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Potassium in PDB 7vte: Uridine Bound Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B

Enzymatic activity of Uridine Bound Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B

All present enzymatic activity of Uridine Bound Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B:
2.7.1.83;

Protein crystallography data

The structure of Uridine Bound Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B, PDB code: 7vte 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) 36.89 / 2.15
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 185.689, 185.689, 50.754, 90, 90, 120
R / Rfree (%) 25 / 28.7

Potassium Binding Sites:

The binding sites of Potassium atom in the Uridine Bound Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B (pdb code 7vte). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Uridine Bound Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B, PDB code: 7vte:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 7vte

Go back to Potassium Binding Sites List in 7vte
Potassium binding site 1 out of 4 in the Uridine Bound 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 Uridine Bound Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K401

b:161.5
occ:1.00
 O A:TYR291 2.6 122.1 1.0
O A:ALA286 2.6 133.8 1.0
OD1 A:ASN250 2.6 127.5 1.0
O A:THR252 2.6 117.5 1.0
O A:CYS289 3.0 140.1 1.0
CG A:ASN250 3.6 119.0 1.0
C A:ALA286 3.6 127.1 1.0
C A:TYR291 3.7 122.5 1.0
O A:THR292 3.7 93.2 1.0
OG1 A:THR252 3.7 118.5 1.0
C A:THR252 3.7 116.8 1.0
ND2 A:ASN250 3.8 115.8 1.0
C A:THR292 4.0 113.8 1.0
CA A:THR292 4.0 107.8 1.0
O A:ASN250 4.1 91.1 1.0
C A:CYS289 4.1 133.2 1.0
CA A:ALA286 4.1 126.4 1.0
N A:THR292 4.3 114.7 1.0
CB A:ALA286 4.3 121.1 1.0
CB A:CYS289 4.4 117.4 1.0
N A:THR252 4.5 108.6 1.0
CA A:THR252 4.5 110.6 1.0
CA A:CYS289 4.6 124.7 1.0
N A:LEU287 4.6 116.8 1.0
N A:CYS289 4.6 119.1 1.0
N A:TYR291 4.7 124.6 1.0
N A:GLY253 4.7 112.2 1.0
C A:ASN250 4.7 100.2 1.0
CB A:THR252 4.7 105.2 1.0
CA A:GLY253 4.7 106.7 1.0
CA A:TYR291 4.8 125.6 1.0
N A:ASN293 4.8 130.1 1.0
CA A:LEU287 4.9 103.6 1.0
C A:VAL251 4.9 107.3 1.0
C A:GLU290 4.9 127.2 1.0
CB A:ASN250 5.0 97.6 1.0

Potassium binding site 2 out of 4 in 7vte

Go back to Potassium Binding Sites List in 7vte
Potassium binding site 2 out of 4 in the Uridine Bound 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 Uridine Bound Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K401

b:119.5
occ:1.00
 OD1 B:ASN250 2.6 134.9 1.0
O B:ALA286 2.7 118.1 1.0
O B:THR252 2.7 125.6 1.0
O B:CYS289 2.7 145.2 1.0
O B:ASN250 3.0 93.6 1.0
O B:TYR291 3.0 104.6 1.0
CG B:ASN250 3.7 127.4 1.0
C B:ALA286 3.7 116.9 1.0
OG1 B:THR252 3.8 123.1 1.0
C B:THR252 3.8 125.2 1.0
C B:ASN250 3.8 106.8 1.0
C B:CYS289 3.9 145.1 1.0
N B:THR252 4.0 117.0 1.0
C B:TYR291 4.1 123.8 1.0
ND2 B:ASN250 4.3 132.8 1.0
C B:VAL251 4.3 115.3 1.0
CA B:THR252 4.4 117.8 1.0
N B:LEU287 4.5 111.4 1.0
CA B:LEU287 4.6 106.2 1.0
N B:VAL251 4.6 114.6 1.0
N B:CYS289 4.6 120.9 1.0
CA B:ALA286 4.6 115.3 1.0
CA B:CYS289 4.6 132.2 1.0
O B:THR292 4.7 123.0 1.0
N B:TYR291 4.7 140.2 1.0
CA B:VAL251 4.7 121.0 1.0
CA B:ASN250 4.7 117.1 1.0
CA B:THR292 4.7 132.8 1.0
C B:LEU287 4.7 98.3 1.0
CB B:THR252 4.7 110.5 1.0
C B:GLU290 4.7 141.1 1.0
CB B:CYS289 4.8 131.7 1.0
CB B:ASN250 4.8 113.7 1.0
O B:VAL251 4.8 111.9 1.0
CB B:ALA286 4.8 111.6 1.0
O B:LEU287 4.9 101.7 1.0
N B:THR292 4.9 130.5 1.0
C B:THR292 4.9 131.1 1.0
N B:GLY253 4.9 117.0 1.0
O B:GLU290 4.9 140.6 1.0
N B:GLU290 5.0 146.4 1.0

Potassium binding site 3 out of 4 in 7vte

Go back to Potassium Binding Sites List in 7vte
Potassium binding site 3 out of 4 in the Uridine Bound 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 Uridine Bound Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K401

b:189.2
occ:1.00
 O C:THR252 2.6 127.2 1.0
O C:TYR291 2.6 108.3 1.0
O C:ALA286 2.6 120.9 1.0
OD1 C:ASN250 2.7 133.8 1.0
ND2 C:ASN250 3.2 134.4 1.0
O C:CYS289 3.2 140.3 1.0
CG C:ASN250 3.3 134.4 1.0
C C:ALA286 3.5 120.7 1.0
O C:THR292 3.6 106.8 1.0
C C:TYR291 3.7 123.9 1.0
C C:THR252 3.7 125.3 1.0
C C:THR292 3.9 118.7 1.0
OG1 C:THR252 3.9 126.6 1.0
CA C:THR292 3.9 123.4 1.0
CA C:ALA286 4.1 117.6 1.0
CB C:ALA286 4.1 110.4 1.0
N C:THR292 4.3 123.9 1.0
C C:CYS289 4.3 135.9 1.0
O C:ASN250 4.5 120.2 1.0
CA C:GLY253 4.6 108.5 1.0
N C:LEU287 4.6 118.4 1.0
N C:GLY253 4.6 118.4 1.0
CA C:THR252 4.6 122.1 1.0
N C:THR252 4.6 120.3 1.0
CB C:CYS289 4.6 120.7 1.0
N C:ASN293 4.8 114.8 1.0
N C:TYR291 4.8 131.3 1.0
CB C:ASN250 4.8 124.6 1.0
CA C:CYS289 4.9 125.7 1.0
N C:CYS289 4.9 121.8 1.0
CA C:TYR291 4.9 126.3 1.0
CB C:THR252 4.9 118.4 1.0
C C:GLY253 4.9 93.1 1.0
C C:ASN250 4.9 118.3 1.0
CA C:LEU287 4.9 111.8 1.0

Potassium binding site 4 out of 4 in 7vte

Go back to Potassium Binding Sites List in 7vte
Potassium binding site 4 out of 4 in the Uridine Bound 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 Uridine Bound Structure of Pseudouridine Kinase (Puki) From Escherichia Coli Strain B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K401

b:207.2
occ:1.00
 O D:TYR291 2.6 159.6 1.0
O D:ALA286 2.6 120.8 1.0
O D:THR252 2.7 123.0 1.0
OD1 D:ASN250 2.7 134.7 1.0
O D:CYS289 3.2 139.5 1.0
O D:THR292 3.5 124.3 1.0
CG D:ASN250 3.6 132.6 1.0
C D:ALA286 3.6 115.7 1.0
ND2 D:ASN250 3.6 135.9 1.0
C D:TYR291 3.8 158.4 1.0
C D:THR252 3.8 119.8 1.0
C D:THR292 3.8 130.7 1.0
CA D:THR292 4.0 143.3 1.0
CA D:ALA286 4.1 110.3 1.0
OG1 D:THR252 4.2 122.1 1.0
CB D:ALA286 4.2 100.8 1.0
C D:CYS289 4.3 132.5 1.0
N D:THR292 4.4 153.6 1.0
O D:ASN250 4.4 107.9 1.0
CA D:GLY253 4.6 106.9 1.0
CB D:CYS289 4.6 122.3 1.0
N D:GLY253 4.7 114.5 1.0
N D:ASN293 4.7 127.2 1.0
N D:LEU287 4.7 114.3 1.0
N D:TYR291 4.7 158.8 1.0
CA D:THR252 4.8 118.3 1.0
N D:THR252 4.8 117.8 1.0
CA D:CYS289 4.8 125.4 1.0
N D:CYS289 4.8 114.9 1.0
C D:GLY253 4.9 92.8 1.0
CA D:TYR291 4.9 161.3 1.0
C D:ASN250 5.0 114.1 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: Mon Aug 12 21:29:00 2024

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