Potassium in PDB 7zkn: X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Gamma
Enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Gamma
All present enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Gamma:
3.4.21.5;
Protein crystallography data
The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Gamma, PDB code: 7zkn
was solved by
R.Troisi,
F.Sica,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
68.13 /
3.03
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
76.62,
114.86,
83.44,
90,
117.25,
90
|
R / Rfree (%)
|
20.1 /
24.3
|
Potassium Binding Sites:
The binding sites of Potassium atom in the X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Gamma
(pdb code 7zkn). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the
X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Gamma, PDB code: 7zkn:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 7zkn
Go back to
Potassium Binding Sites List in 7zkn
Potassium binding site 1 out
of 4 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Gamma
![](/pictures/K/pdb/zk/7zkn-K-sphere_01.jpg) Mono view
![](/pictures/K/pdb/zk/7zkn-K-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Gamma within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:K103
b:84.3
occ:1.00
|
O6
|
E:DG10
|
2.7
|
62.2
|
1.0
|
O6
|
E:DG6
|
2.8
|
118.3
|
1.0
|
O6
|
E:DG1
|
2.9
|
67.3
|
1.0
|
O6
|
E:DG5
|
2.9
|
88.0
|
1.0
|
O6
|
E:DG14
|
3.0
|
55.9
|
1.0
|
O6
|
E:DG15
|
3.1
|
61.3
|
1.0
|
O6
|
E:DG2
|
3.2
|
65.6
|
1.0
|
O6
|
E:DG11
|
3.3
|
73.7
|
1.0
|
N1
|
E:DG1
|
3.6
|
69.6
|
1.0
|
N1
|
E:DG6
|
3.6
|
106.8
|
1.0
|
C6
|
E:DG6
|
3.6
|
115.6
|
1.0
|
C6
|
E:DG1
|
3.6
|
71.4
|
1.0
|
C6
|
E:DG10
|
3.6
|
63.5
|
1.0
|
N1
|
E:DG15
|
3.7
|
62.4
|
1.0
|
C6
|
E:DG5
|
3.7
|
92.2
|
1.0
|
C6
|
E:DG15
|
3.8
|
64.1
|
1.0
|
C6
|
E:DG14
|
3.9
|
58.5
|
1.0
|
N1
|
E:DG10
|
3.9
|
61.7
|
1.0
|
N1
|
E:DG5
|
4.0
|
93.4
|
1.0
|
C6
|
E:DG2
|
4.0
|
62.7
|
1.0
|
C6
|
E:DG11
|
4.2
|
72.9
|
1.0
|
N1
|
E:DG2
|
4.3
|
62.6
|
1.0
|
N1
|
E:DG11
|
4.3
|
71.2
|
1.0
|
C36
|
E:JL0101
|
4.3
|
91.0
|
1.0
|
N1
|
E:DG14
|
4.3
|
59.1
|
1.0
|
O
|
E:HOH201
|
4.4
|
71.4
|
1.0
|
C35
|
E:JL0101
|
4.6
|
92.8
|
1.0
|
C37
|
E:JL0101
|
4.7
|
90.8
|
1.0
|
C5
|
E:DG5
|
4.8
|
94.7
|
1.0
|
C2
|
E:DG1
|
4.8
|
70.1
|
1.0
|
C2
|
E:DG6
|
4.8
|
102.2
|
1.0
|
C2
|
E:DG15
|
4.9
|
63.4
|
1.0
|
C5
|
E:DG14
|
4.9
|
60.1
|
1.0
|
C5
|
E:DG10
|
4.9
|
64.4
|
1.0
|
C5
|
E:DG6
|
5.0
|
115.2
|
1.0
|
C5
|
E:DG1
|
5.0
|
73.2
|
1.0
|
|
Potassium binding site 2 out
of 4 in 7zkn
Go back to
Potassium Binding Sites List in 7zkn
Potassium binding site 2 out
of 4 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Gamma
![](/pictures/K/pdb/zk/7zkn-K-sphere_02.jpg) Mono view
![](/pictures/K/pdb/zk/7zkn-K-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Gamma within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:K103
b:78.9
occ:1.00
|
O6
|
F:DG1
|
2.6
|
71.3
|
1.0
|
O6
|
F:DG5
|
2.7
|
72.5
|
1.0
|
O6
|
F:DG15
|
2.8
|
54.5
|
1.0
|
O6
|
F:DG10
|
2.8
|
46.3
|
1.0
|
O6
|
F:DG6
|
3.0
|
86.1
|
1.0
|
O6
|
F:DG2
|
3.1
|
67.7
|
1.0
|
O6
|
F:DG11
|
3.1
|
70.5
|
1.0
|
O6
|
F:DG14
|
3.2
|
46.3
|
1.0
|
N1
|
F:DG15
|
3.2
|
56.5
|
1.0
|
C6
|
F:DG15
|
3.4
|
58.5
|
1.0
|
C6
|
F:DG1
|
3.5
|
74.2
|
1.0
|
C6
|
F:DG5
|
3.6
|
75.1
|
1.0
|
C6
|
F:DG10
|
3.6
|
46.1
|
1.0
|
N1
|
F:DG1
|
3.7
|
73.4
|
1.0
|
N1
|
F:DG10
|
3.7
|
44.0
|
1.0
|
C6
|
F:DG6
|
3.9
|
91.0
|
1.0
|
N1
|
F:DG6
|
3.9
|
86.3
|
1.0
|
C6
|
F:DG11
|
3.9
|
70.9
|
1.0
|
C6
|
F:DG14
|
4.0
|
48.6
|
1.0
|
C6
|
F:DG2
|
4.0
|
69.8
|
1.0
|
N1
|
F:DG11
|
4.1
|
68.3
|
1.0
|
N1
|
F:DG5
|
4.1
|
71.1
|
1.0
|
C36
|
F:JL0101
|
4.1
|
79.8
|
1.0
|
N1
|
F:DG14
|
4.2
|
46.9
|
1.0
|
C37
|
F:JL0101
|
4.2
|
82.4
|
1.0
|
N1
|
F:DG2
|
4.3
|
69.1
|
1.0
|
C35
|
F:JL0101
|
4.3
|
78.7
|
1.0
|
C2
|
F:DG15
|
4.5
|
58.9
|
1.0
|
C42
|
F:JL0101
|
4.5
|
79.4
|
1.0
|
C34
|
F:JL0101
|
4.6
|
76.9
|
1.0
|
C5
|
F:DG5
|
4.7
|
77.3
|
1.0
|
C38
|
F:JL0101
|
4.7
|
86.8
|
1.0
|
C43
|
F:JL0101
|
4.7
|
76.2
|
1.0
|
N2
|
F:DG15
|
4.8
|
56.2
|
1.0
|
C5
|
F:DG1
|
4.8
|
75.5
|
1.0
|
C5
|
F:DG15
|
4.8
|
60.1
|
1.0
|
C5
|
F:DG10
|
5.0
|
48.6
|
1.0
|
|
Potassium binding site 3 out
of 4 in 7zkn
Go back to
Potassium Binding Sites List in 7zkn
Potassium binding site 3 out
of 4 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Gamma
![](/pictures/K/pdb/zk/7zkn-K-sphere_03.jpg) Mono view
![](/pictures/K/pdb/zk/7zkn-K-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Gamma within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:K103
b:76.2
occ:1.00
|
O6
|
G:DG1
|
2.5
|
58.4
|
1.0
|
O6
|
G:DG10
|
2.6
|
67.9
|
1.0
|
O6
|
G:DG14
|
2.9
|
52.5
|
1.0
|
O6
|
G:DG5
|
3.0
|
71.0
|
1.0
|
O6
|
G:DG15
|
3.0
|
57.8
|
1.0
|
O6
|
G:DG11
|
3.2
|
69.9
|
1.0
|
O6
|
G:DG2
|
3.3
|
51.9
|
1.0
|
C6
|
G:DG1
|
3.4
|
64.0
|
1.0
|
O6
|
G:DG6
|
3.4
|
86.0
|
1.0
|
C6
|
G:DG10
|
3.5
|
65.2
|
1.0
|
N1
|
G:DG15
|
3.5
|
57.5
|
1.0
|
C6
|
G:DG14
|
3.7
|
54.7
|
1.0
|
C6
|
G:DG15
|
3.7
|
59.8
|
1.0
|
N1
|
G:DG1
|
3.7
|
65.0
|
1.0
|
N1
|
G:DG10
|
3.7
|
59.9
|
1.0
|
C6
|
G:DG5
|
3.7
|
74.6
|
1.0
|
N1
|
G:DG6
|
3.8
|
87.4
|
1.0
|
N1
|
G:DG14
|
3.9
|
54.4
|
1.0
|
N1
|
G:DG5
|
4.0
|
72.8
|
1.0
|
C6
|
G:DG11
|
4.1
|
67.5
|
1.0
|
C6
|
G:DG6
|
4.1
|
89.2
|
1.0
|
C6
|
G:DG2
|
4.1
|
48.9
|
1.0
|
C36
|
G:JL0101
|
4.1
|
77.6
|
1.0
|
N1
|
G:DG11
|
4.2
|
64.5
|
1.0
|
N1
|
G:DG2
|
4.2
|
47.3
|
1.0
|
C35
|
G:JL0101
|
4.2
|
77.5
|
1.0
|
C37
|
G:JL0101
|
4.5
|
77.8
|
1.0
|
O
|
G:HOH201
|
4.6
|
74.2
|
1.0
|
C34
|
G:JL0101
|
4.7
|
80.7
|
1.0
|
C5
|
G:DG1
|
4.7
|
65.3
|
1.0
|
C2
|
G:DG15
|
4.7
|
60.2
|
1.0
|
C5
|
G:DG14
|
4.8
|
56.2
|
1.0
|
C5
|
G:DG10
|
4.8
|
66.2
|
1.0
|
C5
|
G:DG5
|
4.9
|
77.9
|
1.0
|
C42
|
G:JL0101
|
4.9
|
76.8
|
1.0
|
|
Potassium binding site 4 out
of 4 in 7zkn
Go back to
Potassium Binding Sites List in 7zkn
Potassium binding site 4 out
of 4 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Gamma
![](/pictures/K/pdb/zk/7zkn-K-sphere_04.jpg) Mono view
![](/pictures/K/pdb/zk/7zkn-K-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Gamma within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:K103
b:91.5
occ:1.00
|
O6
|
I:DG1
|
2.5
|
85.3
|
1.0
|
O6
|
I:DG10
|
2.5
|
64.9
|
1.0
|
O6
|
I:DG5
|
2.6
|
101.5
|
1.0
|
O6
|
I:DG14
|
2.9
|
58.0
|
1.0
|
O6
|
I:DG15
|
3.0
|
47.8
|
1.0
|
O6
|
I:DG6
|
3.1
|
111.6
|
1.0
|
O6
|
I:DG11
|
3.2
|
72.0
|
1.0
|
O6
|
I:DG2
|
3.2
|
61.6
|
1.0
|
C6
|
I:DG1
|
3.4
|
84.9
|
1.0
|
C6
|
I:DG5
|
3.4
|
103.9
|
1.0
|
C6
|
I:DG10
|
3.5
|
65.4
|
1.0
|
N1
|
I:DG1
|
3.6
|
79.5
|
1.0
|
N1
|
I:DG15
|
3.6
|
44.9
|
1.0
|
C6
|
I:DG15
|
3.7
|
48.2
|
1.0
|
N1
|
I:DG10
|
3.7
|
63.9
|
1.0
|
C6
|
I:DG14
|
3.7
|
57.1
|
1.0
|
N1
|
I:DG5
|
3.9
|
101.0
|
1.0
|
C6
|
I:DG6
|
3.9
|
114.1
|
1.0
|
N1
|
I:DG6
|
4.0
|
108.0
|
1.0
|
N1
|
I:DG14
|
4.0
|
53.1
|
1.0
|
C6
|
I:DG11
|
4.1
|
76.0
|
1.0
|
C6
|
I:DG2
|
4.1
|
64.1
|
1.0
|
C36
|
I:JL0101
|
4.2
|
74.2
|
1.0
|
N1
|
I:DG11
|
4.3
|
75.4
|
1.0
|
N1
|
I:DG2
|
4.3
|
62.1
|
1.0
|
C35
|
I:JL0101
|
4.3
|
71.6
|
1.0
|
C5
|
I:DG5
|
4.6
|
102.9
|
1.0
|
C37
|
I:JL0101
|
4.7
|
73.4
|
1.0
|
C5
|
I:DG1
|
4.7
|
82.4
|
1.0
|
C5
|
I:DG10
|
4.7
|
68.1
|
1.0
|
C2
|
I:DG15
|
4.9
|
47.1
|
1.0
|
C2
|
I:DG1
|
4.9
|
80.3
|
1.0
|
C34
|
I:JL0101
|
4.9
|
73.7
|
1.0
|
C5
|
I:DG14
|
5.0
|
56.5
|
1.0
|
|
Reference:
R.Troisi,
C.Riccardi,
K.Perez De Carvasal,
M.Smietana,
F.Morvan,
P.Del Vecchio,
D.Montesarchio,
F.Sica.
A Terminal Functionalization Strategy Reveals Unusual Binding Abilities of Anti-Thrombin Anticoagulant Aptamers. Mol Ther Nucleic Acids V. 30 585 2022.
ISSN: ISSN 2162-2531
PubMed: 36457701
DOI: 10.1016/J.OMTN.2022.11.007
Page generated: Mon Aug 12 21:50:12 2024
|