1.0
C C:LEU348 4.0 27.4 1.0
O C:LEU85 4.0 42.9 1.0
C C:ALA349 4.1 26.4 1.0
N C:ALA351 4.4 24.4 1.0
CA C:ALA349 4.5 23.2 1.0
CA C:ALA351 4.7 20.6 1.0
N C:ALA349 4.7 23.9 1.0
N C:ALA350 4.8 24.2 1.0
O C:SER86 4.8 38.2 1.0
O C:HOH735 4.8 43.1 1.0
C C:ALA350 4.8 26.2 1.0
N C:GLU352 4.9 22.1 1.0
CA C:GLU352 4.9 28.2 1.0

Rubidium binding site 6 out of 6 in 7o5l

Go back to Rubidium Binding Sites List in 7o5l
Rubidium binding site 6 out of 6 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations


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 S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb503

b:60.5
occ:0.70
 O C:SER420 2.8 64.0 1.0
O C:TYR417 3.0 49.3 1.0
O C:HOH802 3.1 53.8 1.0
CE1 C:TYR417 3.4 44.4 1.0
CZ C:TYR417 3.5 41.5 1.0
OG C:SER420 3.7 70.7 1.0
CD1 C:TYR417 3.7 43.9 1.0
C C:SER420 3.8 61.3 1.0
CE2 C:TYR417 3.8 37.5 1.0
OH C:TYR417 4.0 44.3 1.0
CG C:TYR417 4.0 37.0 1.0
CD2 C:TYR417 4.0 43.4 1.0
C C:TYR417 4.1 46.2 1.0
N C:TRP421 4.6 51.5 1.0
CB C:SER420 4.6 68.2 1.0
CA C:SER420 4.6 64.6 1.0
CA C:TRP421 4.6 61.3 1.0
CA C:TYR417 4.7 46.7 1.0
N C:SER420 4.8 58.5 1.0
CB C:TYR417 5.0 43.0 1.0

Reference:

P.H.Malecki, B.Imiolczyk, J.Barciszewski, J.Czyrko-Horczak, J.Sliwiak, M.Gawel, K.Wozniak, M.Jaskolski, K.Brzezinski. Biochemical and Structural Insights Into An Unusual, Alkali-Metal-Independent S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803. Acta Crystallogr D Struct V. 78 865 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35775986
DOI: 10.1107/S2059798322005605
Page generated: Thu Oct 10 12:19:00 2024

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