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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


Mono view


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

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Potassium binding site 2 out of 4 in the Unliganded Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B


Mono view


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


Mono view


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


Mono view


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
Page generated: Sat Aug 9 15:08:56 2025

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