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Potassium in PDB 6f3p: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with 3'-Deoxyadenosine and K+ Cation

Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with 3'-Deoxyadenosine and K+ Cation

All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with 3'-Deoxyadenosine and K+ 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 3'-Deoxyadenosine and K+ Cation, PDB code: 6f3p 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) 30.00 / 1.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.900, 85.740, 112.010, 90.00, 122.20, 90.00
R / Rfree (%) 10.1 / 12.7

Other elements in 6f3p:

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with 3'-Deoxyadenosine and K+ Cation also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with 3'-Deoxyadenosine and K+ Cation (pdb code 6f3p). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with 3'-Deoxyadenosine and K+ Cation, PDB code: 6f3p:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6f3p

Go back to Potassium Binding Sites List in 6f3p
Potassium binding site 1 out of 2 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with 3'-Deoxyadenosine and K+ Cation


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with 3'-Deoxyadenosine and K+ Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:11.2
occ:1.00
O A:THR380 2.7 11.5 1.0
O A:HOH863 2.7 12.8 1.0
O A:HIS382 2.7 10.4 1.0
O A:HOH826 2.8 12.8 1.0
OG1 A:THR380 2.8 11.8 1.0
O C:HOH827 3.1 12.6 1.0
OE1 A:GLN65 3.2 11.3 1.0
NE2 A:GLN65 3.4 11.2 1.0
CD A:GLN65 3.5 10.2 1.0
CB A:THR380 3.5 11.5 1.0
C A:THR380 3.6 10.5 1.0
C A:HIS382 3.6 9.3 1.0
O A:GLY381 3.7 10.1 1.0
CA A:PRO383 4.0 9.4 1.0
N6 A:3AD502 4.0 10.6 1.0
C A:GLY381 4.1 9.2 1.0
N A:PRO383 4.2 8.9 1.0
CA A:THR380 4.2 10.9 1.0
CB C:ASP216 4.3 12.4 1.0
O A:HOH965 4.4 16.9 1.0
N A:HIS382 4.5 10.0 1.0
N A:GLY381 4.5 9.3 1.0
CG C:ASP216 4.6 13.0 1.0
CG A:GLN65 4.6 11.3 1.0
OD1 C:ASP216 4.7 12.8 1.0
C A:PRO383 4.7 10.0 1.0
CA A:HIS382 4.7 9.8 1.0
CA A:GLY381 4.7 10.6 1.0
N A:SER384 4.7 9.4 1.0
CG2 A:THR380 4.8 12.4 1.0
OE1 A:GLN91 4.9 11.8 1.0
O C:ASP216 5.0 12.2 1.0

Potassium binding site 2 out of 2 in 6f3p

Go back to Potassium Binding Sites List in 6f3p
Potassium binding site 2 out of 2 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with 3'-Deoxyadenosine and K+ Cation


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa in Complex with 3'-Deoxyadenosine and K+ Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K503

b:10.7
occ:1.00
O C:THR380 2.7 10.7 1.0
O C:HIS382 2.7 10.1 1.0
O C:HOH842 2.8 12.0 1.0
O C:HOH890 2.8 12.6 1.0
OG1 C:THR380 2.8 11.8 1.0
O A:HOH780 3.1 12.3 1.0
OE1 C:GLN65 3.2 10.1 1.0
NE2 C:GLN65 3.3 10.6 1.0
CD C:GLN65 3.4 10.4 1.0
CB C:THR380 3.6 10.9 1.0
C C:THR380 3.6 10.2 1.0
C C:HIS382 3.6 8.9 1.0
O C:GLY381 3.7 10.3 1.0
CA C:PRO383 4.0 8.9 1.0
N6 C:3AD502 4.0 9.6 1.0
C C:GLY381 4.1 9.6 1.0
N C:PRO383 4.2 8.7 1.0
CA C:THR380 4.2 10.7 1.0
CB A:ASP216 4.3 12.1 1.0
O C:HOH1016 4.4 16.3 1.0
N C:HIS382 4.4 8.7 1.0
N C:GLY381 4.5 9.4 1.0
CG C:GLN65 4.6 10.3 1.0
CG A:ASP216 4.6 12.0 1.0
CA C:HIS382 4.7 9.0 1.0
OD1 A:ASP216 4.7 12.4 1.0
C C:PRO383 4.7 9.1 1.0
CA C:GLY381 4.7 10.0 1.0
N C:SER384 4.8 8.6 1.0
CG2 C:THR380 4.8 12.0 1.0
OE1 C:GLN91 4.9 10.9 1.0
O A:ASP216 5.0 11.8 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: Mon Aug 12 16:06:05 2024

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