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Rubidium in PDB 7zd7: Crystal Structure of the R24E/E352T Double Mutant 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 the R24E/E352T Double Mutant 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 the R24E/E352T Double Mutant 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 the R24E/E352T Double Mutant of S-Adenosyl-L- Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations, PDB code: 7zd7 was solved by P.H.Malecki, B.Imiolczyk, K.Wozniak, K.Brzezinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.51 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 120.897, 196.825, 81.92, 90, 90, 90
R / Rfree (%) 16.6 / 20

Other elements in 7zd7:

The structure of Crystal Structure of the R24E/E352T Double Mutant 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) 3 atoms

Rubidium Binding Sites:

The binding sites of Rubidium atom in the Crystal Structure of the R24E/E352T Double Mutant of S-Adenosyl-L- Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations (pdb code 7zd7). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 3 binding sites of Rubidium where determined in the Crystal Structure of the R24E/E352T Double Mutant of S-Adenosyl-L- Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations, PDB code: 7zd7:
Jump to Rubidium binding site number: 1; 2; 3;

Rubidium binding site 1 out of 3 in 7zd7

Go back to Rubidium Binding Sites List in 7zd7
Rubidium binding site 1 out of 3 in the Crystal Structure of the R24E/E352T Double Mutant 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 the R24E/E352T Double Mutant 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:Rb505

b:48.3
occ:0.60
O A:HOH681 2.8 29.4 1.0
OG1 A:THR61 2.9 31.4 1.0
O C:HOH672 3.0 52.2 1.0
OE1 A:GLN88 3.4 31.2 1.0
O A:HOH690 3.5 36.5 1.0
O A:HOH666 3.5 39.1 1.0
CG2 A:THR61 3.6 27.2 1.0
O A:HOH754 3.7 40.6 1.0
ND2 C:ASN209 3.7 43.1 1.0
CB A:THR61 3.8 27.7 1.0
NE2 A:GLN88 3.9 33.8 1.0
O A:HOH640 3.9 39.0 1.0
CD A:GLN88 4.0 34.6 1.0
CB A:THR352 4.1 33.1 1.0
CG2 A:THR352 4.4 36.7 1.0
OG1 A:THR352 4.5 37.9 1.0
OE2 A:GLU62 4.6 33.5 1.0
N A:THR61 4.6 29.3 1.0
CG C:ASN209 4.7 40.8 1.0
OE1 A:GLU24 4.7 42.4 1.0
OE1 A:GLU62 4.8 30.2 1.0
CA A:THR61 4.9 29.9 1.0
O A:HOH694 4.9 33.7 1.0
O A:THR352 5.0 28.8 1.0

Rubidium binding site 2 out of 3 in 7zd7

Go back to Rubidium Binding Sites List in 7zd7
Rubidium binding site 2 out of 3 in the Crystal Structure of the R24E/E352T Double Mutant 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 the R24E/E352T Double Mutant 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:Rb506

b:57.4
occ:0.50
O A:HOH807 2.9 47.4 1.0
O A:TYR417 3.1 44.4 1.0
O A:SER420 3.3 53.5 1.0
O A:HOH615 3.5 50.2 1.0
CE1 A:TYR417 3.5 48.3 1.0
CZ A:TYR417 3.7 43.5 1.0
CD1 A:TYR417 3.7 44.4 1.0
C A:SER420 3.9 53.3 1.0
CB A:SER420 4.1 51.1 1.0
CE2 A:TYR417 4.1 44.1 1.0
CG A:TYR417 4.1 43.6 1.0
C A:TYR417 4.2 45.6 1.0
OH A:TYR417 4.2 51.6 1.0
CD2 A:TYR417 4.3 42.6 1.0
CA A:SER420 4.5 51.8 1.0
OG A:SER420 4.5 64.5 1.0
N A:TRP421 4.6 45.8 1.0
CA A:TYR417 4.7 44.5 1.0
CA A:TRP421 4.8 47.7 1.0
O A:HOH740 4.8 52.5 1.0
N A:SER420 4.9 49.6 1.0

Rubidium binding site 3 out of 3 in 7zd7

Go back to Rubidium Binding Sites List in 7zd7
Rubidium binding site 3 out of 3 in the Crystal Structure of the R24E/E352T Double Mutant 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 the R24E/E352T Double Mutant 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:Rb505

b:55.5
occ:0.58
O C:HOH674 2.8 33.6 1.0
OG1 C:THR61 2.9 32.8 1.0
O C:HOH639 3.4 38.4 1.0
O C:HOH694 3.4 37.8 1.0
OE1 C:GLN88 3.6 33.6 1.0
CG2 C:THR61 3.6 31.9 1.0
ND2 A:ASN209 3.6 43.1 1.0
O A:HOH782 3.7 40.8 1.0
CB C:THR61 3.8 32.5 1.0
NE2 C:GLN88 4.0 35.8 1.0
O C:HOH741 4.0 42.7 1.0
CD C:GLN88 4.1 40.1 1.0
CB C:THR352 4.2 35.3 1.0
CG2 C:THR352 4.4 39.6 1.0
OE2 C:GLU62 4.5 34.3 1.0
OE1 C:GLU24 4.5 45.9 1.0
OG1 C:THR352 4.6 39.0 1.0
N C:THR61 4.6 35.4 1.0
CG A:ASN209 4.6 37.6 1.0
OE1 C:GLU62 4.8 35.7 1.0
NH1 A:ARG323 4.8 57.9 1.0
O C:HOH698 4.8 34.9 1.0
CA C:THR61 4.9 34.2 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 12:22:07 2024

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