Atomistry » Potassium » PDB 7u1y-7w93 » 7vtd
Atomistry »
  Potassium »
    PDB 7u1y-7w93 »
      7vtd »

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

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


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: Mon Aug 12 21:28:21 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy