Potassium in PDB 8cfg: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment C04
Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment C04
All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment C04:
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 C04, PDB code: 8cfg
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)
|
37.12 /
1.73
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.94,
132.8,
98.78,
90,
101.13,
90
|
R / Rfree (%)
|
16.2 /
20.1
|
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 C04
(pdb code 8cfg). 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 C04, PDB code: 8cfg:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 8cfg
Go back to
Potassium Binding Sites List in 8cfg
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 C04
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 C04 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K504
b:20.4
occ:1.00
|
O
|
A:THR380
|
2.7
|
19.7
|
1.0
|
O
|
A:HIS382
|
2.7
|
20.1
|
1.0
|
O
|
A:HOH655
|
2.9
|
20.0
|
1.0
|
O
|
A:HOH792
|
2.9
|
17.1
|
1.0
|
OG1
|
A:THR380
|
2.9
|
17.4
|
1.0
|
O
|
B:HOH784
|
3.1
|
20.4
|
1.0
|
OE1
|
A:GLN65
|
3.2
|
21.1
|
1.0
|
NE2
|
A:GLN65
|
3.3
|
19.3
|
1.0
|
CD
|
A:GLN65
|
3.4
|
21.9
|
1.0
|
CB
|
A:THR380
|
3.5
|
16.5
|
1.0
|
C
|
A:THR380
|
3.6
|
16.5
|
1.0
|
C
|
A:HIS382
|
3.6
|
16.9
|
1.0
|
O
|
A:GLY381
|
3.8
|
18.2
|
1.0
|
N6
|
A:ADE502
|
4.0
|
18.0
|
1.0
|
CA
|
A:PRO383
|
4.0
|
19.3
|
1.0
|
C
|
A:GLY381
|
4.1
|
17.0
|
1.0
|
N
|
A:PRO383
|
4.2
|
17.6
|
1.0
|
CA
|
A:THR380
|
4.2
|
15.2
|
1.0
|
CB
|
B:ASP216
|
4.3
|
17.1
|
1.0
|
N
|
A:HIS382
|
4.5
|
18.2
|
1.0
|
O
|
A:HOH902
|
4.5
|
21.1
|
1.0
|
N
|
A:GLY381
|
4.5
|
17.8
|
1.0
|
CG
|
A:GLN65
|
4.6
|
20.2
|
1.0
|
CG
|
B:ASP216
|
4.6
|
19.5
|
1.0
|
CA
|
A:HIS382
|
4.7
|
20.9
|
1.0
|
OD1
|
B:ASP216
|
4.7
|
20.1
|
1.0
|
CA
|
A:GLY381
|
4.7
|
16.8
|
1.0
|
C
|
A:PRO383
|
4.7
|
20.7
|
1.0
|
N
|
A:SER384
|
4.8
|
19.9
|
1.0
|
OE1
|
A:GLN91
|
4.8
|
19.6
|
1.0
|
CG2
|
A:THR380
|
4.8
|
18.5
|
1.0
|
|
Potassium binding site 2 out
of 4 in 8cfg
Go back to
Potassium Binding Sites List in 8cfg
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 C04
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 C04 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K506
b:19.6
occ:1.00
|
O
|
B:THR380
|
2.7
|
19.6
|
1.0
|
O
|
B:HIS382
|
2.7
|
20.1
|
1.0
|
O
|
B:HOH727
|
2.8
|
22.0
|
1.0
|
OG1
|
B:THR380
|
2.8
|
19.6
|
1.0
|
O
|
B:HOH766
|
2.8
|
18.1
|
1.0
|
O
|
A:HOH768
|
3.0
|
20.1
|
1.0
|
OE1
|
B:GLN65
|
3.2
|
19.1
|
1.0
|
NE2
|
B:GLN65
|
3.4
|
16.5
|
1.0
|
CB
|
B:THR380
|
3.4
|
20.5
|
1.0
|
CD
|
B:GLN65
|
3.4
|
21.2
|
1.0
|
C
|
B:THR380
|
3.6
|
18.8
|
1.0
|
C
|
B:HIS382
|
3.6
|
18.4
|
1.0
|
O
|
B:GLY381
|
3.8
|
19.3
|
1.0
|
CA
|
B:PRO383
|
4.0
|
15.6
|
1.0
|
N6
|
B:ADE503
|
4.0
|
19.8
|
1.0
|
C
|
B:GLY381
|
4.1
|
21.9
|
1.0
|
N
|
B:PRO383
|
4.2
|
19.5
|
1.0
|
CA
|
B:THR380
|
4.2
|
18.2
|
1.0
|
CB
|
A:ASP216
|
4.3
|
18.9
|
1.0
|
O
|
B:HOH918
|
4.4
|
20.0
|
1.0
|
N
|
B:HIS382
|
4.5
|
21.6
|
1.0
|
CG
|
A:ASP216
|
4.6
|
20.2
|
1.0
|
N
|
B:GLY381
|
4.6
|
16.9
|
1.0
|
CG
|
B:GLN65
|
4.6
|
16.0
|
1.0
|
OD1
|
A:ASP216
|
4.6
|
21.0
|
1.0
|
C
|
B:PRO383
|
4.7
|
19.9
|
1.0
|
CA
|
B:HIS382
|
4.7
|
20.8
|
1.0
|
CG2
|
B:THR380
|
4.7
|
20.4
|
1.0
|
N
|
B:SER384
|
4.8
|
16.4
|
1.0
|
CA
|
B:GLY381
|
4.8
|
17.9
|
1.0
|
OE1
|
B:GLN91
|
4.9
|
19.2
|
1.0
|
O
|
A:ASP216
|
5.0
|
17.5
|
1.0
|
|
Potassium binding site 3 out
of 4 in 8cfg
Go back to
Potassium Binding Sites List in 8cfg
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 C04
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 C04 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K503
b:23.2
occ:1.00
|
O
|
C:THR380
|
2.8
|
21.8
|
1.0
|
OG1
|
C:THR380
|
2.8
|
23.1
|
1.0
|
O
|
C:HOH755
|
2.8
|
22.3
|
1.0
|
O
|
C:HIS382
|
2.8
|
21.5
|
1.0
|
O
|
C:HOH796
|
2.8
|
23.7
|
1.0
|
OE1
|
C:GLN65
|
3.2
|
22.5
|
1.0
|
O
|
D:HOH666
|
3.3
|
22.3
|
1.0
|
NE2
|
C:GLN65
|
3.4
|
20.9
|
1.0
|
CD
|
C:GLN65
|
3.5
|
23.7
|
1.0
|
CB
|
C:THR380
|
3.5
|
23.5
|
1.0
|
C
|
C:THR380
|
3.6
|
21.0
|
1.0
|
C
|
C:HIS382
|
3.7
|
20.4
|
1.0
|
O
|
C:GLY381
|
3.8
|
20.8
|
1.0
|
CA
|
C:PRO383
|
4.0
|
22.8
|
1.0
|
N6
|
C:ADE502
|
4.0
|
23.4
|
1.0
|
C
|
C:GLY381
|
4.1
|
22.7
|
1.0
|
N
|
C:PRO383
|
4.2
|
22.9
|
1.0
|
CA
|
C:THR380
|
4.2
|
19.0
|
1.0
|
CB
|
D:ASP216
|
4.3
|
24.6
|
1.0
|
O
|
C:HOH862
|
4.5
|
29.0
|
1.0
|
N
|
C:HIS382
|
4.5
|
19.5
|
1.0
|
N
|
C:GLY381
|
4.5
|
22.6
|
1.0
|
CG
|
D:ASP216
|
4.6
|
25.4
|
1.0
|
CG
|
C:GLN65
|
4.7
|
23.9
|
1.0
|
OD1
|
D:ASP216
|
4.7
|
21.4
|
1.0
|
C
|
C:PRO383
|
4.7
|
24.8
|
1.0
|
CA
|
C:HIS382
|
4.7
|
18.9
|
1.0
|
CA
|
C:GLY381
|
4.7
|
23.1
|
1.0
|
CG2
|
C:THR380
|
4.8
|
21.5
|
1.0
|
N
|
C:SER384
|
4.8
|
20.8
|
1.0
|
OE1
|
C:GLN91
|
4.8
|
27.9
|
1.0
|
O
|
D:ASP216
|
4.9
|
23.2
|
1.0
|
|
Potassium binding site 4 out
of 4 in 8cfg
Go back to
Potassium Binding Sites List in 8cfg
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 C04
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 C04 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K504
b:21.9
occ:0.96
|
O
|
D:THR380
|
2.7
|
21.6
|
1.0
|
O
|
D:HIS382
|
2.7
|
21.6
|
1.0
|
O
|
D:HOH793
|
2.8
|
19.6
|
1.0
|
OG1
|
D:THR380
|
2.8
|
20.8
|
1.0
|
O
|
D:HOH811
|
2.9
|
21.2
|
1.0
|
O
|
C:HOH730
|
3.1
|
19.2
|
1.0
|
OE1
|
D:GLN65
|
3.2
|
22.2
|
1.0
|
NE2
|
D:GLN65
|
3.4
|
22.6
|
1.0
|
CB
|
D:THR380
|
3.5
|
23.0
|
1.0
|
CD
|
D:GLN65
|
3.5
|
21.6
|
1.0
|
C
|
D:THR380
|
3.6
|
22.7
|
1.0
|
C
|
D:HIS382
|
3.6
|
22.1
|
1.0
|
O
|
D:GLY381
|
3.8
|
21.0
|
1.0
|
CA
|
D:PRO383
|
4.0
|
23.8
|
1.0
|
N6
|
D:ADE502
|
4.0
|
21.9
|
1.0
|
C
|
D:GLY381
|
4.1
|
21.7
|
1.0
|
N
|
D:PRO383
|
4.2
|
19.5
|
1.0
|
CA
|
D:THR380
|
4.2
|
21.8
|
1.0
|
CB
|
C:ASP216
|
4.3
|
17.9
|
1.0
|
O
|
D:HOH905
|
4.4
|
27.4
|
1.0
|
N
|
D:HIS382
|
4.5
|
20.8
|
1.0
|
CG
|
C:ASP216
|
4.6
|
23.4
|
1.0
|
N
|
D:GLY381
|
4.6
|
22.8
|
1.0
|
OD1
|
C:ASP216
|
4.6
|
20.9
|
1.0
|
CG
|
D:GLN65
|
4.7
|
21.5
|
1.0
|
C
|
D:PRO383
|
4.7
|
22.8
|
1.0
|
CA
|
D:HIS382
|
4.7
|
21.6
|
1.0
|
N
|
D:SER384
|
4.7
|
19.5
|
1.0
|
CG2
|
D:THR380
|
4.7
|
23.4
|
1.0
|
CA
|
D:GLY381
|
4.8
|
20.2
|
1.0
|
OE1
|
D:GLN91
|
4.8
|
27.1
|
1.0
|
O
|
C:ASP216
|
4.9
|
23.7
|
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 C04 To Be Published.
Page generated: Mon Aug 12 22:26:15 2024
|