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Rubidium in PDB 7zd8: Crystal Structure of the R24E 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 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 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 Mutant of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations, PDB code: 7zd8 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) 62.84 / 2.03
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 120.31, 195.837, 81.943, 90, 90, 90
R / Rfree (%) 16.8 / 20.3

Other elements in 7zd8:

The structure of Crystal Structure of the R24E 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 Mutant of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations (pdb code 7zd8). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 4 binding sites of Rubidium where determined in the Crystal Structure of the R24E Mutant of S-Adenosyl-L-Homocysteine Hydrolase From Synechocystis Sp. Pcc 6803 Cocrystallized with Adenosine in the Presence of Rb+ Cations, PDB code: 7zd8:
Jump to Rubidium binding site number: 1; 2; 3; 4;

Rubidium binding site 1 out of 4 in 7zd8

Go back to Rubidium Binding Sites List in 7zd8
Rubidium binding site 1 out of 4 in the Crystal Structure of the R24E 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 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:52.8
occ:0.64
 O A:HOH654 2.8 34.5 1.0
OG1 A:THR61 2.9 39.6 1.0
OE1 A:GLU352 3.0 49.7 1.0
O A:HOH649 3.0 36.9 0.5
O A:HOH625 3.1 37.4 1.0
O A:HOH627 3.4 44.0 1.0
CG2 A:THR61 3.5 31.7 1.0
OE1 A:GLN88 3.8 40.8 1.0
CB A:THR61 3.8 37.2 1.0
NH1 C:ARG323 4.1 42.2 1.0
NE2 A:GLN88 4.1 40.7 1.0
CD A:GLU352 4.1 51.2 1.0
OE1 A:GLU24 4.2 47.4 1.0
O A:HOH649 4.2 33.9 0.5
CB A:GLU352 4.3 41.2 1.0
CD A:GLN88 4.3 39.5 1.0
OE2 A:GLU62 4.5 40.7 1.0
N A:THR61 4.7 31.8 1.0
OE1 A:GLU62 4.7 38.4 1.0
CG A:GLU352 4.8 43.8 1.0
ND2 C:ASN209 4.9 42.2 1.0
CA A:THR61 4.9 35.6 1.0
O A:GLU352 4.9 36.0 1.0

Rubidium binding site 2 out of 4 in 7zd8

Go back to Rubidium Binding Sites List in 7zd8
Rubidium binding site 2 out of 4 in the Crystal Structure of the R24E 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 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:Rb507

b:74.2
occ:0.48
 O A:TYR417 3.1 54.0 1.0
O A:SER420 3.3 71.3 1.0
O A:SER423 3.3 84.3 1.0
CE1 A:TYR417 3.4 57.1 1.0
CZ A:TYR417 3.5 55.8 1.0
OG A:SER423 3.6 89.1 1.0
CD1 A:TYR417 3.7 48.4 1.0
C A:SER420 3.9 66.9 1.0
CE2 A:TYR417 3.9 51.5 1.0
OH A:TYR417 4.0 64.7 1.0
CG A:TYR417 4.1 54.1 1.0
CB A:SER420 4.1 65.0 1.0
C A:TYR417 4.2 55.5 1.0
CD2 A:TYR417 4.2 52.1 1.0
C A:SER423 4.3 90.1 1.0
OG A:SER420 4.3 77.7 1.0
CA A:SER420 4.5 63.9 1.0
N A:TRP421 4.6 57.9 1.0
CA A:TRP421 4.7 57.4 1.0
CB A:SER423 4.8 89.7 1.0
CA A:TYR417 4.8 52.0 1.0
N A:SER420 4.9 59.4 1.0
CA A:SER423 4.9 87.1 1.0
N A:SER423 5.0 74.9 1.0

Rubidium binding site 3 out of 4 in 7zd8

Go back to Rubidium Binding Sites List in 7zd8
Rubidium binding site 3 out of 4 in the Crystal Structure of the R24E 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 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:Rb508

b:78.0
occ:0.60
 O A:HOH805 2.8 42.3 0.5
O A:LYS313 2.8 47.3 1.0
O A:ALA316 2.8 54.4 1.0
O A:GLU314 2.9 53.2 1.0
C A:GLU314 3.5 52.7 1.0
CA A:GLU314 3.7 54.3 1.0
C A:LYS313 3.9 49.1 1.0
C A:ALA316 4.0 49.5 1.0
N A:GLU314 4.3 50.2 1.0
O A:HOH805 4.4 44.5 0.5
N A:ALA316 4.5 44.5 1.0
N A:GLN315 4.6 51.3 1.0
C A:GLN315 4.6 50.2 1.0
CA A:ALA316 4.8 46.5 1.0
O A:GLN315 5.0 49.6 1.0

Rubidium binding site 4 out of 4 in 7zd8

Go back to Rubidium Binding Sites List in 7zd8
Rubidium binding site 4 out of 4 in the Crystal Structure of the R24E 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 4 of Crystal Structure of the R24E 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:Rb506

b:57.0
occ:0.70
 O C:HOH662 2.8 40.4 1.0
O C:HOH722 2.8 39.8 0.5
OE1 C:GLU352 2.9 56.6 1.0
OG1 C:THR61 2.9 38.1 1.0
O C:HOH632 3.0 43.6 1.0
O C:HOH712 3.0 43.4 1.0
CG2 C:THR61 3.8 38.9 1.0
NH1 A:ARG323 3.8 51.3 1.0
CB C:THR61 4.0 40.8 1.0
CD C:GLU352 4.0 52.3 1.0
OE1 C:GLN88 4.0 43.6 1.0
CB C:GLU352 4.2 41.5 1.0
NE2 C:GLN88 4.3 43.3 1.0
OE2 C:GLU62 4.3 39.0 1.0
CG C:GLU352 4.4 46.1 1.0
OE1 C:GLU24 4.5 49.3 1.0
CD C:GLN88 4.6 45.6 1.0
O C:HOH722 4.6 44.5 0.5
ND2 A:ASN209 4.7 39.7 1.0
OE1 C:GLU62 4.7 40.9 1.0
CZ A:ARG323 4.9 47.8 1.0
N C:THR61 4.9 40.6 1.0
O C:GLU352 5.0 40.3 1.0
CD C:GLU62 5.0 44.0 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 12:22:07 2024

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