Potassium in PDB 7vtd: Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B
Enzymatic activity of Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B
All present enzymatic activity of Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B:
2.7.1.83;
Protein crystallography data
The structure of Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B, PDB code: 7vtd
was solved by
S.H.Kim,
S.Rhee,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.29 /
2.15
|
Space group
|
P 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
186.805,
186.805,
49.648,
90,
90,
120
|
R / Rfree (%)
|
23.2 /
26.8
|
Potassium Binding Sites:
The binding sites of Potassium atom in the Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B
(pdb code 7vtd). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the
Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B, PDB code: 7vtd:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 7vtd
Go back to
Potassium Binding Sites List in 7vtd
Potassium binding site 1 out
of 4 in the Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B
![](/pictures/K/pdb/vt/7vtd-K-sphere_01.jpg) Mono view
![](/pictures/K/pdb/vt/7vtd-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 Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K401
b:89.9
occ:1.00
|
O
|
A:CYS289
|
2.8
|
117.0
|
1.0
|
O
|
A:THR252
|
2.8
|
105.6
|
1.0
|
O
|
A:ASN250
|
2.8
|
104.0
|
1.0
|
O
|
A:ALA286
|
2.9
|
78.8
|
1.0
|
O
|
A:TYR291
|
2.9
|
88.5
|
1.0
|
CB
|
A:ASN250
|
3.2
|
105.4
|
1.0
|
CG2
|
A:THR252
|
3.4
|
110.6
|
1.0
|
C
|
A:ASN250
|
3.5
|
108.2
|
1.0
|
C
|
A:CYS289
|
3.8
|
109.2
|
1.0
|
C
|
A:TYR291
|
3.8
|
105.5
|
1.0
|
C
|
A:THR252
|
3.8
|
105.8
|
1.0
|
CA
|
A:ASN250
|
3.9
|
108.2
|
1.0
|
N
|
A:THR252
|
3.9
|
85.6
|
1.0
|
CG
|
A:ASN250
|
3.9
|
117.2
|
1.0
|
C
|
A:ALA286
|
4.0
|
91.8
|
1.0
|
CA
|
A:THR252
|
4.3
|
101.4
|
1.0
|
C
|
A:GLU290
|
4.3
|
101.4
|
1.0
|
ND2
|
A:ASN250
|
4.3
|
115.9
|
1.0
|
N
|
A:VAL251
|
4.4
|
92.3
|
1.0
|
O
|
A:GLU290
|
4.4
|
90.9
|
1.0
|
N
|
A:TYR291
|
4.5
|
101.1
|
1.0
|
CB
|
A:THR252
|
4.5
|
103.5
|
1.0
|
C
|
A:VAL251
|
4.5
|
95.8
|
1.0
|
N
|
A:ASN250
|
4.5
|
102.5
|
1.0
|
N
|
A:THR292
|
4.5
|
88.9
|
1.0
|
CA
|
A:THR292
|
4.5
|
97.2
|
1.0
|
CA
|
A:CYS289
|
4.6
|
101.5
|
1.0
|
OD1
|
A:ASN250
|
4.6
|
126.5
|
1.0
|
N
|
A:CYS289
|
4.6
|
101.5
|
1.0
|
CA
|
A:LEU287
|
4.7
|
99.3
|
1.0
|
N
|
A:GLU290
|
4.7
|
99.8
|
1.0
|
CB
|
A:CYS289
|
4.7
|
96.6
|
1.0
|
CA
|
A:TYR291
|
4.7
|
113.1
|
1.0
|
O
|
A:LEU287
|
4.7
|
108.5
|
1.0
|
CA
|
A:GLU290
|
4.7
|
106.1
|
1.0
|
N
|
A:LEU287
|
4.7
|
91.4
|
1.0
|
O
|
A:THR292
|
4.8
|
75.7
|
1.0
|
C
|
A:LEU287
|
4.8
|
103.9
|
1.0
|
CA
|
A:VAL251
|
4.9
|
98.6
|
1.0
|
CA
|
A:ALA286
|
4.9
|
84.5
|
1.0
|
C
|
A:THR292
|
4.9
|
100.5
|
1.0
|
N
|
A:GLY253
|
5.0
|
90.4
|
1.0
|
|
Potassium binding site 2 out
of 4 in 7vtd
Go back to
Potassium Binding Sites List in 7vtd
Potassium binding site 2 out
of 4 in the Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B
![](/pictures/K/pdb/vt/7vtd-K-sphere_02.jpg) Mono view
![](/pictures/K/pdb/vt/7vtd-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 Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K401
b:92.4
occ:1.00
|
O
|
B:CYS289
|
2.8
|
120.9
|
1.0
|
O
|
B:THR252
|
2.8
|
108.0
|
1.0
|
O
|
B:TYR291
|
2.8
|
86.3
|
1.0
|
O
|
B:ASN250
|
2.9
|
100.2
|
1.0
|
O
|
B:ALA286
|
2.9
|
83.4
|
1.0
|
CB
|
B:ASN250
|
3.2
|
115.8
|
1.0
|
CG2
|
B:THR252
|
3.5
|
111.7
|
1.0
|
C
|
B:ASN250
|
3.5
|
112.5
|
1.0
|
C
|
B:TYR291
|
3.8
|
109.7
|
1.0
|
C
|
B:CYS289
|
3.8
|
113.6
|
1.0
|
C
|
B:THR252
|
3.8
|
104.9
|
1.0
|
CA
|
B:ASN250
|
3.9
|
117.8
|
1.0
|
CG
|
B:ASN250
|
4.0
|
123.9
|
1.0
|
N
|
B:THR252
|
4.0
|
93.3
|
1.0
|
C
|
B:ALA286
|
4.0
|
97.1
|
1.0
|
C
|
B:GLU290
|
4.3
|
100.7
|
1.0
|
CA
|
B:THR252
|
4.3
|
97.9
|
1.0
|
ND2
|
B:ASN250
|
4.4
|
122.8
|
1.0
|
O
|
B:GLU290
|
4.4
|
94.2
|
1.0
|
CA
|
B:THR292
|
4.4
|
105.9
|
1.0
|
N
|
B:VAL251
|
4.4
|
101.9
|
1.0
|
N
|
B:ASN250
|
4.4
|
115.7
|
1.0
|
N
|
B:THR292
|
4.4
|
105.4
|
1.0
|
N
|
B:TYR291
|
4.4
|
92.6
|
1.0
|
CB
|
B:THR252
|
4.5
|
96.3
|
1.0
|
C
|
B:VAL251
|
4.6
|
97.3
|
1.0
|
CA
|
B:CYS289
|
4.6
|
107.4
|
1.0
|
N
|
B:CYS289
|
4.6
|
107.6
|
1.0
|
O
|
B:THR292
|
4.6
|
87.1
|
1.0
|
CB
|
B:CYS289
|
4.7
|
101.0
|
1.0
|
N
|
B:GLU290
|
4.7
|
99.4
|
1.0
|
OD1
|
B:ASN250
|
4.7
|
127.0
|
1.0
|
CA
|
B:TYR291
|
4.7
|
107.6
|
1.0
|
CA
|
B:LEU287
|
4.7
|
103.3
|
1.0
|
CA
|
B:GLU290
|
4.7
|
106.2
|
1.0
|
C
|
B:THR292
|
4.8
|
106.7
|
1.0
|
N
|
B:LEU287
|
4.8
|
103.5
|
1.0
|
O
|
B:LEU287
|
4.8
|
106.3
|
1.0
|
C
|
B:LEU287
|
4.9
|
103.0
|
1.0
|
CA
|
B:VAL251
|
4.9
|
102.5
|
1.0
|
CA
|
B:ALA286
|
5.0
|
92.2
|
1.0
|
N
|
B:GLY253
|
5.0
|
91.5
|
1.0
|
|
Potassium binding site 3 out
of 4 in 7vtd
Go back to
Potassium Binding Sites List in 7vtd
Potassium binding site 3 out
of 4 in the Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B
![](/pictures/K/pdb/vt/7vtd-K-sphere_03.jpg) Mono view
![](/pictures/K/pdb/vt/7vtd-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 Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K401
b:86.0
occ:1.00
|
O
|
C:CYS289
|
2.7
|
124.4
|
1.0
|
O
|
C:THR252
|
2.8
|
93.3
|
1.0
|
O
|
C:TYR291
|
2.8
|
83.2
|
1.0
|
O
|
C:ALA286
|
2.8
|
79.2
|
1.0
|
O
|
C:ASN250
|
2.9
|
101.4
|
1.0
|
CB
|
C:ASN250
|
3.3
|
104.5
|
1.0
|
CG2
|
C:THR252
|
3.4
|
113.8
|
1.0
|
C
|
C:ASN250
|
3.5
|
110.3
|
1.0
|
C
|
C:CYS289
|
3.8
|
125.2
|
1.0
|
C
|
C:THR252
|
3.8
|
96.9
|
1.0
|
C
|
C:TYR291
|
3.8
|
111.8
|
1.0
|
N
|
C:THR252
|
3.9
|
89.5
|
1.0
|
C
|
C:ALA286
|
4.0
|
87.2
|
1.0
|
CA
|
C:ASN250
|
4.0
|
107.0
|
1.0
|
CG
|
C:ASN250
|
4.0
|
118.4
|
1.0
|
C
|
C:GLU290
|
4.2
|
127.8
|
1.0
|
CA
|
C:THR252
|
4.3
|
94.5
|
1.0
|
O
|
C:GLU290
|
4.3
|
119.0
|
1.0
|
ND2
|
C:ASN250
|
4.4
|
120.3
|
1.0
|
N
|
C:TYR291
|
4.4
|
111.8
|
1.0
|
CB
|
C:THR252
|
4.5
|
100.7
|
1.0
|
N
|
C:VAL251
|
4.5
|
98.6
|
1.0
|
N
|
C:ASN250
|
4.5
|
102.3
|
1.0
|
C
|
C:VAL251
|
4.5
|
97.5
|
1.0
|
N
|
C:THR292
|
4.6
|
102.9
|
1.0
|
CA
|
C:CYS289
|
4.6
|
115.2
|
1.0
|
CA
|
C:THR292
|
4.6
|
97.2
|
1.0
|
CA
|
C:LEU287
|
4.6
|
90.6
|
1.0
|
N
|
C:CYS289
|
4.6
|
110.6
|
1.0
|
N
|
C:GLU290
|
4.7
|
134.9
|
1.0
|
OD1
|
C:ASN250
|
4.7
|
124.9
|
1.0
|
CA
|
C:GLU290
|
4.7
|
136.1
|
1.0
|
O
|
C:LEU287
|
4.7
|
106.1
|
1.0
|
CA
|
C:TYR291
|
4.7
|
117.3
|
1.0
|
N
|
C:LEU287
|
4.7
|
74.8
|
1.0
|
CB
|
C:CYS289
|
4.7
|
114.2
|
1.0
|
O
|
C:THR292
|
4.8
|
87.2
|
1.0
|
C
|
C:LEU287
|
4.8
|
92.9
|
1.0
|
CA
|
C:VAL251
|
4.9
|
103.7
|
1.0
|
CA
|
C:ALA286
|
4.9
|
87.2
|
1.0
|
C
|
C:THR292
|
4.9
|
104.7
|
1.0
|
N
|
C:GLY253
|
5.0
|
83.7
|
1.0
|
|
Potassium binding site 4 out
of 4 in 7vtd
Go back to
Potassium Binding Sites List in 7vtd
Potassium binding site 4 out
of 4 in the Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B
![](/pictures/K/pdb/vt/7vtd-K-sphere_04.jpg) Mono view
![](/pictures/K/pdb/vt/7vtd-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 Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K401
b:92.2
occ:1.00
|
O
|
D:CYS289
|
2.7
|
119.2
|
1.0
|
O
|
D:THR252
|
2.8
|
106.9
|
1.0
|
O
|
D:ASN250
|
2.9
|
105.6
|
1.0
|
O
|
D:ALA286
|
2.9
|
87.4
|
1.0
|
O
|
D:TYR291
|
2.9
|
94.0
|
1.0
|
CB
|
D:ASN250
|
3.3
|
106.0
|
1.0
|
CG2
|
D:THR252
|
3.4
|
119.2
|
1.0
|
C
|
D:ASN250
|
3.5
|
110.5
|
1.0
|
C
|
D:THR252
|
3.8
|
105.6
|
1.0
|
C
|
D:CYS289
|
3.8
|
111.2
|
1.0
|
N
|
D:THR252
|
3.9
|
88.8
|
1.0
|
C
|
D:TYR291
|
3.9
|
114.5
|
1.0
|
CG
|
D:ASN250
|
3.9
|
114.4
|
1.0
|
CA
|
D:ASN250
|
4.0
|
110.1
|
1.0
|
C
|
D:ALA286
|
4.0
|
88.7
|
1.0
|
CA
|
D:THR252
|
4.2
|
101.1
|
1.0
|
ND2
|
D:ASN250
|
4.3
|
119.1
|
1.0
|
C
|
D:GLU290
|
4.3
|
106.9
|
1.0
|
O
|
D:GLU290
|
4.4
|
98.2
|
1.0
|
N
|
D:VAL251
|
4.4
|
88.9
|
1.0
|
CB
|
D:THR252
|
4.4
|
110.3
|
1.0
|
C
|
D:VAL251
|
4.5
|
92.9
|
1.0
|
N
|
D:TYR291
|
4.5
|
101.9
|
1.0
|
OD1
|
D:ASN250
|
4.6
|
114.3
|
1.0
|
CA
|
D:THR292
|
4.6
|
108.7
|
1.0
|
N
|
D:THR292
|
4.6
|
113.7
|
1.0
|
N
|
D:ASN250
|
4.6
|
110.4
|
1.0
|
CA
|
D:CYS289
|
4.6
|
102.8
|
1.0
|
N
|
D:CYS289
|
4.7
|
101.7
|
1.0
|
N
|
D:GLU290
|
4.7
|
107.3
|
1.0
|
CA
|
D:GLU290
|
4.7
|
113.8
|
1.0
|
CA
|
D:LEU287
|
4.7
|
96.2
|
1.0
|
O
|
D:LEU287
|
4.7
|
111.4
|
1.0
|
CB
|
D:CYS289
|
4.8
|
101.2
|
1.0
|
O
|
D:THR292
|
4.8
|
91.0
|
1.0
|
N
|
D:LEU287
|
4.8
|
86.6
|
1.0
|
CA
|
D:TYR291
|
4.8
|
113.3
|
1.0
|
C
|
D:LEU287
|
4.9
|
107.4
|
1.0
|
CA
|
D:VAL251
|
4.9
|
97.3
|
1.0
|
C
|
D:THR292
|
4.9
|
110.7
|
1.0
|
N
|
D:GLY253
|
5.0
|
91.3
|
1.0
|
CA
|
D:ALA286
|
5.0
|
90.4
|
1.0
|
|
Reference:
S.H.Kim,
M.Kim,
D.Park,
S.Byun,
S.Rhee.
Substrate-Binding Loop Interactions with Pseudouridine Trigger Conformational Changes That Promote Catalytic Efficiency of Pseudouridine Kinase Puki. J.Biol.Chem. V. 298 01869 2022.
ISSN: ESSN 1083-351X
PubMed: 35346685
DOI: 10.1016/J.JBC.2022.101869
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