Potassium in PDB 6f3n: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations
Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations
All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations:
3.3.1.1;
Protein crystallography data
The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations, PDB code: 6f3n
was solved by
J.Czyrko,
K.Brzezinski,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.82 /
1.85
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
170.585,
99.275,
111.721,
90.00,
101.90,
90.00
|
R / Rfree (%)
|
15.1 /
17.6
|
Other elements in 6f3n:
The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations
(pdb code 6f3n). 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 Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations, PDB code: 6f3n:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 6f3n
Go back to
Potassium Binding Sites List in 6f3n
Potassium binding site 1 out
of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations
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 Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K501
b:14.7
occ:1.00
|
OG1
|
A:THR380
|
2.7
|
14.7
|
1.0
|
O
|
A:THR380
|
2.7
|
15.9
|
1.0
|
O
|
A:HIS382
|
2.8
|
14.8
|
1.0
|
O
|
A:HOH859
|
2.9
|
16.3
|
1.0
|
O
|
A:HOH820
|
2.9
|
16.0
|
1.0
|
O
|
C:HOH799
|
3.0
|
16.3
|
1.0
|
OE1
|
A:GLN65
|
3.2
|
14.8
|
1.0
|
NE2
|
A:GLN65
|
3.4
|
15.4
|
1.0
|
CB
|
A:THR380
|
3.5
|
15.7
|
1.0
|
CD
|
A:GLN65
|
3.5
|
14.9
|
1.0
|
C
|
A:THR380
|
3.6
|
15.8
|
1.0
|
C
|
A:HIS382
|
3.7
|
14.7
|
1.0
|
O
|
A:GLY381
|
3.8
|
16.6
|
1.0
|
CA
|
A:PRO383
|
4.1
|
14.8
|
1.0
|
N6
|
A:ADN505
|
4.1
|
17.2
|
0.7
|
C
|
A:GLY381
|
4.1
|
16.1
|
1.0
|
N6
|
A:ADN505
|
4.1
|
16.7
|
0.3
|
CA
|
A:THR380
|
4.2
|
15.5
|
1.0
|
N
|
A:PRO383
|
4.2
|
14.7
|
1.0
|
CB
|
C:ASP216
|
4.3
|
16.3
|
1.0
|
O
|
A:HOH925
|
4.4
|
17.6
|
1.0
|
N
|
A:GLY381
|
4.5
|
15.8
|
1.0
|
N
|
A:HIS382
|
4.5
|
15.8
|
1.0
|
CG
|
C:ASP216
|
4.5
|
16.4
|
1.0
|
OD1
|
C:ASP216
|
4.6
|
16.1
|
1.0
|
CG
|
A:GLN65
|
4.7
|
14.6
|
1.0
|
CA
|
A:HIS382
|
4.7
|
15.2
|
1.0
|
C
|
A:PRO383
|
4.7
|
14.4
|
1.0
|
CA
|
A:GLY381
|
4.7
|
15.9
|
1.0
|
N
|
A:SER384
|
4.8
|
14.7
|
1.0
|
CG2
|
A:THR380
|
4.8
|
16.1
|
1.0
|
OE1
|
A:GLN91
|
4.8
|
16.7
|
1.0
|
O
|
C:ASP216
|
5.0
|
17.1
|
1.0
|
|
Potassium binding site 2 out
of 4 in 6f3n
Go back to
Potassium Binding Sites List in 6f3n
Potassium binding site 2 out
of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations
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 Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K501
b:14.0
occ:1.00
|
O
|
B:THR380
|
2.7
|
14.6
|
1.0
|
OG1
|
B:THR380
|
2.8
|
13.5
|
1.0
|
O
|
B:HOH777
|
2.8
|
12.1
|
1.0
|
O
|
B:HIS382
|
2.8
|
12.9
|
1.0
|
O
|
B:HOH802
|
2.9
|
11.7
|
1.0
|
O
|
D:HOH785
|
3.1
|
11.4
|
1.0
|
OE1
|
B:GLN65
|
3.2
|
13.2
|
1.0
|
NE2
|
B:GLN65
|
3.4
|
13.7
|
1.0
|
CD
|
B:GLN65
|
3.5
|
13.9
|
1.0
|
CB
|
B:THR380
|
3.5
|
14.2
|
1.0
|
C
|
B:THR380
|
3.6
|
14.0
|
1.0
|
C
|
B:HIS382
|
3.6
|
13.6
|
1.0
|
O
|
B:GLY381
|
3.7
|
14.1
|
1.0
|
CA
|
B:PRO383
|
4.1
|
13.8
|
1.0
|
N6
|
B:ADN505
|
4.1
|
14.5
|
0.7
|
C
|
B:GLY381
|
4.1
|
14.3
|
1.0
|
N6
|
B:ADN505
|
4.1
|
14.9
|
0.3
|
CA
|
B:THR380
|
4.2
|
13.9
|
1.0
|
N
|
B:PRO383
|
4.2
|
13.3
|
1.0
|
CB
|
D:ASP216
|
4.3
|
14.8
|
1.0
|
N
|
B:HIS382
|
4.5
|
14.6
|
1.0
|
N
|
B:GLY381
|
4.5
|
13.8
|
1.0
|
O
|
B:HOH946
|
4.5
|
15.4
|
1.0
|
CG
|
D:ASP216
|
4.5
|
15.0
|
1.0
|
OD1
|
D:ASP216
|
4.6
|
15.8
|
1.0
|
CG
|
B:GLN65
|
4.6
|
13.6
|
1.0
|
CA
|
B:HIS382
|
4.7
|
14.3
|
1.0
|
C
|
B:PRO383
|
4.7
|
13.4
|
1.0
|
CA
|
B:GLY381
|
4.8
|
14.2
|
1.0
|
CG2
|
B:THR380
|
4.8
|
14.5
|
1.0
|
N
|
B:SER384
|
4.8
|
14.4
|
1.0
|
OE1
|
B:GLN91
|
4.8
|
17.3
|
1.0
|
O
|
D:ASP216
|
4.9
|
14.2
|
1.0
|
|
Potassium binding site 3 out
of 4 in 6f3n
Go back to
Potassium Binding Sites List in 6f3n
Potassium binding site 3 out
of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations
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 Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K501
b:17.3
occ:1.00
|
O
|
C:THR380
|
2.7
|
16.6
|
1.0
|
OG1
|
C:THR380
|
2.7
|
16.4
|
1.0
|
O
|
C:HIS382
|
2.8
|
17.4
|
1.0
|
O
|
C:HOH784
|
2.8
|
14.3
|
1.0
|
O
|
C:HOH734
|
2.9
|
17.0
|
1.0
|
O
|
A:HOH787
|
3.1
|
18.1
|
1.0
|
OE1
|
C:GLN65
|
3.2
|
16.8
|
1.0
|
NE2
|
C:GLN65
|
3.4
|
17.3
|
1.0
|
CB
|
C:THR380
|
3.5
|
16.8
|
1.0
|
CD
|
C:GLN65
|
3.5
|
16.6
|
1.0
|
C
|
C:THR380
|
3.5
|
16.2
|
1.0
|
C
|
C:HIS382
|
3.7
|
17.8
|
1.0
|
O
|
C:GLY381
|
3.7
|
16.0
|
1.0
|
N6
|
C:ADN505
|
4.0
|
17.7
|
0.7
|
C
|
C:GLY381
|
4.1
|
16.7
|
1.0
|
CA
|
C:PRO383
|
4.1
|
16.5
|
1.0
|
N6
|
C:ADN505
|
4.1
|
17.2
|
0.3
|
CA
|
C:THR380
|
4.2
|
16.4
|
1.0
|
N
|
C:PRO383
|
4.2
|
16.1
|
1.0
|
CB
|
A:ASP216
|
4.3
|
17.5
|
1.0
|
N
|
C:GLY381
|
4.5
|
16.1
|
1.0
|
O
|
C:HOH864
|
4.5
|
19.8
|
1.0
|
N
|
C:HIS382
|
4.5
|
17.6
|
1.0
|
CG
|
A:ASP216
|
4.5
|
17.8
|
1.0
|
OD1
|
A:ASP216
|
4.6
|
17.3
|
1.0
|
CG
|
C:GLN65
|
4.6
|
16.0
|
1.0
|
CA
|
C:GLY381
|
4.7
|
16.4
|
1.0
|
CA
|
C:HIS382
|
4.7
|
17.6
|
1.0
|
CG2
|
C:THR380
|
4.7
|
16.7
|
1.0
|
C
|
C:PRO383
|
4.8
|
16.5
|
1.0
|
N
|
C:SER384
|
4.8
|
16.9
|
1.0
|
OE1
|
C:GLN91
|
4.8
|
20.3
|
1.0
|
O
|
A:ASP216
|
5.0
|
17.6
|
1.0
|
|
Potassium binding site 4 out
of 4 in 6f3n
Go back to
Potassium Binding Sites List in 6f3n
Potassium binding site 4 out
of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations
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 Pseudomonas Aeruginosa Cocrystallized with Sah in the Presence of K+ and ZN2+ Cations within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K501
b:15.1
occ:1.00
|
O
|
D:THR380
|
2.8
|
13.7
|
1.0
|
OG1
|
D:THR380
|
2.8
|
14.8
|
1.0
|
O
|
D:HOH835
|
2.8
|
14.7
|
1.0
|
O
|
D:HIS382
|
2.8
|
13.2
|
1.0
|
O
|
D:HOH752
|
2.9
|
13.5
|
1.0
|
O
|
B:HOH847
|
3.0
|
14.4
|
1.0
|
OE1
|
D:GLN65
|
3.2
|
14.3
|
1.0
|
NE2
|
D:GLN65
|
3.4
|
13.6
|
1.0
|
CD
|
D:GLN65
|
3.4
|
13.6
|
1.0
|
CB
|
D:THR380
|
3.5
|
14.9
|
1.0
|
C
|
D:THR380
|
3.6
|
14.2
|
1.0
|
C
|
D:HIS382
|
3.7
|
13.2
|
1.0
|
O
|
D:GLY381
|
3.8
|
13.8
|
1.0
|
CA
|
D:PRO383
|
4.0
|
13.6
|
1.0
|
N6
|
D:ADN506
|
4.1
|
17.1
|
0.7
|
C
|
D:GLY381
|
4.1
|
14.1
|
1.0
|
N6
|
D:ADN506
|
4.2
|
17.4
|
0.3
|
CB
|
B:ASP216
|
4.2
|
14.5
|
1.0
|
N
|
D:PRO383
|
4.2
|
13.5
|
1.0
|
CA
|
D:THR380
|
4.2
|
14.3
|
1.0
|
O
|
D:HOH939
|
4.4
|
16.3
|
1.0
|
CG
|
B:ASP216
|
4.5
|
14.4
|
1.0
|
N
|
D:GLY381
|
4.5
|
14.1
|
1.0
|
N
|
D:HIS382
|
4.5
|
13.7
|
1.0
|
OD1
|
B:ASP216
|
4.6
|
13.6
|
1.0
|
CG
|
D:GLN65
|
4.6
|
13.3
|
1.0
|
C
|
D:PRO383
|
4.7
|
13.8
|
1.0
|
CA
|
D:HIS382
|
4.7
|
13.7
|
1.0
|
N
|
D:SER384
|
4.7
|
13.6
|
1.0
|
CG2
|
D:THR380
|
4.8
|
14.8
|
1.0
|
CA
|
D:GLY381
|
4.8
|
14.3
|
1.0
|
OE1
|
D:GLN91
|
4.9
|
15.0
|
1.0
|
O
|
B:ASP216
|
4.9
|
15.1
|
1.0
|
|
Reference:
J.Czyrko,
J.Sliwiak,
B.Imiolczyk,
Z.Gdaniec,
M.Jaskolski,
K.Brzezinski.
Metal-Cation Regulation of Enzyme Dynamics Is A Key Factor Influencing the Activity of S-Adenosyl-L-Homocysteine Hydrolase From Pseudomonas Aeruginosa. Sci Rep V. 8 11334 2018.
ISSN: ESSN 2045-2322
PubMed: 30054521
DOI: 10.1038/S41598-018-29535-Y
Page generated: Mon Aug 12 16:04:59 2024
|