Potassium in PDB 8cfm: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment E08
Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment E08
All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From P. Aeruginosa in Complex with F2X-Entry Library Fragment E08:
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 E08, PDB code: 8cfm
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)
|
36.37 /
1.84
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.05,
133.22,
98.28,
90,
100.94,
90
|
R / Rfree (%)
|
16.7 /
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 E08
(pdb code 8cfm). 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 E08, PDB code: 8cfm:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 8cfm
Go back to
Potassium Binding Sites List in 8cfm
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 E08
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 E08 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K504
b:24.3
occ:1.00
|
O
|
A:THR380
|
2.7
|
20.8
|
1.0
|
O
|
A:HOH739
|
2.8
|
21.3
|
1.0
|
O
|
A:HIS382
|
2.8
|
22.6
|
1.0
|
O
|
A:HOH654
|
2.8
|
22.0
|
1.0
|
OG1
|
A:THR380
|
2.9
|
23.1
|
1.0
|
O
|
B:HOH821
|
3.0
|
22.2
|
1.0
|
OE1
|
A:GLN65
|
3.2
|
21.2
|
1.0
|
NE2
|
A:GLN65
|
3.4
|
22.5
|
1.0
|
CB
|
A:THR380
|
3.5
|
25.1
|
1.0
|
CD
|
A:GLN65
|
3.5
|
24.2
|
1.0
|
C
|
A:THR380
|
3.6
|
23.9
|
1.0
|
C
|
A:HIS382
|
3.6
|
22.4
|
1.0
|
O
|
A:GLY381
|
3.7
|
22.0
|
1.0
|
CA
|
A:PRO383
|
4.0
|
24.6
|
1.0
|
N6
|
A:ADE502
|
4.1
|
23.0
|
1.0
|
C
|
A:GLY381
|
4.1
|
20.4
|
1.0
|
CA
|
A:THR380
|
4.2
|
23.4
|
1.0
|
N
|
A:PRO383
|
4.2
|
23.3
|
1.0
|
CB
|
B:ASP216
|
4.3
|
22.4
|
1.0
|
N
|
A:HIS382
|
4.5
|
21.6
|
1.0
|
O
|
A:HOH884
|
4.5
|
23.9
|
1.0
|
N
|
A:GLY381
|
4.5
|
20.6
|
1.0
|
CG
|
B:ASP216
|
4.6
|
24.1
|
1.0
|
CG
|
A:GLN65
|
4.6
|
20.4
|
1.0
|
OD1
|
B:ASP216
|
4.7
|
22.6
|
1.0
|
CA
|
A:HIS382
|
4.7
|
22.7
|
1.0
|
CA
|
A:GLY381
|
4.7
|
22.1
|
1.0
|
C
|
A:PRO383
|
4.7
|
25.6
|
1.0
|
OE1
|
A:GLN91
|
4.8
|
23.6
|
1.0
|
CG2
|
A:THR380
|
4.8
|
24.7
|
1.0
|
N
|
A:SER384
|
4.8
|
25.1
|
1.0
|
O
|
B:ASP216
|
5.0
|
25.6
|
1.0
|
|
Potassium binding site 2 out
of 4 in 8cfm
Go back to
Potassium Binding Sites List in 8cfm
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 E08
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 E08 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K506
b:22.8
occ:1.00
|
O
|
B:THR380
|
2.7
|
22.5
|
1.0
|
O
|
B:HIS382
|
2.7
|
22.7
|
1.0
|
O
|
B:HOH693
|
2.8
|
21.5
|
1.0
|
OG1
|
B:THR380
|
2.9
|
22.6
|
1.0
|
O
|
B:HOH671
|
2.9
|
25.2
|
1.0
|
O
|
A:HOH750
|
3.1
|
24.3
|
1.0
|
OE1
|
B:GLN65
|
3.2
|
19.8
|
1.0
|
NE2
|
B:GLN65
|
3.4
|
19.4
|
1.0
|
CD
|
B:GLN65
|
3.5
|
24.4
|
1.0
|
CB
|
B:THR380
|
3.5
|
20.1
|
1.0
|
C
|
B:THR380
|
3.6
|
20.6
|
1.0
|
C
|
B:HIS382
|
3.6
|
19.8
|
1.0
|
O
|
B:GLY381
|
3.7
|
23.4
|
1.0
|
N6
|
B:ADE503
|
4.0
|
25.4
|
1.0
|
C
|
B:GLY381
|
4.0
|
21.7
|
1.0
|
CA
|
B:PRO383
|
4.0
|
20.4
|
1.0
|
CA
|
B:THR380
|
4.2
|
19.8
|
1.0
|
N
|
B:PRO383
|
4.2
|
22.4
|
1.0
|
CB
|
A:ASP216
|
4.4
|
22.3
|
1.0
|
O
|
B:HOH895
|
4.4
|
27.6
|
1.0
|
N
|
B:HIS382
|
4.4
|
22.8
|
1.0
|
N
|
B:GLY381
|
4.5
|
19.9
|
1.0
|
CG
|
A:ASP216
|
4.6
|
23.7
|
1.0
|
CG
|
B:GLN65
|
4.7
|
19.4
|
1.0
|
CA
|
B:GLY381
|
4.7
|
22.6
|
1.0
|
CA
|
B:HIS382
|
4.7
|
22.3
|
1.0
|
OD1
|
A:ASP216
|
4.7
|
22.7
|
1.0
|
C
|
B:PRO383
|
4.7
|
21.2
|
1.0
|
CG2
|
B:THR380
|
4.8
|
22.8
|
1.0
|
OE1
|
B:GLN91
|
4.8
|
22.7
|
1.0
|
N
|
B:SER384
|
4.8
|
21.2
|
1.0
|
|
Potassium binding site 3 out
of 4 in 8cfm
Go back to
Potassium Binding Sites List in 8cfm
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 E08
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 E08 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K504
b:32.6
occ:1.00
|
O
|
C:HIS382
|
2.8
|
25.0
|
1.0
|
O
|
C:HOH801
|
2.8
|
30.8
|
1.0
|
O
|
C:HOH722
|
2.8
|
23.6
|
1.0
|
O
|
C:THR380
|
2.8
|
26.1
|
1.0
|
OG1
|
C:THR380
|
3.0
|
26.6
|
1.0
|
O
|
D:HOH701
|
3.2
|
27.9
|
1.0
|
OE1
|
C:GLN65
|
3.3
|
28.4
|
1.0
|
NE2
|
C:GLN65
|
3.4
|
29.3
|
1.0
|
CD
|
C:GLN65
|
3.5
|
25.9
|
1.0
|
CB
|
C:THR380
|
3.6
|
23.9
|
1.0
|
C
|
C:HIS382
|
3.6
|
26.1
|
1.0
|
C
|
C:THR380
|
3.7
|
26.2
|
1.0
|
O
|
C:GLY381
|
3.8
|
25.2
|
1.0
|
CA
|
C:PRO383
|
3.9
|
27.3
|
1.0
|
N
|
C:PRO383
|
4.1
|
23.4
|
1.0
|
N6
|
C:ADE503
|
4.2
|
31.1
|
1.0
|
C
|
C:GLY381
|
4.2
|
27.3
|
1.0
|
CB
|
D:ASP216
|
4.3
|
25.5
|
1.0
|
CA
|
C:THR380
|
4.3
|
25.9
|
1.0
|
O
|
C:HOH849
|
4.5
|
34.5
|
1.0
|
N
|
C:HIS382
|
4.5
|
27.3
|
1.0
|
CG
|
D:ASP216
|
4.6
|
27.5
|
1.0
|
N
|
C:GLY381
|
4.6
|
22.1
|
1.0
|
C
|
C:PRO383
|
4.7
|
25.3
|
1.0
|
CA
|
C:HIS382
|
4.7
|
25.2
|
1.0
|
CG
|
C:GLN65
|
4.7
|
25.5
|
1.0
|
OD1
|
D:ASP216
|
4.7
|
25.1
|
1.0
|
N
|
C:SER384
|
4.8
|
24.3
|
1.0
|
O
|
D:ASP216
|
4.9
|
24.3
|
1.0
|
CA
|
C:GLY381
|
4.9
|
26.9
|
1.0
|
CG2
|
C:THR380
|
4.9
|
24.9
|
1.0
|
OE1
|
C:GLN91
|
4.9
|
38.0
|
1.0
|
|
Potassium binding site 4 out
of 4 in 8cfm
Go back to
Potassium Binding Sites List in 8cfm
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 E08
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 E08 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K505
b:25.2
occ:1.00
|
O
|
D:THR380
|
2.6
|
25.8
|
1.0
|
OG1
|
D:THR380
|
2.7
|
23.3
|
1.0
|
O
|
D:HIS382
|
2.7
|
20.2
|
1.0
|
O
|
D:HOH747
|
2.8
|
24.4
|
1.0
|
O
|
D:HOH811
|
2.9
|
22.4
|
1.0
|
O
|
C:HOH736
|
3.1
|
23.4
|
1.0
|
OE1
|
D:GLN65
|
3.2
|
23.1
|
1.0
|
NE2
|
D:GLN65
|
3.4
|
23.6
|
1.0
|
CB
|
D:THR380
|
3.4
|
25.5
|
1.0
|
CD
|
D:GLN65
|
3.5
|
23.9
|
1.0
|
C
|
D:THR380
|
3.5
|
24.8
|
1.0
|
C
|
D:HIS382
|
3.6
|
24.5
|
1.0
|
O
|
D:GLY381
|
3.8
|
22.2
|
1.0
|
CA
|
D:PRO383
|
3.9
|
24.3
|
1.0
|
N6
|
D:ADE503
|
4.0
|
27.0
|
1.0
|
C
|
D:GLY381
|
4.1
|
21.8
|
1.0
|
CA
|
D:THR380
|
4.1
|
24.7
|
1.0
|
N
|
D:PRO383
|
4.1
|
23.3
|
1.0
|
CB
|
C:ASP216
|
4.3
|
23.8
|
1.0
|
O
|
D:HOH891
|
4.4
|
31.8
|
1.0
|
N
|
D:HIS382
|
4.5
|
22.7
|
1.0
|
N
|
D:GLY381
|
4.5
|
24.4
|
1.0
|
CG
|
C:ASP216
|
4.6
|
25.2
|
1.0
|
CG
|
D:GLN65
|
4.6
|
21.7
|
1.0
|
OD1
|
C:ASP216
|
4.6
|
24.3
|
1.0
|
CA
|
D:HIS382
|
4.7
|
24.6
|
1.0
|
C
|
D:PRO383
|
4.7
|
25.4
|
1.0
|
CA
|
D:GLY381
|
4.7
|
20.6
|
1.0
|
CG2
|
D:THR380
|
4.7
|
24.4
|
1.0
|
N
|
D:SER384
|
4.8
|
25.5
|
1.0
|
OE1
|
D:GLN91
|
4.8
|
28.0
|
1.0
|
O
|
C:ASP216
|
5.0
|
23.8
|
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 E08 To Be Published.
Page generated: Mon Aug 12 22:29:32 2024
|