Potassium in PDB 8cfp: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment F09
Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment F09
All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment F09:
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 F09, PDB code: 8cfp
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)
|
48.44 /
1.61
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
73.83,
132.89,
98.71,
90,
101.06,
90
|
R / Rfree (%)
|
15.8 /
18.9
|
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 F09
(pdb code 8cfp). 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 F09, PDB code: 8cfp:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 8cfp
Go back to
Potassium Binding Sites List in 8cfp
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 F09
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 F09 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K506
b:18.6
occ:1.00
|
O
|
A:THR380
|
2.6
|
18.8
|
1.0
|
O
|
A:HIS382
|
2.7
|
17.1
|
1.0
|
OG1
|
A:THR380
|
2.8
|
18.4
|
1.0
|
O
|
A:HOH685
|
2.8
|
16.8
|
1.0
|
O
|
A:HOH851
|
2.8
|
16.8
|
1.0
|
O
|
B:HOH788
|
3.1
|
16.4
|
1.0
|
OE1
|
A:GLN65
|
3.2
|
19.1
|
1.0
|
NE2
|
A:GLN65
|
3.4
|
16.2
|
1.0
|
CD
|
A:GLN65
|
3.5
|
16.3
|
1.0
|
CB
|
A:THR380
|
3.5
|
15.6
|
1.0
|
C
|
A:THR380
|
3.6
|
16.9
|
1.0
|
C
|
A:HIS382
|
3.6
|
17.5
|
1.0
|
O
|
A:GLY381
|
3.7
|
17.3
|
1.0
|
N6
|
A:ADE502
|
4.0
|
16.9
|
1.0
|
CA
|
A:PRO383
|
4.0
|
16.9
|
1.0
|
C
|
A:GLY381
|
4.0
|
16.9
|
1.0
|
N
|
A:PRO383
|
4.2
|
18.8
|
1.0
|
CA
|
A:THR380
|
4.2
|
17.0
|
1.0
|
CB
|
B:ASP216
|
4.3
|
16.4
|
1.0
|
O
|
A:HOH906
|
4.4
|
23.0
|
1.0
|
N
|
A:HIS382
|
4.4
|
17.0
|
1.0
|
N
|
A:GLY381
|
4.5
|
17.0
|
1.0
|
CG
|
A:GLN65
|
4.6
|
16.5
|
1.0
|
CG
|
B:ASP216
|
4.6
|
17.2
|
1.0
|
CA
|
A:HIS382
|
4.7
|
18.3
|
1.0
|
CA
|
A:GLY381
|
4.7
|
15.8
|
1.0
|
OD1
|
B:ASP216
|
4.7
|
17.2
|
1.0
|
C
|
A:PRO383
|
4.7
|
18.4
|
1.0
|
OE1
|
A:GLN91
|
4.8
|
20.2
|
1.0
|
N
|
A:SER384
|
4.8
|
17.7
|
1.0
|
CG2
|
A:THR380
|
4.8
|
14.7
|
1.0
|
O
|
B:ASP216
|
5.0
|
17.8
|
1.0
|
|
Potassium binding site 2 out
of 4 in 8cfp
Go back to
Potassium Binding Sites List in 8cfp
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 F09
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 F09 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K508
b:16.8
occ:1.00
|
O
|
B:THR380
|
2.7
|
16.0
|
1.0
|
O
|
B:HOH750
|
2.8
|
18.0
|
1.0
|
O
|
B:HIS382
|
2.8
|
16.4
|
1.0
|
OG1
|
B:THR380
|
2.8
|
17.2
|
1.0
|
O
|
B:HOH815
|
2.8
|
15.6
|
1.0
|
O
|
A:HOH781
|
3.1
|
18.5
|
1.0
|
OE1
|
B:GLN65
|
3.2
|
17.3
|
1.0
|
CB
|
B:THR380
|
3.4
|
15.3
|
1.0
|
NE2
|
B:GLN65
|
3.4
|
17.6
|
1.0
|
CD
|
B:GLN65
|
3.5
|
17.3
|
1.0
|
C
|
B:THR380
|
3.6
|
17.3
|
1.0
|
C
|
B:HIS382
|
3.6
|
17.7
|
1.0
|
O
|
B:GLY381
|
3.8
|
17.1
|
1.0
|
CA
|
B:PRO383
|
4.0
|
15.7
|
1.0
|
C
|
B:GLY381
|
4.1
|
16.6
|
1.0
|
N6
|
B:ADE503
|
4.1
|
20.3
|
1.0
|
CA
|
B:THR380
|
4.2
|
17.5
|
1.0
|
N
|
B:PRO383
|
4.2
|
15.1
|
1.0
|
CB
|
A:ASP216
|
4.3
|
17.9
|
1.0
|
O
|
B:HOH933
|
4.4
|
17.8
|
1.0
|
N
|
B:HIS382
|
4.5
|
16.7
|
1.0
|
CG
|
A:ASP216
|
4.5
|
20.0
|
1.0
|
N
|
B:GLY381
|
4.6
|
14.9
|
1.0
|
OD1
|
A:ASP216
|
4.6
|
18.1
|
1.0
|
CG
|
B:GLN65
|
4.7
|
16.3
|
1.0
|
C
|
B:PRO383
|
4.7
|
16.9
|
1.0
|
CA
|
B:HIS382
|
4.7
|
17.3
|
1.0
|
CA
|
B:GLY381
|
4.7
|
16.4
|
1.0
|
CG2
|
B:THR380
|
4.7
|
17.6
|
1.0
|
N
|
B:SER384
|
4.7
|
17.6
|
1.0
|
OE1
|
B:GLN91
|
4.8
|
18.0
|
1.0
|
O
|
A:ASP216
|
5.0
|
16.2
|
1.0
|
|
Potassium binding site 3 out
of 4 in 8cfp
Go back to
Potassium Binding Sites List in 8cfp
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 F09
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 F09 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K504
b:19.6
occ:1.00
|
O
|
C:HOH707
|
2.7
|
20.2
|
1.0
|
O
|
C:THR380
|
2.8
|
19.6
|
1.0
|
O
|
C:HOH705
|
2.8
|
19.3
|
1.0
|
OG1
|
C:THR380
|
2.8
|
20.1
|
1.0
|
O
|
C:HIS382
|
2.8
|
17.5
|
1.0
|
O
|
D:HOH700
|
3.1
|
20.1
|
1.0
|
OE1
|
C:GLN65
|
3.3
|
19.9
|
1.0
|
NE2
|
C:GLN65
|
3.4
|
20.0
|
1.0
|
CB
|
C:THR380
|
3.5
|
15.9
|
1.0
|
CD
|
C:GLN65
|
3.5
|
20.4
|
1.0
|
C
|
C:THR380
|
3.6
|
17.4
|
1.0
|
C
|
C:HIS382
|
3.7
|
17.1
|
1.0
|
O
|
C:GLY381
|
3.8
|
16.3
|
1.0
|
CA
|
C:PRO383
|
4.0
|
19.0
|
1.0
|
N6
|
C:ADE502
|
4.1
|
22.3
|
1.0
|
C
|
C:GLY381
|
4.1
|
17.1
|
1.0
|
CA
|
C:THR380
|
4.2
|
18.5
|
1.0
|
N
|
C:PRO383
|
4.2
|
16.5
|
1.0
|
CB
|
D:ASP216
|
4.2
|
18.6
|
1.0
|
O
|
C:HOH903
|
4.5
|
23.3
|
1.0
|
N
|
C:GLY381
|
4.5
|
18.4
|
1.0
|
N
|
C:HIS382
|
4.5
|
17.2
|
1.0
|
CG
|
D:ASP216
|
4.5
|
18.3
|
1.0
|
CG
|
C:GLN65
|
4.6
|
20.6
|
1.0
|
OD1
|
D:ASP216
|
4.7
|
18.0
|
1.0
|
C
|
C:PRO383
|
4.7
|
21.0
|
1.0
|
OE1
|
C:GLN91
|
4.7
|
23.1
|
1.0
|
CG2
|
C:THR380
|
4.7
|
17.6
|
1.0
|
CA
|
C:HIS382
|
4.7
|
16.5
|
1.0
|
N
|
C:SER384
|
4.8
|
17.6
|
1.0
|
CA
|
C:GLY381
|
4.8
|
17.6
|
1.0
|
O
|
D:ASP216
|
4.9
|
18.5
|
1.0
|
|
Potassium binding site 4 out
of 4 in 8cfp
Go back to
Potassium Binding Sites List in 8cfp
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 F09
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 F09 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K505
b:18.2
occ:1.00
|
O
|
D:THR380
|
2.7
|
19.4
|
1.0
|
O
|
D:HOH768
|
2.8
|
18.9
|
1.0
|
OG1
|
D:THR380
|
2.8
|
17.9
|
1.0
|
O
|
D:HIS382
|
2.8
|
18.0
|
1.0
|
O
|
D:HOH851
|
2.8
|
18.0
|
1.0
|
O
|
C:HOH750
|
3.1
|
18.3
|
1.0
|
OE1
|
D:GLN65
|
3.3
|
19.4
|
1.0
|
NE2
|
D:GLN65
|
3.4
|
16.3
|
1.0
|
CB
|
D:THR380
|
3.5
|
21.4
|
1.0
|
CD
|
D:GLN65
|
3.5
|
19.4
|
1.0
|
C
|
D:THR380
|
3.6
|
18.7
|
1.0
|
C
|
D:HIS382
|
3.6
|
19.9
|
1.0
|
O
|
D:GLY381
|
3.8
|
18.5
|
1.0
|
CA
|
D:PRO383
|
4.0
|
17.3
|
1.0
|
N6
|
D:ADE502
|
4.1
|
17.9
|
1.0
|
C
|
D:GLY381
|
4.1
|
17.2
|
1.0
|
CA
|
D:THR380
|
4.2
|
19.5
|
1.0
|
N
|
D:PRO383
|
4.2
|
18.1
|
1.0
|
CB
|
C:ASP216
|
4.3
|
21.1
|
1.0
|
O
|
D:HOH918
|
4.4
|
22.4
|
1.0
|
N
|
D:HIS382
|
4.5
|
17.6
|
1.0
|
CG
|
C:ASP216
|
4.5
|
21.1
|
1.0
|
OD1
|
C:ASP216
|
4.6
|
21.2
|
1.0
|
N
|
D:GLY381
|
4.6
|
19.2
|
1.0
|
CG
|
D:GLN65
|
4.6
|
18.4
|
1.0
|
CA
|
D:HIS382
|
4.7
|
19.8
|
1.0
|
C
|
D:PRO383
|
4.7
|
17.0
|
1.0
|
CG2
|
D:THR380
|
4.7
|
19.4
|
1.0
|
N
|
D:SER384
|
4.8
|
17.8
|
1.0
|
CA
|
D:GLY381
|
4.8
|
16.6
|
1.0
|
OE1
|
D:GLN91
|
4.8
|
21.5
|
1.0
|
O
|
C:ASP216
|
4.9
|
18.2
|
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 F09 To Be Published.
Page generated: Mon Aug 12 22:31:06 2024
|