Potassium in PDB 8cfv: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H04
Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H04
All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H04:
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 H04, PDB code: 8cfv
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)
|
48.50 /
1.88
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.019,
132.869,
98.904,
90,
101.2,
90
|
R / Rfree (%)
|
16 /
20.2
|
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 H04
(pdb code 8cfv). 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 H04, PDB code: 8cfv:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 8cfv
Go back to
Potassium Binding Sites List in 8cfv
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 H04
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 H04 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K504
b:24.6
occ:1.00
|
O
|
A:THR380
|
2.7
|
22.4
|
1.0
|
O
|
A:HIS382
|
2.7
|
22.6
|
1.0
|
OG1
|
A:THR380
|
2.8
|
21.0
|
1.0
|
O
|
A:HOH824
|
2.9
|
23.4
|
1.0
|
O
|
A:HOH631
|
2.9
|
22.1
|
1.0
|
O
|
B:HOH796
|
3.2
|
24.6
|
1.0
|
OE1
|
A:GLN65
|
3.2
|
26.4
|
1.0
|
NE2
|
A:GLN65
|
3.5
|
22.1
|
1.0
|
CD
|
A:GLN65
|
3.5
|
24.3
|
1.0
|
CB
|
A:THR380
|
3.5
|
23.6
|
1.0
|
C
|
A:THR380
|
3.6
|
23.2
|
1.0
|
C
|
A:HIS382
|
3.6
|
22.6
|
1.0
|
O
|
A:GLY381
|
3.8
|
21.9
|
1.0
|
CA
|
A:PRO383
|
4.0
|
24.2
|
1.0
|
N6
|
A:ADE502
|
4.0
|
23.6
|
1.0
|
C
|
A:GLY381
|
4.1
|
22.4
|
1.0
|
N
|
A:PRO383
|
4.2
|
24.0
|
1.0
|
CA
|
A:THR380
|
4.2
|
23.6
|
1.0
|
CB
|
B:ASP216
|
4.3
|
22.7
|
1.0
|
O
|
A:HOH863
|
4.4
|
25.1
|
1.0
|
N
|
A:HIS382
|
4.5
|
24.3
|
1.0
|
N
|
A:GLY381
|
4.5
|
21.1
|
1.0
|
CG
|
B:ASP216
|
4.5
|
24.7
|
1.0
|
CG
|
A:GLN65
|
4.6
|
20.9
|
1.0
|
OD1
|
B:ASP216
|
4.6
|
22.1
|
1.0
|
CA
|
A:HIS382
|
4.6
|
24.3
|
1.0
|
C
|
A:PRO383
|
4.7
|
26.9
|
1.0
|
CA
|
A:GLY381
|
4.7
|
24.3
|
1.0
|
OE1
|
A:GLN91
|
4.8
|
25.8
|
1.0
|
N
|
A:SER384
|
4.8
|
21.5
|
1.0
|
CG2
|
A:THR380
|
4.8
|
21.9
|
1.0
|
O
|
B:ASP216
|
5.0
|
26.7
|
1.0
|
|
Potassium binding site 2 out
of 4 in 8cfv
Go back to
Potassium Binding Sites List in 8cfv
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 H04
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 H04 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K507
b:22.9
occ:1.00
|
O
|
B:THR380
|
2.7
|
21.9
|
1.0
|
O
|
B:HIS382
|
2.8
|
21.6
|
1.0
|
OG1
|
B:THR380
|
2.8
|
21.7
|
1.0
|
O
|
B:HOH820
|
2.8
|
20.9
|
1.0
|
O
|
B:HOH708
|
2.8
|
23.9
|
1.0
|
O
|
A:HOH724
|
3.2
|
24.2
|
1.0
|
OE1
|
B:GLN65
|
3.2
|
21.9
|
1.0
|
NE2
|
B:GLN65
|
3.4
|
23.8
|
1.0
|
CD
|
B:GLN65
|
3.4
|
23.9
|
1.0
|
CB
|
B:THR380
|
3.5
|
24.0
|
1.0
|
C
|
B:THR380
|
3.6
|
23.0
|
1.0
|
C
|
B:HIS382
|
3.6
|
21.1
|
1.0
|
O
|
B:GLY381
|
3.9
|
23.9
|
1.0
|
N6
|
B:ADE503
|
4.0
|
23.7
|
1.0
|
CA
|
B:PRO383
|
4.0
|
18.8
|
1.0
|
C
|
B:GLY381
|
4.1
|
23.3
|
1.0
|
CA
|
B:THR380
|
4.2
|
18.8
|
1.0
|
N
|
B:PRO383
|
4.2
|
22.0
|
1.0
|
CB
|
A:ASP216
|
4.3
|
21.7
|
1.0
|
O
|
B:HOH887
|
4.4
|
26.6
|
1.0
|
N
|
B:HIS382
|
4.5
|
24.6
|
1.0
|
N
|
B:GLY381
|
4.6
|
19.8
|
1.0
|
CG
|
A:ASP216
|
4.6
|
23.2
|
1.0
|
CG
|
B:GLN65
|
4.6
|
22.7
|
1.0
|
C
|
B:PRO383
|
4.7
|
21.9
|
1.0
|
OD1
|
A:ASP216
|
4.7
|
22.9
|
1.0
|
CA
|
B:HIS382
|
4.7
|
22.8
|
1.0
|
N
|
B:SER384
|
4.7
|
21.3
|
1.0
|
CG2
|
B:THR380
|
4.8
|
22.6
|
1.0
|
CA
|
B:GLY381
|
4.8
|
23.0
|
1.0
|
OE1
|
B:GLN91
|
4.8
|
24.6
|
1.0
|
O
|
A:ASP216
|
5.0
|
21.3
|
1.0
|
|
Potassium binding site 3 out
of 4 in 8cfv
Go back to
Potassium Binding Sites List in 8cfv
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 H04
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 H04 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K503
b:30.5
occ:1.00
|
O
|
C:THR380
|
2.7
|
25.8
|
1.0
|
O
|
C:HOH722
|
2.7
|
24.3
|
1.0
|
O
|
C:HOH769
|
2.8
|
27.3
|
1.0
|
OG1
|
C:THR380
|
2.8
|
23.1
|
1.0
|
O
|
C:HIS382
|
2.9
|
24.1
|
1.0
|
O
|
D:HOH626
|
3.2
|
26.9
|
1.0
|
OE1
|
C:GLN65
|
3.3
|
26.1
|
1.0
|
NE2
|
C:GLN65
|
3.4
|
22.1
|
1.0
|
CB
|
C:THR380
|
3.5
|
26.4
|
1.0
|
CD
|
C:GLN65
|
3.5
|
25.8
|
1.0
|
C
|
C:THR380
|
3.6
|
26.7
|
1.0
|
C
|
C:HIS382
|
3.7
|
24.9
|
1.0
|
O
|
C:GLY381
|
3.8
|
24.4
|
1.0
|
CA
|
C:PRO383
|
4.0
|
27.0
|
1.0
|
C
|
C:GLY381
|
4.1
|
27.7
|
1.0
|
N6
|
C:ADE502
|
4.1
|
36.9
|
1.0
|
CA
|
C:THR380
|
4.2
|
25.2
|
1.0
|
N
|
C:PRO383
|
4.2
|
26.6
|
1.0
|
CB
|
D:ASP216
|
4.3
|
25.7
|
1.0
|
N
|
C:GLY381
|
4.5
|
25.1
|
1.0
|
N
|
C:HIS382
|
4.5
|
23.9
|
1.0
|
CG
|
D:ASP216
|
4.5
|
28.1
|
1.0
|
O
|
C:HOH844
|
4.6
|
32.4
|
1.0
|
CG
|
C:GLN65
|
4.7
|
25.9
|
1.0
|
OE1
|
C:GLN91
|
4.7
|
29.9
|
1.0
|
OD1
|
D:ASP216
|
4.7
|
27.1
|
1.0
|
CA
|
C:GLY381
|
4.7
|
24.0
|
1.0
|
C
|
C:PRO383
|
4.7
|
27.1
|
1.0
|
CA
|
C:HIS382
|
4.7
|
24.0
|
1.0
|
CG2
|
C:THR380
|
4.8
|
25.8
|
1.0
|
N
|
C:SER384
|
4.8
|
26.9
|
1.0
|
O
|
D:ASP216
|
4.9
|
26.6
|
1.0
|
|
Potassium binding site 4 out
of 4 in 8cfv
Go back to
Potassium Binding Sites List in 8cfv
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 H04
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 H04 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K504
b:25.3
occ:1.00
|
O
|
D:THR380
|
2.7
|
27.7
|
1.0
|
O
|
D:HIS382
|
2.8
|
26.1
|
1.0
|
OG1
|
D:THR380
|
2.8
|
25.1
|
1.0
|
O
|
D:HOH756
|
2.8
|
26.3
|
1.0
|
O
|
D:HOH829
|
2.8
|
21.4
|
1.0
|
O
|
C:HOH715
|
3.0
|
23.0
|
1.0
|
OE1
|
D:GLN65
|
3.2
|
24.8
|
1.0
|
NE2
|
D:GLN65
|
3.4
|
22.6
|
1.0
|
CB
|
D:THR380
|
3.4
|
28.5
|
1.0
|
CD
|
D:GLN65
|
3.5
|
26.8
|
1.0
|
C
|
D:THR380
|
3.6
|
29.6
|
1.0
|
C
|
D:HIS382
|
3.6
|
25.7
|
1.0
|
O
|
D:GLY381
|
3.9
|
25.3
|
1.0
|
CA
|
D:PRO383
|
4.0
|
22.2
|
1.0
|
N6
|
D:ADE502
|
4.1
|
26.1
|
1.0
|
C
|
D:GLY381
|
4.1
|
23.2
|
1.0
|
CA
|
D:THR380
|
4.1
|
27.5
|
1.0
|
N
|
D:PRO383
|
4.2
|
25.1
|
1.0
|
O
|
D:HOH874
|
4.3
|
32.7
|
1.0
|
CB
|
C:ASP216
|
4.3
|
22.7
|
1.0
|
N
|
D:HIS382
|
4.5
|
25.7
|
1.0
|
N
|
D:GLY381
|
4.5
|
24.4
|
1.0
|
CG
|
C:ASP216
|
4.6
|
24.7
|
1.0
|
OD1
|
C:ASP216
|
4.6
|
24.5
|
1.0
|
CG
|
D:GLN65
|
4.7
|
21.1
|
1.0
|
CA
|
D:HIS382
|
4.7
|
25.0
|
1.0
|
CG2
|
D:THR380
|
4.7
|
26.0
|
1.0
|
C
|
D:PRO383
|
4.7
|
23.8
|
1.0
|
OE1
|
D:GLN91
|
4.7
|
27.0
|
1.0
|
CA
|
D:GLY381
|
4.8
|
23.7
|
1.0
|
N
|
D:SER384
|
4.8
|
25.9
|
1.0
|
O
|
C:ASP216
|
4.9
|
26.2
|
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 H04 To Be Published.
Page generated: Mon Aug 12 22:33:36 2024
|