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Potassium in PDB 8cfx: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06

Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06

All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06:
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 H06, PDB code: 8cfx 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) 35.94 / 1.98
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.574, 103.99, 176.086, 90, 99.58, 90
R / Rfree (%) 16.8 / 20.3

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 H06 (pdb code 8cfx). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 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 H06, PDB code: 8cfx:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 8cfx

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Potassium binding site 1 out of 8 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06


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 H06 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K504

b:23.7
occ:1.00
O A:HIS382 2.7 24.3 1.0
O A:THR380 2.8 25.3 1.0
O A:HOH739 2.8 18.6 1.0
OG1 A:THR380 2.9 29.9 1.0
O A:HOH768 2.9 24.9 1.0
O B:HOH678 3.1 25.6 1.0
OE1 A:GLN65 3.2 23.5 1.0
NE2 A:GLN65 3.3 22.9 1.0
CD A:GLN65 3.4 22.7 1.0
CB A:THR380 3.5 26.9 1.0
C A:HIS382 3.6 26.1 1.0
C A:THR380 3.6 25.7 1.0
O A:GLY381 3.7 27.2 1.0
CA A:PRO383 3.9 23.2 1.0
N6 A:ADE502 4.0 24.9 1.0
C A:GLY381 4.1 23.5 1.0
N A:PRO383 4.1 26.4 1.0
CA A:THR380 4.2 24.4 1.0
CB B:ASP216 4.4 25.0 1.0
N A:HIS382 4.5 23.1 1.0
O A:HOH893 4.5 24.4 1.0
N A:GLY381 4.5 24.9 1.0
CG B:ASP216 4.6 27.2 1.0
OD1 B:ASP216 4.6 21.8 1.0
CG A:GLN65 4.6 21.6 1.0
C A:PRO383 4.7 26.1 1.0
CA A:HIS382 4.7 24.6 1.0
CA A:GLY381 4.7 23.9 1.0
CG2 A:THR380 4.8 25.1 1.0
N A:SER384 4.8 23.9 1.0
OE1 A:GLN91 4.9 25.3 1.0
O B:ASP216 4.9 23.9 1.0

Potassium binding site 2 out of 8 in 8cfx

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Potassium binding site 2 out of 8 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06


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 H06 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:28.1
occ:1.00
OG1 B:THR380 2.7 25.9 1.0
O B:HIS382 2.7 27.1 1.0
O B:THR380 2.8 26.8 1.0
O B:HOH706 2.9 27.3 1.0
O B:HOH639 3.0 26.5 1.0
O A:HOH631 3.1 25.7 1.0
OE1 B:GLN65 3.2 30.0 1.0
CB B:THR380 3.5 30.1 1.0
NE2 B:GLN65 3.5 23.2 1.0
CD B:GLN65 3.5 27.0 1.0
C B:THR380 3.6 26.2 1.0
C B:HIS382 3.6 26.6 1.0
O B:GLY381 3.8 24.8 1.0
CA B:PRO383 4.0 25.2 1.0
C B:GLY381 4.1 28.7 1.0
N6 B:ADE502 4.2 30.6 1.0
N B:PRO383 4.2 24.6 1.0
CA B:THR380 4.2 27.4 1.0
CB A:ASP216 4.3 28.9 1.0
CG A:ASP216 4.5 27.8 1.0
N B:HIS382 4.5 27.3 1.0
O B:HOH855 4.5 31.6 1.0
N B:GLY381 4.5 27.2 1.0
OD1 A:ASP216 4.6 26.6 1.0
CA B:HIS382 4.7 29.2 1.0
CG B:GLN65 4.7 22.7 1.0
C B:PRO383 4.7 27.7 1.0
CG2 B:THR380 4.7 28.3 1.0
CA B:GLY381 4.8 26.1 1.0
N B:SER384 4.8 26.3 1.0
OE1 B:GLN91 4.8 28.7 1.0
O A:ASP216 4.9 27.8 1.0

Potassium binding site 3 out of 8 in 8cfx

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Potassium binding site 3 out of 8 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06


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 H06 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K506

b:28.1
occ:1.00
O C:THR380 2.7 29.6 1.0
O C:HIS382 2.8 30.8 1.0
OG1 C:THR380 2.8 33.0 1.0
O C:HOH766 2.8 24.9 1.0
O C:HOH758 2.9 30.4 1.0
O D:HOH636 2.9 28.9 1.0
OE1 C:GLN65 3.1 28.9 1.0
NE2 C:GLN65 3.4 28.8 1.0
CD C:GLN65 3.4 29.2 1.0
CB C:THR380 3.6 29.8 1.0
C C:THR380 3.6 33.8 1.0
C C:HIS382 3.7 30.2 1.0
O C:GLY381 3.9 29.9 1.0
N6 C:ADE502 4.0 30.0 1.0
CA C:PRO383 4.1 29.1 1.0
C C:GLY381 4.1 31.1 1.0
N C:PRO383 4.3 28.3 1.0
CA C:THR380 4.3 33.3 1.0
CB D:ASP216 4.4 29.9 1.0
N C:HIS382 4.5 32.1 1.0
N C:GLY381 4.6 30.4 1.0
CG D:ASP216 4.6 32.5 1.0
O C:HOH872 4.6 34.4 1.0
CG C:GLN65 4.7 27.3 1.0
CA C:HIS382 4.7 30.1 1.0
OD1 D:ASP216 4.7 31.1 1.0
CA C:GLY381 4.7 30.3 1.0
C C:PRO383 4.8 31.9 1.0
OE1 C:GLN91 4.8 31.6 1.0
N C:SER384 4.8 28.5 1.0
CG2 C:THR380 4.9 32.6 1.0
O D:ASP216 4.9 27.9 1.0

Potassium binding site 4 out of 8 in 8cfx

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Potassium binding site 4 out of 8 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06


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 H06 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K505

b:28.4
occ:1.00
O D:HOH777 2.8 27.1 1.0
O D:THR380 2.8 28.4 1.0
O D:HIS382 2.8 28.5 1.0
O D:HOH824 2.8 26.9 1.0
OG1 D:THR380 2.9 28.8 1.0
O C:HOH765 3.0 29.9 1.0
OE1 D:GLN65 3.2 29.5 1.0
NE2 D:GLN65 3.4 24.3 1.0
CB D:THR380 3.5 29.0 1.0
CD D:GLN65 3.5 29.4 1.0
C D:THR380 3.7 31.0 1.0
C D:HIS382 3.7 29.6 1.0
O D:GLY381 3.8 26.1 1.0
CA D:PRO383 3.9 28.5 1.0
N6 D:ADE502 4.1 33.0 1.0
C D:GLY381 4.2 25.9 1.0
N D:PRO383 4.2 27.1 1.0
CA D:THR380 4.2 28.4 1.0
CB C:ASP216 4.3 28.3 1.0
O D:HOH872 4.5 34.5 1.0
CG C:ASP216 4.5 29.3 1.0
N D:GLY381 4.6 26.8 1.0
N D:HIS382 4.6 29.1 1.0
OD1 C:ASP216 4.7 30.9 1.0
C D:PRO383 4.7 30.8 1.0
CG D:GLN65 4.7 28.3 1.0
N D:SER384 4.7 25.8 1.0
CG2 D:THR380 4.8 29.4 1.0
CA D:HIS382 4.8 30.2 1.0
CA D:GLY381 4.8 27.3 1.0
OE1 D:GLN91 4.9 34.5 1.0
O C:ASP216 5.0 29.3 1.0

Potassium binding site 5 out of 8 in 8cfx

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Potassium binding site 5 out of 8 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K504

b:26.7
occ:1.00
O G:HIS382 2.7 25.7 1.0
O G:THR380 2.7 25.0 1.0
O G:HOH781 2.8 24.4 1.0
O G:HOH747 2.9 23.6 1.0
OG1 G:THR380 2.9 25.0 1.0
O H:HOH726 3.0 27.6 1.0
OE1 G:GLN65 3.1 26.3 1.0
NE2 G:GLN65 3.3 23.0 1.0
CD G:GLN65 3.4 28.8 1.0
CB G:THR380 3.6 26.3 1.0
C G:HIS382 3.6 27.7 1.0
C G:THR380 3.7 24.6 1.0
O G:GLY381 3.8 27.3 1.0
CA G:PRO383 3.9 25.6 1.0
N6 G:ADE502 4.0 25.2 1.0
C G:GLY381 4.1 25.5 1.0
N G:PRO383 4.2 23.7 1.0
CA G:THR380 4.3 25.9 1.0
CB H:ASP216 4.3 24.3 1.0
O G:HOH867 4.4 28.6 1.0
N G:HIS382 4.5 26.7 1.0
CG H:ASP216 4.6 27.5 1.0
CG G:GLN65 4.6 21.8 1.0
N G:GLY381 4.6 24.6 1.0
OD1 H:ASP216 4.6 24.3 1.0
C G:PRO383 4.7 26.1 1.0
CA G:HIS382 4.7 28.3 1.0
CA G:GLY381 4.7 23.1 1.0
N G:SER384 4.8 24.5 1.0
OE1 G:GLN91 4.8 28.3 1.0
CG2 G:THR380 4.9 24.2 1.0
O H:ASP216 4.9 23.4 1.0

Potassium binding site 6 out of 8 in 8cfx

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Potassium binding site 6 out of 8 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K503

b:28.3
occ:1.00
O H:THR380 2.7 26.5 1.0
O H:HOH654 2.8 24.1 1.0
O H:HIS382 2.8 26.1 1.0
OG1 H:THR380 2.8 25.2 1.0
O H:HOH651 2.9 27.6 1.0
O G:HOH726 3.0 27.4 1.0
OE1 H:GLN65 3.2 27.7 1.0
NE2 H:GLN65 3.4 27.1 1.0
CD H:GLN65 3.5 29.1 1.0
CB H:THR380 3.6 27.4 1.0
C H:THR380 3.6 28.1 1.0
C H:HIS382 3.7 27.1 1.0
O H:GLY381 3.8 29.0 1.0
CA H:PRO383 4.0 28.6 1.0
N6 H:ADE502 4.1 29.2 1.0
C H:GLY381 4.1 29.7 1.0
N H:PRO383 4.2 26.8 1.0
CA H:THR380 4.3 26.3 1.0
CB G:ASP216 4.3 27.3 1.0
N H:HIS382 4.5 27.9 1.0
CG G:ASP216 4.5 28.1 1.0
N H:GLY381 4.6 22.9 1.0
O H:HOH866 4.6 32.4 1.0
CG H:GLN65 4.6 25.4 1.0
OD1 G:ASP216 4.7 28.8 1.0
C H:PRO383 4.7 28.5 1.0
CA H:HIS382 4.7 29.0 1.0
CA H:GLY381 4.7 27.2 1.0
N H:SER384 4.8 27.5 1.0
CG2 H:THR380 4.9 27.7 1.0
OE1 H:GLN91 4.9 25.8 1.0
O G:ASP216 5.0 29.3 1.0

Potassium binding site 7 out of 8 in 8cfx

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Potassium binding site 7 out of 8 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K506

b:26.7
occ:1.00
OG1 I:THR380 2.7 29.8 1.0
O I:THR380 2.8 29.9 1.0
O I:HIS382 2.8 30.4 1.0
O I:HOH771 2.8 29.9 1.0
O I:HOH789 2.9 23.1 1.0
O J:HOH698 3.0 27.5 1.0
OE1 I:GLN65 3.2 25.1 1.0
NE2 I:GLN65 3.2 24.9 1.0
CD I:GLN65 3.4 28.2 1.0
CB I:THR380 3.5 32.6 1.0
C I:THR380 3.6 30.1 1.0
C I:HIS382 3.7 31.2 1.0
O I:GLY381 3.8 27.6 1.0
CA I:PRO383 4.1 26.4 1.0
N6 I:ADE502 4.1 26.7 1.0
C I:GLY381 4.1 29.1 1.0
CA I:THR380 4.2 28.2 1.0
N I:PRO383 4.3 26.3 1.0
CB J:ASP216 4.4 27.0 1.0
N I:HIS382 4.5 28.0 1.0
O I:HOH886 4.5 36.1 1.0
N I:GLY381 4.6 24.4 1.0
CG I:GLN65 4.6 24.0 1.0
CG J:ASP216 4.6 30.3 1.0
C I:PRO383 4.7 27.1 1.0
CA I:HIS382 4.7 26.8 1.0
OD1 J:ASP216 4.7 26.5 1.0
CA I:GLY381 4.8 25.5 1.0
CG2 I:THR380 4.8 31.4 1.0
N I:SER384 4.8 25.6 1.0
OE1 I:GLN91 4.8 32.2 1.0
O J:ASP216 5.0 28.4 1.0

Potassium binding site 8 out of 8 in 8cfx

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Potassium binding site 8 out of 8 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H06 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K505

b:27.3
occ:1.00
O J:THR380 2.7 28.6 1.0
O J:HIS382 2.7 28.6 1.0
OG1 J:THR380 2.8 23.4 1.0
O J:HOH772 2.8 28.8 1.0
O J:HOH740 2.9 27.3 1.0
OE1 J:GLN65 3.1 26.7 1.0
O I:HOH631 3.3 28.9 1.0
NE2 J:GLN65 3.4 25.3 1.0
CD J:GLN65 3.5 30.2 1.0
CB J:THR380 3.5 26.6 1.0
C J:THR380 3.6 28.9 1.0
C J:HIS382 3.6 28.6 1.0
O J:GLY381 3.7 25.5 1.0
CA J:PRO383 4.0 26.7 1.0
N6 J:ADE502 4.1 33.7 1.0
C J:GLY381 4.1 27.5 1.0
N J:PRO383 4.2 27.0 1.0
CA J:THR380 4.2 27.4 1.0
CB I:ASP216 4.4 27.4 1.0
O J:HOH831 4.5 31.3 1.0
N J:HIS382 4.5 27.9 1.0
N J:GLY381 4.6 26.1 1.0
CG I:ASP216 4.6 28.1 1.0
OD1 I:ASP216 4.7 29.4 1.0
CG J:GLN65 4.7 28.0 1.0
CA J:HIS382 4.7 28.1 1.0
C J:PRO383 4.7 26.4 1.0
CA J:GLY381 4.8 26.1 1.0
N J:SER384 4.8 28.9 1.0
CG2 J:THR380 4.8 27.7 1.0
OE1 J:GLN91 4.9 29.6 1.0
O I:ASP216 5.0 27.7 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 H06 To Be Published.
Page generated: Mon Aug 12 22:41:30 2024

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