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Potassium in PDB 8cfi: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment D07

Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment D07

All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment D07:
3.3.1.1;

Protein crystallography data

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment D07, PDB code: 8cfi was solved by P.H.Malecki, M.Gawel, M.Stepniewska, K.Brzezinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.88 / 2.02
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 176.42, 104.11, 107.88, 90, 100.21, 90
R / Rfree (%) 19.2 / 23.4

Other elements in 8cfi:

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment D07 also contains other interesting chemical elements:

Fluorine (F) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment D07 (pdb code 8cfi). 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 P. Aeruginosa in Complex with F2X-Entry Library Fragment D07, PDB code: 8cfi:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8cfi

Go back to Potassium Binding Sites List in 8cfi
Potassium binding site 1 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment D07


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 P. Aeruginosa in Complex with F2X-Entry Library Fragment D07 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K504

b:35.2
occ:1.00
 OG1 A:THR380 2.7 34.8 1.0
O A:HIS382 2.7 34.6 1.0
O A:THR380 2.8 34.4 1.0
O A:HOH746 2.8 31.5 1.0
O A:HOH663 2.9 33.4 1.0
O B:HOH680 3.0 35.5 1.0
OE1 A:GLN65 3.3 32.5 1.0
CB A:THR380 3.4 36.1 1.0
NE2 A:GLN65 3.4 31.2 1.0
CD A:GLN65 3.5 32.1 1.0
C A:THR380 3.6 32.1 1.0
C A:HIS382 3.7 33.5 1.0
O A:GLY381 3.8 33.9 1.0
CA A:PRO383 4.0 30.6 1.0
C A:GLY381 4.1 34.8 1.0
CA A:THR380 4.1 33.6 1.0
N6 A:ADE502 4.2 33.6 1.0
N A:PRO383 4.2 33.4 1.0
CB B:ASP216 4.2 33.7 1.0
CG B:ASP216 4.5 36.5 1.0
O A:HOH850 4.5 36.1 1.0
N A:HIS382 4.5 31.9 1.0
N A:GLY381 4.5 33.9 1.0
OD1 B:ASP216 4.6 36.3 1.0
CG2 A:THR380 4.7 32.4 1.0
C A:PRO383 4.7 32.5 1.0
CA A:HIS382 4.7 31.6 1.0
CG A:GLN65 4.7 34.1 1.0
CA A:GLY381 4.8 32.1 1.0
OE1 A:GLN91 4.8 36.4 1.0
N A:SER384 4.8 33.1 1.0
O B:ASP216 4.8 34.6 1.0

Potassium binding site 2 out of 4 in 8cfi

Go back to Potassium Binding Sites List in 8cfi
Potassium binding site 2 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment D07


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 P. Aeruginosa in Complex with F2X-Entry Library Fragment D07 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:42.2
occ:1.00
 O B:HIS382 2.7 41.9 1.0
O B:HOH722 2.8 40.9 1.0
O B:THR380 2.8 39.8 1.0
O B:HOH655 2.8 41.1 1.0
OG1 B:THR380 2.9 39.6 1.0
O A:HOH749 3.0 38.2 1.0
NE2 B:GLN65 3.3 42.4 1.0
OE1 B:GLN65 3.4 43.0 1.0
CD B:GLN65 3.6 45.5 1.0
CB B:THR380 3.6 41.3 1.0
C B:HIS382 3.6 41.0 1.0
C B:THR380 3.6 41.1 1.0
O B:GLY381 3.9 42.0 1.0
CA B:PRO383 4.0 37.9 1.0
C B:GLY381 4.1 43.6 1.0
N6 B:ADE502 4.1 45.6 1.0
N B:PRO383 4.1 40.0 1.0
CB A:ASP216 4.3 35.1 1.0
CA B:THR380 4.3 42.0 1.0
N B:HIS382 4.4 39.3 1.0
O B:HOH763 4.4 39.7 1.0
CG A:ASP216 4.5 40.3 1.0
N B:GLY381 4.5 40.8 1.0
C B:PRO383 4.6 42.0 1.0
CA B:HIS382 4.6 38.4 1.0
CA B:GLY381 4.7 41.9 1.0
OE1 B:GLN91 4.7 48.4 1.0
OD1 A:ASP216 4.7 38.3 1.0
CG B:GLN65 4.8 45.1 1.0
N B:SER384 4.8 43.0 1.0
OD2 A:ASP216 4.8 44.8 1.0
O A:ASP216 4.9 38.4 1.0
CG2 B:THR380 4.9 41.3 1.0

Potassium binding site 3 out of 4 in 8cfi

Go back to Potassium Binding Sites List in 8cfi
Potassium binding site 3 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment D07


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 P. Aeruginosa in Complex with F2X-Entry Library Fragment D07 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K504

b:39.6
occ:1.00
 O C:THR380 2.7 40.3 1.0
O C:HIS382 2.8 48.0 1.0
OG1 C:THR380 2.8 44.9 1.0
O C:HOH744 2.9 34.1 1.0
O C:HOH675 2.9 41.5 1.0
OE1 C:GLN65 3.0 45.1 1.0
O D:HOH709 3.1 39.1 1.0
NE2 C:GLN65 3.4 39.1 1.0
CD C:GLN65 3.4 40.1 1.0
CB C:THR380 3.5 39.5 1.0
C C:THR380 3.6 43.7 1.0
C C:HIS382 3.7 39.7 1.0
O C:GLY381 3.9 37.6 1.0
N6 C:ADE502 4.0 45.6 1.0
CA C:PRO383 4.1 41.4 1.0
C C:GLY381 4.1 42.7 1.0
CA C:THR380 4.2 41.3 1.0
N C:PRO383 4.3 40.2 1.0
O C:HOH813 4.4 40.3 1.0
CB D:ASP216 4.4 41.7 1.0
N C:HIS382 4.5 40.2 1.0
N C:GLY381 4.5 37.9 1.0
CG C:GLN65 4.6 38.3 1.0
CG D:ASP216 4.6 43.4 1.0
C C:PRO383 4.7 42.6 1.0
OE1 C:GLN91 4.7 43.2 1.0
CA C:GLY381 4.7 39.6 1.0
CA C:HIS382 4.7 38.9 1.0
OD1 D:ASP216 4.7 43.2 1.0
CG2 C:THR380 4.8 39.9 1.0
N C:SER384 4.8 39.3 1.0
O D:ASP216 5.0 38.1 1.0

Potassium binding site 4 out of 4 in 8cfi

Go back to Potassium Binding Sites List in 8cfi
Potassium binding site 4 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment D07


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 P. Aeruginosa in Complex with F2X-Entry Library Fragment D07 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K504

b:32.2
occ:0.99
 O D:HOH764 2.7 42.6 1.0
O D:THR380 2.8 38.6 1.0
O D:HIS382 2.8 39.0 1.0
OG1 D:THR380 2.9 39.6 1.0
O D:HOH686 2.9 35.0 1.0
O D:HOH734 3.0 36.0 1.0
OE1 D:GLN65 3.2 36.9 1.0
NE2 D:GLN65 3.3 33.4 1.0
CD D:GLN65 3.4 39.2 1.0
CB D:THR380 3.5 41.7 1.0
C D:THR380 3.6 37.7 1.0
C D:HIS382 3.7 40.0 1.0
O D:GLY381 3.8 35.9 1.0
N6 D:ADE502 3.9 46.6 1.0
CA D:PRO383 4.1 36.9 1.0
C D:GLY381 4.1 38.4 1.0
CA D:THR380 4.2 35.6 1.0
N D:PRO383 4.3 38.6 1.0
CB C:ASP216 4.3 37.9 1.0
N D:HIS382 4.5 37.2 1.0
CG C:ASP216 4.5 39.4 1.0
N D:GLY381 4.5 36.4 1.0
OD1 C:ASP216 4.6 41.3 1.0
CG D:GLN65 4.6 35.8 1.0
C D:PRO383 4.7 40.9 1.0
O D:HOH853 4.7 39.6 1.0
CA D:HIS382 4.7 35.3 1.0
CA D:GLY381 4.7 39.7 1.0
CG2 D:THR380 4.7 39.6 1.0
OE1 D:GLN91 4.8 38.8 1.0
N D:SER384 4.8 37.1 1.0
O C:ASP216 5.0 37.5 1.0

Reference:

P.H.Malecki, M.Gawel, M.Stepniewska, K.Brzezinski. Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with Fragment F2X-Entry D07 To Be Published.
Page generated: Sat Aug 9 16:01:11 2025

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