Potassium in PDB 7zd4: Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions
Enzymatic activity of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions
All present enzymatic activity of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions:
3.3.1.1;
Protein crystallography data
The structure of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions, PDB code: 7zd4
was solved by
P.H.Malecki,
M.Gawel,
K.Brzezinski,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.29 /
2.14
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
175.68,
133.57,
107.04,
90,
105.22,
90
|
R / Rfree (%)
|
18.3 /
22.7
|
Other elements in 7zd4:
The structure of Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions
(pdb code 7zd4). 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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions, PDB code: 7zd4:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 7zd4
Go back to
Potassium Binding Sites List in 7zd4
Potassium binding site 1 out
of 4 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions
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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K504
b:35.4
occ:1.00
|
O
|
A:THR380
|
2.7
|
22.6
|
1.0
|
O
|
A:HOH767
|
2.7
|
26.7
|
1.0
|
O
|
A:HIS382
|
2.8
|
25.1
|
1.0
|
OG1
|
A:THR380
|
2.8
|
26.8
|
1.0
|
O
|
A:HOH732
|
2.9
|
23.7
|
1.0
|
OE1
|
A:GLN65
|
3.2
|
25.9
|
1.0
|
NE2
|
A:GLN65
|
3.4
|
25.7
|
1.0
|
CD
|
A:GLN65
|
3.5
|
27.4
|
1.0
|
CB
|
A:THR380
|
3.5
|
28.1
|
1.0
|
O
|
B:HOH609
|
3.5
|
27.3
|
1.0
|
C
|
A:THR380
|
3.5
|
24.9
|
1.0
|
C
|
A:HIS382
|
3.6
|
26.5
|
1.0
|
O
|
A:GLY381
|
3.7
|
23.4
|
1.0
|
C
|
A:GLY381
|
4.0
|
23.8
|
1.0
|
N6
|
A:ADN502
|
4.0
|
26.9
|
1.0
|
CA
|
A:PRO383
|
4.1
|
26.3
|
1.0
|
CA
|
A:THR380
|
4.2
|
26.8
|
1.0
|
N
|
A:PRO383
|
4.2
|
27.6
|
1.0
|
CB
|
B:ASP216
|
4.3
|
25.7
|
1.0
|
N
|
A:GLY381
|
4.4
|
28.2
|
1.0
|
N
|
A:HIS382
|
4.4
|
26.5
|
1.0
|
CG
|
B:ASP216
|
4.4
|
25.2
|
1.0
|
OD1
|
B:ASP216
|
4.5
|
25.8
|
1.0
|
CA
|
A:GLY381
|
4.6
|
26.6
|
1.0
|
CG
|
A:GLN65
|
4.6
|
23.3
|
1.0
|
CA
|
A:HIS382
|
4.7
|
24.7
|
1.0
|
O
|
A:HOH885
|
4.7
|
25.8
|
1.0
|
OE1
|
A:GLN91
|
4.7
|
29.2
|
1.0
|
C
|
A:PRO383
|
4.7
|
25.7
|
1.0
|
CG2
|
A:THR380
|
4.8
|
27.3
|
1.0
|
N
|
A:SER384
|
4.9
|
25.8
|
1.0
|
O
|
B:ASP216
|
4.9
|
27.1
|
1.0
|
OD2
|
B:ASP216
|
5.0
|
26.5
|
1.0
|
|
Potassium binding site 2 out
of 4 in 7zd4
Go back to
Potassium Binding Sites List in 7zd4
Potassium binding site 2 out
of 4 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions
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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K504
b:39.2
occ:1.00
|
O
|
B:HIS382
|
2.7
|
26.2
|
1.0
|
O
|
B:THR380
|
2.7
|
27.5
|
1.0
|
O
|
B:HOH626
|
2.8
|
32.9
|
1.0
|
O
|
B:HOH641
|
2.8
|
26.2
|
1.0
|
OG1
|
B:THR380
|
2.9
|
27.7
|
1.0
|
OE1
|
B:GLN65
|
3.2
|
32.1
|
1.0
|
O
|
A:HOH699
|
3.2
|
29.8
|
1.0
|
NE2
|
B:GLN65
|
3.3
|
29.7
|
1.0
|
CD
|
B:GLN65
|
3.4
|
31.9
|
1.0
|
CB
|
B:THR380
|
3.5
|
30.8
|
1.0
|
C
|
B:THR380
|
3.6
|
28.6
|
1.0
|
C
|
B:HIS382
|
3.6
|
29.0
|
1.0
|
O
|
B:GLY381
|
3.7
|
25.2
|
1.0
|
N6
|
B:ADN502
|
3.9
|
33.9
|
1.0
|
C
|
B:GLY381
|
4.0
|
29.9
|
1.0
|
CA
|
B:PRO383
|
4.1
|
27.2
|
1.0
|
CA
|
B:THR380
|
4.2
|
31.1
|
1.0
|
N
|
B:PRO383
|
4.2
|
27.9
|
1.0
|
CB
|
A:ASP216
|
4.3
|
28.6
|
1.0
|
N
|
B:HIS382
|
4.4
|
30.9
|
1.0
|
N
|
B:GLY381
|
4.5
|
25.5
|
1.0
|
CG
|
B:GLN65
|
4.5
|
29.2
|
1.0
|
CG
|
A:ASP216
|
4.5
|
28.3
|
1.0
|
O
|
B:HOH826
|
4.6
|
31.8
|
1.0
|
CA
|
B:HIS382
|
4.6
|
31.0
|
1.0
|
OD1
|
A:ASP216
|
4.7
|
26.6
|
1.0
|
OE1
|
B:GLN91
|
4.7
|
33.9
|
1.0
|
CA
|
B:GLY381
|
4.7
|
27.2
|
1.0
|
C
|
B:PRO383
|
4.7
|
26.6
|
1.0
|
CG2
|
B:THR380
|
4.8
|
30.0
|
1.0
|
N
|
B:SER384
|
4.9
|
28.8
|
1.0
|
|
Potassium binding site 3 out
of 4 in 7zd4
Go back to
Potassium Binding Sites List in 7zd4
Potassium binding site 3 out
of 4 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions
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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K504
b:33.5
occ:1.00
|
O
|
C:THR380
|
2.7
|
30.1
|
1.0
|
O
|
C:HIS382
|
2.7
|
30.1
|
1.0
|
O
|
C:HOH778
|
2.8
|
23.6
|
1.0
|
O
|
C:HOH690
|
2.8
|
27.5
|
1.0
|
OG1
|
C:THR380
|
2.9
|
26.1
|
1.0
|
OE1
|
C:GLN65
|
3.2
|
24.1
|
1.0
|
O
|
D:HOH709
|
3.4
|
27.7
|
1.0
|
NE2
|
C:GLN65
|
3.4
|
22.1
|
1.0
|
CB
|
C:THR380
|
3.5
|
29.3
|
1.0
|
CD
|
C:GLN65
|
3.5
|
25.2
|
1.0
|
C
|
C:THR380
|
3.5
|
27.2
|
1.0
|
C
|
C:HIS382
|
3.6
|
25.9
|
1.0
|
O
|
C:GLY381
|
3.6
|
26.2
|
1.0
|
N6
|
C:ADN502
|
3.9
|
25.7
|
1.0
|
C
|
C:GLY381
|
4.0
|
25.8
|
1.0
|
CA
|
C:PRO383
|
4.0
|
24.1
|
1.0
|
CA
|
C:THR380
|
4.1
|
28.1
|
1.0
|
N
|
C:PRO383
|
4.2
|
24.6
|
1.0
|
CB
|
D:ASP216
|
4.2
|
27.4
|
1.0
|
N
|
C:HIS382
|
4.4
|
26.2
|
1.0
|
N
|
C:GLY381
|
4.4
|
26.3
|
1.0
|
CG
|
D:ASP216
|
4.5
|
26.8
|
1.0
|
OD1
|
D:ASP216
|
4.5
|
27.3
|
1.0
|
O
|
C:HOH854
|
4.5
|
32.3
|
1.0
|
OE1
|
C:GLN91
|
4.6
|
29.8
|
1.0
|
CA
|
C:HIS382
|
4.6
|
25.1
|
1.0
|
CA
|
C:GLY381
|
4.6
|
28.9
|
1.0
|
CG
|
C:GLN65
|
4.7
|
25.8
|
1.0
|
C
|
C:PRO383
|
4.7
|
26.4
|
1.0
|
CG2
|
C:THR380
|
4.8
|
25.1
|
1.0
|
N
|
C:SER384
|
4.9
|
25.3
|
1.0
|
O
|
D:ASP216
|
5.0
|
27.1
|
1.0
|
|
Potassium binding site 4 out
of 4 in 7zd4
Go back to
Potassium Binding Sites List in 7zd4
Potassium binding site 4 out
of 4 in the Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions
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 Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K504
b:38.8
occ:1.00
|
O
|
D:HIS382
|
2.7
|
29.3
|
1.0
|
O
|
D:HOH778
|
2.7
|
30.2
|
1.0
|
O
|
D:THR380
|
2.7
|
31.4
|
1.0
|
O
|
D:HOH686
|
2.7
|
34.4
|
1.0
|
OG1
|
D:THR380
|
2.9
|
33.5
|
1.0
|
O
|
C:HOH755
|
3.2
|
27.9
|
1.0
|
OE1
|
D:GLN65
|
3.3
|
33.1
|
1.0
|
NE2
|
D:GLN65
|
3.4
|
31.4
|
1.0
|
CB
|
D:THR380
|
3.4
|
34.7
|
1.0
|
CD
|
D:GLN65
|
3.5
|
31.9
|
1.0
|
C
|
D:HIS382
|
3.6
|
29.2
|
1.0
|
C
|
D:THR380
|
3.6
|
31.9
|
1.0
|
O
|
D:GLY381
|
3.8
|
29.7
|
1.0
|
CA
|
D:PRO383
|
3.9
|
27.8
|
1.0
|
N6
|
D:ADN502
|
3.9
|
30.4
|
1.0
|
C
|
D:GLY381
|
4.1
|
30.8
|
1.0
|
N
|
D:PRO383
|
4.1
|
28.9
|
1.0
|
CA
|
D:THR380
|
4.1
|
33.2
|
1.0
|
CB
|
C:ASP216
|
4.3
|
29.9
|
1.0
|
O
|
D:HOH801
|
4.4
|
30.6
|
1.0
|
N
|
D:HIS382
|
4.4
|
29.8
|
1.0
|
CG
|
C:ASP216
|
4.4
|
33.0
|
1.0
|
N
|
D:GLY381
|
4.5
|
32.0
|
1.0
|
OD1
|
C:ASP216
|
4.5
|
32.0
|
1.0
|
C
|
D:PRO383
|
4.6
|
30.8
|
1.0
|
CA
|
D:HIS382
|
4.6
|
28.7
|
1.0
|
CG
|
D:GLN65
|
4.7
|
31.6
|
1.0
|
OE1
|
D:GLN91
|
4.7
|
37.2
|
1.0
|
CG2
|
D:THR380
|
4.7
|
34.1
|
1.0
|
CA
|
D:GLY381
|
4.7
|
30.2
|
1.0
|
N
|
D:SER384
|
4.8
|
30.3
|
1.0
|
O
|
C:ASP216
|
4.9
|
29.1
|
1.0
|
OD2
|
C:ASP216
|
5.0
|
33.1
|
1.0
|
|
Reference:
P.H.Malecki,
M.Gawel,
K.Brzezinski.
Crystal Structure of Pseudomonas Aeruginosa S-Adenosyl-L-Homocysteine Hydrolase Soaked with Cu+ Ions To Be Published.
Page generated: Mon Aug 12 21:47:58 2024
|