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Potassium in PDB 6f3n: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations

Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations

All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations:
3.3.1.1;

Protein crystallography data

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations, PDB code: 6f3n 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) 24.82 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.585, 99.275, 111.721, 90.00, 101.90, 90.00
R / Rfree (%) 15.1 / 17.6

Other elements in 6f3n:

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations (pdb code 6f3n). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations, PDB code: 6f3n:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6f3n

Go back to Potassium Binding Sites List in 6f3n
Potassium binding site 1 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations


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 Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K501

b:14.7
occ:1.00
OG1 A:THR380 2.7 14.7 1.0
O A:THR380 2.7 15.9 1.0
O A:HIS382 2.8 14.8 1.0
O A:HOH859 2.9 16.3 1.0
O A:HOH820 2.9 16.0 1.0
O C:HOH799 3.0 16.3 1.0
OE1 A:GLN65 3.2 14.8 1.0
NE2 A:GLN65 3.4 15.4 1.0
CB A:THR380 3.5 15.7 1.0
CD A:GLN65 3.5 14.9 1.0
C A:THR380 3.6 15.8 1.0
C A:HIS382 3.7 14.7 1.0
O A:GLY381 3.8 16.6 1.0
CA A:PRO383 4.1 14.8 1.0
N6 A:ADN505 4.1 17.2 0.7
C A:GLY381 4.1 16.1 1.0
N6 A:ADN505 4.1 16.7 0.3
CA A:THR380 4.2 15.5 1.0
N A:PRO383 4.2 14.7 1.0
CB C:ASP216 4.3 16.3 1.0
O A:HOH925 4.4 17.6 1.0
N A:GLY381 4.5 15.8 1.0
N A:HIS382 4.5 15.8 1.0
CG C:ASP216 4.5 16.4 1.0
OD1 C:ASP216 4.6 16.1 1.0
CG A:GLN65 4.7 14.6 1.0
CA A:HIS382 4.7 15.2 1.0
C A:PRO383 4.7 14.4 1.0
CA A:GLY381 4.7 15.9 1.0
N A:SER384 4.8 14.7 1.0
CG2 A:THR380 4.8 16.1 1.0
OE1 A:GLN91 4.8 16.7 1.0
O C:ASP216 5.0 17.1 1.0

Potassium binding site 2 out of 4 in 6f3n

Go back to Potassium Binding Sites List in 6f3n
Potassium binding site 2 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations


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 Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K501

b:14.0
occ:1.00
O B:THR380 2.7 14.6 1.0
OG1 B:THR380 2.8 13.5 1.0
O B:HOH777 2.8 12.1 1.0
O B:HIS382 2.8 12.9 1.0
O B:HOH802 2.9 11.7 1.0
O D:HOH785 3.1 11.4 1.0
OE1 B:GLN65 3.2 13.2 1.0
NE2 B:GLN65 3.4 13.7 1.0
CD B:GLN65 3.5 13.9 1.0
CB B:THR380 3.5 14.2 1.0
C B:THR380 3.6 14.0 1.0
C B:HIS382 3.6 13.6 1.0
O B:GLY381 3.7 14.1 1.0
CA B:PRO383 4.1 13.8 1.0
N6 B:ADN505 4.1 14.5 0.7
C B:GLY381 4.1 14.3 1.0
N6 B:ADN505 4.1 14.9 0.3
CA B:THR380 4.2 13.9 1.0
N B:PRO383 4.2 13.3 1.0
CB D:ASP216 4.3 14.8 1.0
N B:HIS382 4.5 14.6 1.0
N B:GLY381 4.5 13.8 1.0
O B:HOH946 4.5 15.4 1.0
CG D:ASP216 4.5 15.0 1.0
OD1 D:ASP216 4.6 15.8 1.0
CG B:GLN65 4.6 13.6 1.0
CA B:HIS382 4.7 14.3 1.0
C B:PRO383 4.7 13.4 1.0
CA B:GLY381 4.8 14.2 1.0
CG2 B:THR380 4.8 14.5 1.0
N B:SER384 4.8 14.4 1.0
OE1 B:GLN91 4.8 17.3 1.0
O D:ASP216 4.9 14.2 1.0

Potassium binding site 3 out of 4 in 6f3n

Go back to Potassium Binding Sites List in 6f3n
Potassium binding site 3 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K501

b:17.3
occ:1.00
O C:THR380 2.7 16.6 1.0
OG1 C:THR380 2.7 16.4 1.0
O C:HIS382 2.8 17.4 1.0
O C:HOH784 2.8 14.3 1.0
O C:HOH734 2.9 17.0 1.0
O A:HOH787 3.1 18.1 1.0
OE1 C:GLN65 3.2 16.8 1.0
NE2 C:GLN65 3.4 17.3 1.0
CB C:THR380 3.5 16.8 1.0
CD C:GLN65 3.5 16.6 1.0
C C:THR380 3.5 16.2 1.0
C C:HIS382 3.7 17.8 1.0
O C:GLY381 3.7 16.0 1.0
N6 C:ADN505 4.0 17.7 0.7
C C:GLY381 4.1 16.7 1.0
CA C:PRO383 4.1 16.5 1.0
N6 C:ADN505 4.1 17.2 0.3
CA C:THR380 4.2 16.4 1.0
N C:PRO383 4.2 16.1 1.0
CB A:ASP216 4.3 17.5 1.0
N C:GLY381 4.5 16.1 1.0
O C:HOH864 4.5 19.8 1.0
N C:HIS382 4.5 17.6 1.0
CG A:ASP216 4.5 17.8 1.0
OD1 A:ASP216 4.6 17.3 1.0
CG C:GLN65 4.6 16.0 1.0
CA C:GLY381 4.7 16.4 1.0
CA C:HIS382 4.7 17.6 1.0
CG2 C:THR380 4.7 16.7 1.0
C C:PRO383 4.8 16.5 1.0
N C:SER384 4.8 16.9 1.0
OE1 C:GLN91 4.8 20.3 1.0
O A:ASP216 5.0 17.6 1.0

Potassium binding site 4 out of 4 in 6f3n

Go back to Potassium Binding Sites List in 6f3n
Potassium binding site 4 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K501

b:15.1
occ:1.00
O D:THR380 2.8 13.7 1.0
OG1 D:THR380 2.8 14.8 1.0
O D:HOH835 2.8 14.7 1.0
O D:HIS382 2.8 13.2 1.0
O D:HOH752 2.9 13.5 1.0
O B:HOH847 3.0 14.4 1.0
OE1 D:GLN65 3.2 14.3 1.0
NE2 D:GLN65 3.4 13.6 1.0
CD D:GLN65 3.4 13.6 1.0
CB D:THR380 3.5 14.9 1.0
C D:THR380 3.6 14.2 1.0
C D:HIS382 3.7 13.2 1.0
O D:GLY381 3.8 13.8 1.0
CA D:PRO383 4.0 13.6 1.0
N6 D:ADN506 4.1 17.1 0.7
C D:GLY381 4.1 14.1 1.0
N6 D:ADN506 4.2 17.4 0.3
CB B:ASP216 4.2 14.5 1.0
N D:PRO383 4.2 13.5 1.0
CA D:THR380 4.2 14.3 1.0
O D:HOH939 4.4 16.3 1.0
CG B:ASP216 4.5 14.4 1.0
N D:GLY381 4.5 14.1 1.0
N D:HIS382 4.5 13.7 1.0
OD1 B:ASP216 4.6 13.6 1.0
CG D:GLN65 4.6 13.3 1.0
C D:PRO383 4.7 13.8 1.0
CA D:HIS382 4.7 13.7 1.0
N D:SER384 4.7 13.6 1.0
CG2 D:THR380 4.8 14.8 1.0
CA D:GLY381 4.8 14.3 1.0
OE1 D:GLN91 4.9 15.0 1.0
O B:ASP216 4.9 15.1 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: Sat Aug 9 10:57:25 2025

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