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Rubidium in PDB 6f3q: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation

Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation

All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation:
3.3.1.1;

Protein crystallography data

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation, PDB code: 6f3q was solved by J.Czyrko, K.Brzezinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.53 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.492, 99.442, 111.714, 90.00, 101.93, 90.00
R / Rfree (%) 9.3 / 12.4

Rubidium Binding Sites:

The binding sites of Rubidium atom in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation (pdb code 6f3q). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 5 binding sites of Rubidium where determined in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation, PDB code: 6f3q:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5;

Rubidium binding site 1 out of 5 in 6f3q

Go back to Rubidium Binding Sites List in 6f3q
Rubidium binding site 1 out of 5 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation


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 Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb501

b:11.8
occ:1.00
 O A:THR380 2.8 12.4 1.0
O A:HIS382 2.9 10.4 1.0
OG1 A:THR380 2.9 12.8 1.0
O A:HOH861 2.9 12.7 1.0
O A:HOH846 3.0 11.6 1.0
O C:HOH777 3.1 12.4 1.0
OE1 A:GLN65 3.2 11.3 1.0
NE2 A:GLN65 3.4 11.4 1.0
CD A:GLN65 3.5 11.4 1.0
CB A:THR380 3.6 11.8 1.0
C A:THR380 3.7 11.5 1.0
C A:HIS382 3.7 9.6 1.0
O A:GLY381 3.8 11.2 1.0
CA A:PRO383 4.1 10.0 1.0
N6 A:ADE505 4.1 10.9 1.0
C A:GLY381 4.1 10.2 1.0
CB C:ASP216 4.2 13.7 1.0
N A:PRO383 4.3 10.1 1.0
CA A:THR380 4.3 12.0 1.0
O A:HOH986 4.4 16.1 1.0
CG C:ASP216 4.5 12.8 1.0
N A:HIS382 4.6 10.9 1.0
N A:GLY381 4.6 10.8 1.0
CG A:GLN65 4.6 10.5 1.0
OD1 C:ASP216 4.6 13.4 1.0
C A:PRO383 4.7 10.0 1.0
N A:SER384 4.7 10.5 1.0
CA A:HIS382 4.8 10.4 1.0
CA A:GLY381 4.8 12.2 1.0
CG2 A:THR380 4.9 14.1 1.0
OE1 A:GLN91 4.9 12.7 1.0
O C:ASP216 5.0 12.8 1.0

Rubidium binding site 2 out of 5 in 6f3q

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Rubidium binding site 2 out of 5 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation


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 Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb501

b:9.6
occ:1.00
 O B:THR380 2.8 10.1 1.0
O B:HIS382 2.9 8.4 1.0
OG1 B:THR380 2.9 10.8 1.0
O B:HOH853 2.9 10.7 1.0
O B:HOH848 3.0 10.3 1.0
O D:HOH807 3.2 10.0 1.0
OE1 B:GLN65 3.2 9.0 1.0
NE2 B:GLN65 3.4 9.8 1.0
CD B:GLN65 3.5 8.4 1.0
CB B:THR380 3.6 9.2 1.0
C B:THR380 3.7 8.1 1.0
C B:HIS382 3.7 8.0 1.0
O B:GLY381 3.8 9.6 1.0
N6 B:ADE507 4.0 8.7 1.0
CA B:PRO383 4.1 8.5 1.0
C B:GLY381 4.1 8.8 1.0
CB D:ASP216 4.2 9.7 1.0
CA B:THR380 4.3 8.4 1.0
N B:PRO383 4.3 7.7 1.0
O B:HOH1025 4.5 13.2 1.0
CG D:ASP216 4.5 11.2 1.0
N B:HIS382 4.5 8.2 1.0
N B:GLY381 4.6 9.0 1.0
OD1 D:ASP216 4.6 10.8 1.0
CG B:GLN65 4.6 9.0 1.0
C B:PRO383 4.7 8.3 1.0
N B:SER384 4.8 8.6 1.0
CA B:HIS382 4.8 8.2 1.0
CA B:GLY381 4.8 9.2 1.0
CG2 B:THR380 4.8 11.0 1.0
OE1 B:GLN91 4.9 10.7 1.0
O D:ASP216 5.0 10.6 1.0

Rubidium binding site 3 out of 5 in 6f3q

Go back to Rubidium Binding Sites List in 6f3q
Rubidium binding site 3 out of 5 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation


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 Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rb502

b:22.7
occ:0.50
 O B:HOH1013 2.9 32.9 1.0
O B:THR11 3.1 19.1 1.0
O B:HOH1012 3.4 28.8 1.0
CZ B:PHE10 3.5 22.6 1.0
CE1 B:PHE10 3.6 21.9 1.0
OG1 B:THR11 3.6 27.3 1.0
O B:HOH679 3.7 30.3 1.0
CE2 B:PHE10 4.1 19.8 1.0
C B:THR11 4.2 17.1 1.0
O B:HOH962 4.2 48.2 1.0
CD1 B:PHE10 4.3 21.4 1.0
N B:THR11 4.5 20.2 1.0
O B:TYR13 4.5 14.7 1.0
CB B:THR11 4.7 22.9 1.0
CA B:THR11 4.7 21.6 1.0
CD2 B:PHE10 4.7 19.4 1.0
CG B:PHE10 4.8 18.6 1.0

Rubidium binding site 4 out of 5 in 6f3q

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Rubidium binding site 4 out of 5 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation


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 Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Rb501

b:12.4
occ:1.00
 O C:THR380 2.8 12.7 1.0
O C:HIS382 2.9 11.5 1.0
OG1 C:THR380 2.9 13.1 1.0
O C:HOH816 2.9 13.7 1.0
O C:HOH811 3.0 12.3 1.0
O A:HOH810 3.1 12.7 1.0
OE1 C:GLN65 3.2 12.3 1.0
NE2 C:GLN65 3.4 13.3 1.0
CD C:GLN65 3.5 12.6 1.0
CB C:THR380 3.6 12.8 1.0
C C:THR380 3.7 10.8 1.0
C C:HIS382 3.7 10.7 1.0
O C:GLY381 3.8 11.6 1.0
N6 C:ADE505 4.0 12.0 1.0
CA C:PRO383 4.1 11.2 1.0
C C:GLY381 4.1 11.3 1.0
CB A:ASP216 4.2 14.4 1.0
N C:PRO383 4.3 9.8 1.0
CA C:THR380 4.3 11.8 1.0
O C:HOH954 4.4 16.3 1.0
CG A:ASP216 4.5 13.3 1.0
N C:HIS382 4.5 11.0 1.0
N C:GLY381 4.6 11.5 1.0
CG C:GLN65 4.6 11.9 1.0
OD1 A:ASP216 4.6 14.0 1.0
C C:PRO383 4.7 11.5 1.0
N C:SER384 4.8 11.9 1.0
CA C:GLY381 4.8 12.2 1.0
CA C:HIS382 4.8 10.6 1.0
CG2 C:THR380 4.8 13.8 1.0
OE1 C:GLN91 4.9 13.5 1.0
O A:ASP216 5.0 13.6 1.0

Rubidium binding site 5 out of 5 in 6f3q

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Rubidium binding site 5 out of 5 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation


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 Pseudomonas Aeruginosa in Complex with Adenine and Rb+ Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Rb501

b:10.1
occ:1.00
 O D:THR380 2.8 11.3 1.0
O D:HIS382 2.9 9.4 1.0
OG1 D:THR380 2.9 11.1 1.0
O D:HOH874 2.9 11.4 1.0
O D:HOH837 3.0 10.6 1.0
O B:HOH808 3.1 10.7 1.0
OE1 D:GLN65 3.2 10.5 1.0
NE2 D:GLN65 3.4 9.8 1.0
CD D:GLN65 3.5 9.4 1.0
CB D:THR380 3.6 10.9 1.0
C D:THR380 3.7 9.0 1.0
C D:HIS382 3.7 9.0 1.0
O D:GLY381 3.8 9.9 1.0
N6 D:ADE506 4.1 9.6 1.0
CA D:PRO383 4.1 8.8 1.0
C D:GLY381 4.1 9.7 1.0
CB B:ASP216 4.1 10.5 1.0
N D:PRO383 4.3 8.6 1.0
CA D:THR380 4.3 9.3 1.0
O D:HOH1007 4.4 13.3 1.0
CG B:ASP216 4.5 10.7 1.0
N D:HIS382 4.5 8.4 1.0
N D:GLY381 4.6 8.9 1.0
CG D:GLN65 4.6 10.2 1.0
OD1 B:ASP216 4.6 11.1 1.0
C D:PRO383 4.7 9.3 1.0
N D:SER384 4.7 9.0 1.0
CA D:GLY381 4.8 9.4 1.0
CA D:HIS382 4.8 8.9 1.0
CG2 D:THR380 4.8 12.0 1.0
OE1 D:GLN91 5.0 12.1 1.0
O B:ASP216 5.0 11.2 1.0

Reference:

J.Czyrko, J.Sliwiak, B.Imiolczyk, Z.Gdaniec, M.Jaskolski, K.Brzezinski. Metal-Cation Regulation of Enzyme Dynamics Is A Key Factor Influencing the Activity of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa. Sci Rep V. 8 11334 2018.
ISSN: ESSN 2045-2322
PubMed: 30054521
DOI: 10.1038/S41598-018-29535-Y
Page generated: Thu Oct 10 12:12:53 2024

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