Potassium in PDB 8cfu: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H02
Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H02
All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment H02:
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 H02, PDB code: 8cfu
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)
|
37.08 /
1.50
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.55,
133.9,
97.95,
90,
101.21,
90
|
R / Rfree (%)
|
15.4 /
18.8
|
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 H02
(pdb code 8cfu). 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 H02, PDB code: 8cfu:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 8cfu
Go back to
Potassium Binding Sites List in 8cfu
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 H02
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 H02 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K505
b:16.5
occ:1.00
|
O
|
A:THR380
|
2.7
|
17.1
|
1.0
|
O
|
A:HOH760
|
2.7
|
16.3
|
1.0
|
O
|
A:HIS382
|
2.8
|
15.4
|
1.0
|
OG1
|
A:THR380
|
2.8
|
17.0
|
1.0
|
O
|
A:HOH799
|
2.9
|
15.1
|
1.0
|
O
|
B:HOH799
|
3.1
|
17.2
|
1.0
|
OE1
|
A:GLN65
|
3.2
|
16.0
|
1.0
|
NE2
|
A:GLN65
|
3.4
|
16.3
|
1.0
|
CD
|
A:GLN65
|
3.4
|
16.7
|
1.0
|
CB
|
A:THR380
|
3.5
|
16.8
|
1.0
|
C
|
A:THR380
|
3.6
|
17.8
|
1.0
|
C
|
A:HIS382
|
3.6
|
15.6
|
1.0
|
O
|
A:GLY381
|
3.7
|
16.5
|
1.0
|
CA
|
A:PRO383
|
4.0
|
16.1
|
1.0
|
N6
|
A:ADE502
|
4.0
|
13.9
|
1.0
|
C
|
A:GLY381
|
4.1
|
15.5
|
1.0
|
CA
|
A:THR380
|
4.2
|
15.5
|
1.0
|
N
|
A:PRO383
|
4.2
|
15.3
|
1.0
|
CB
|
B:ASP216
|
4.3
|
17.2
|
1.0
|
O
|
A:HOH903
|
4.5
|
18.6
|
1.0
|
N
|
A:HIS382
|
4.5
|
14.5
|
1.0
|
N
|
A:GLY381
|
4.5
|
14.4
|
1.0
|
CG
|
B:ASP216
|
4.6
|
17.9
|
1.0
|
CG
|
A:GLN65
|
4.6
|
15.6
|
1.0
|
OD1
|
B:ASP216
|
4.7
|
17.3
|
1.0
|
CA
|
A:HIS382
|
4.7
|
15.7
|
1.0
|
C
|
A:PRO383
|
4.7
|
16.2
|
1.0
|
OE1
|
A:GLN91
|
4.8
|
16.8
|
1.0
|
CA
|
A:GLY381
|
4.8
|
15.0
|
1.0
|
CG2
|
A:THR380
|
4.8
|
17.9
|
1.0
|
N
|
A:SER384
|
4.8
|
15.7
|
1.0
|
O
|
B:ASP216
|
5.0
|
17.5
|
1.0
|
|
Potassium binding site 2 out
of 4 in 8cfu
Go back to
Potassium Binding Sites List in 8cfu
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 H02
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 H02 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K507
b:16.1
occ:1.00
|
O
|
B:THR380
|
2.8
|
15.3
|
1.0
|
O
|
B:HOH831
|
2.8
|
17.7
|
1.0
|
O
|
B:HIS382
|
2.8
|
15.9
|
1.0
|
OG1
|
B:THR380
|
2.8
|
16.1
|
1.0
|
O
|
B:HOH806
|
2.9
|
16.9
|
1.0
|
O
|
A:HOH786
|
3.1
|
16.1
|
1.0
|
OE1
|
B:GLN65
|
3.2
|
17.4
|
1.0
|
NE2
|
B:GLN65
|
3.3
|
16.0
|
1.0
|
CD
|
B:GLN65
|
3.4
|
16.9
|
1.0
|
CB
|
B:THR380
|
3.5
|
16.0
|
1.0
|
C
|
B:THR380
|
3.6
|
15.7
|
1.0
|
C
|
B:HIS382
|
3.7
|
15.3
|
1.0
|
O
|
B:GLY381
|
3.8
|
17.1
|
1.0
|
CA
|
B:PRO383
|
4.0
|
15.4
|
1.0
|
N6
|
B:ADE503
|
4.0
|
17.9
|
1.0
|
C
|
B:GLY381
|
4.1
|
16.9
|
1.0
|
CA
|
B:THR380
|
4.2
|
16.4
|
1.0
|
N
|
B:PRO383
|
4.2
|
14.2
|
1.0
|
CB
|
A:ASP216
|
4.3
|
16.6
|
1.0
|
O
|
B:HOH939
|
4.4
|
18.5
|
1.0
|
N
|
B:HIS382
|
4.5
|
13.9
|
1.0
|
CG
|
A:ASP216
|
4.5
|
16.6
|
1.0
|
N
|
B:GLY381
|
4.6
|
15.8
|
1.0
|
OD1
|
A:ASP216
|
4.6
|
17.1
|
1.0
|
CG
|
B:GLN65
|
4.6
|
15.8
|
1.0
|
C
|
B:PRO383
|
4.7
|
16.3
|
1.0
|
N
|
B:SER384
|
4.7
|
16.1
|
1.0
|
CA
|
B:HIS382
|
4.7
|
16.9
|
1.0
|
CA
|
B:GLY381
|
4.8
|
15.6
|
1.0
|
CG2
|
B:THR380
|
4.8
|
17.9
|
1.0
|
OE1
|
B:GLN91
|
4.9
|
17.0
|
1.0
|
O
|
A:ASP216
|
5.0
|
16.7
|
1.0
|
|
Potassium binding site 3 out
of 4 in 8cfu
Go back to
Potassium Binding Sites List in 8cfu
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 H02
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 H02 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K504
b:19.3
occ:1.00
|
O
|
C:THR380
|
2.7
|
20.9
|
1.0
|
O
|
C:HIS382
|
2.8
|
18.9
|
1.0
|
O
|
C:HOH798
|
2.8
|
22.0
|
1.0
|
O
|
C:HOH799
|
2.8
|
20.1
|
1.0
|
OG1
|
C:THR380
|
2.8
|
20.7
|
1.0
|
O
|
D:HOH657
|
3.1
|
21.0
|
1.0
|
OE1
|
C:GLN65
|
3.2
|
23.4
|
1.0
|
NE2
|
C:GLN65
|
3.4
|
22.1
|
1.0
|
CD
|
C:GLN65
|
3.5
|
22.2
|
1.0
|
CB
|
C:THR380
|
3.5
|
20.1
|
1.0
|
C
|
C:THR380
|
3.6
|
19.5
|
1.0
|
C
|
C:HIS382
|
3.6
|
20.2
|
1.0
|
O
|
C:GLY381
|
3.8
|
20.2
|
1.0
|
CA
|
C:PRO383
|
4.0
|
18.7
|
1.0
|
N6
|
C:ADE502
|
4.1
|
20.2
|
1.0
|
C
|
C:GLY381
|
4.1
|
20.5
|
1.0
|
CA
|
C:THR380
|
4.2
|
21.0
|
1.0
|
N
|
C:PRO383
|
4.2
|
18.0
|
1.0
|
CB
|
D:ASP216
|
4.3
|
18.0
|
1.0
|
N
|
C:HIS382
|
4.5
|
17.8
|
1.0
|
N
|
C:GLY381
|
4.5
|
19.8
|
1.0
|
O
|
C:HOH884
|
4.5
|
23.6
|
1.0
|
CG
|
D:ASP216
|
4.5
|
20.4
|
1.0
|
CG
|
C:GLN65
|
4.6
|
22.5
|
1.0
|
OD1
|
D:ASP216
|
4.6
|
21.1
|
1.0
|
CA
|
C:HIS382
|
4.7
|
19.4
|
1.0
|
C
|
C:PRO383
|
4.7
|
20.8
|
1.0
|
CA
|
C:GLY381
|
4.7
|
19.6
|
1.0
|
CG2
|
C:THR380
|
4.8
|
20.0
|
1.0
|
N
|
C:SER384
|
4.8
|
22.2
|
1.0
|
OE1
|
C:GLN91
|
4.9
|
25.9
|
1.0
|
O
|
D:ASP216
|
4.9
|
20.1
|
1.0
|
|
Potassium binding site 4 out
of 4 in 8cfu
Go back to
Potassium Binding Sites List in 8cfu
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 H02
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 H02 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K504
b:18.2
occ:0.95
|
O
|
D:HIS382
|
2.8
|
18.9
|
1.0
|
O
|
D:THR380
|
2.8
|
19.7
|
1.0
|
O
|
D:HOH708
|
2.8
|
22.4
|
1.0
|
OG1
|
D:THR380
|
2.8
|
20.2
|
1.0
|
O
|
D:HOH795
|
2.8
|
18.7
|
1.0
|
O
|
C:HOH768
|
3.1
|
19.2
|
1.0
|
OE1
|
D:GLN65
|
3.2
|
21.1
|
1.0
|
NE2
|
D:GLN65
|
3.4
|
19.8
|
1.0
|
CD
|
D:GLN65
|
3.4
|
20.9
|
1.0
|
CB
|
D:THR380
|
3.5
|
19.6
|
1.0
|
C
|
D:THR380
|
3.6
|
18.9
|
1.0
|
C
|
D:HIS382
|
3.6
|
18.9
|
1.0
|
O
|
D:GLY381
|
3.8
|
20.6
|
1.0
|
CA
|
D:PRO383
|
4.0
|
17.2
|
1.0
|
N6
|
D:ADE502
|
4.0
|
16.4
|
1.0
|
C
|
D:GLY381
|
4.1
|
18.9
|
1.0
|
N
|
D:PRO383
|
4.2
|
16.4
|
1.0
|
CA
|
D:THR380
|
4.2
|
18.9
|
1.0
|
CB
|
C:ASP216
|
4.2
|
20.3
|
1.0
|
O
|
D:HOH902
|
4.4
|
23.5
|
1.0
|
N
|
D:HIS382
|
4.5
|
16.3
|
1.0
|
CG
|
C:ASP216
|
4.5
|
21.4
|
1.0
|
N
|
D:GLY381
|
4.6
|
18.7
|
1.0
|
OD1
|
C:ASP216
|
4.6
|
21.6
|
1.0
|
CG
|
D:GLN65
|
4.6
|
19.3
|
1.0
|
C
|
D:PRO383
|
4.7
|
20.9
|
1.0
|
CA
|
D:HIS382
|
4.7
|
19.5
|
1.0
|
N
|
D:SER384
|
4.7
|
19.4
|
1.0
|
CG2
|
D:THR380
|
4.8
|
20.8
|
1.0
|
CA
|
D:GLY381
|
4.8
|
18.8
|
1.0
|
OE1
|
D:GLN91
|
4.8
|
22.1
|
1.0
|
O
|
C:ASP216
|
5.0
|
21.0
|
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 H02 To Be Published.
Page generated: Mon Aug 12 22:33:24 2024
|