Atomistry » Rubidium » PDB 5aw4-7w49 » 6f3q
Atomistry »
  Rubidium »
    PDB 5aw4-7w49 »
      6f3q »

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

Go back to Rubidium Binding Sites List in 6f3q
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

Go back to Rubidium Binding Sites List in 6f3q
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

Go back to Rubidium Binding Sites List in 6f3q
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: Wed Dec 16 02:07:17 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy