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Sodium in PDB 3b1q: Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine

Enzymatic activity of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine

All present enzymatic activity of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine:
2.7.1.143;

Protein crystallography data

The structure of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine, PDB code: 3b1q was solved by Y.Yasutake, H.Ota, E.Hino, S.Sakasegawa, T.Tamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.78 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 83.110, 85.897, 86.872, 66.33, 68.47, 67.81
R / Rfree (%) 17.6 / 20.7

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Sodium atom in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine (pdb code 3b1q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 15 binding sites of Sodium where determined in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine, PDB code: 3b1q:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 15 in 3b1q

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Sodium binding site 1 out of 15 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na332

b:21.2
occ:1.00
 O A:ARG213 2.3 22.1 1.0
O A:ALA186 2.3 16.4 1.0
O A:HOH420 2.3 25.4 1.0
O A:GLU184 2.4 18.4 1.0
O A:ILE183 2.6 18.1 1.0
C A:GLU184 3.0 17.6 1.0
C A:ALA186 3.4 15.0 1.0
C A:ARG213 3.5 21.6 1.0
CA A:GLU184 3.5 17.6 1.0
C A:ILE183 3.6 16.6 1.0
CG1 A:VAL214 3.6 18.3 1.0
N A:ALA186 3.6 15.1 1.0
N A:LEU185 3.9 15.5 1.0
C A:LEU185 4.0 16.8 1.0
N A:GLU184 4.1 16.1 1.0
CA A:VAL214 4.1 17.6 1.0
CA A:ALA186 4.1 15.2 1.0
N A:VAL214 4.2 19.8 1.0
O A:HOH778 4.4 37.0 1.0
CA A:LEU185 4.4 15.4 1.0
O A:LEU185 4.5 17.2 1.0
CB A:VAL214 4.5 17.2 1.0
N A:THR187 4.5 13.9 1.0
CA A:ARG213 4.6 24.4 1.0
OE2 A:GLU184 4.6 39.6 1.0
CB A:ARG213 4.7 24.4 1.0
CB A:ALA186 4.7 15.6 1.0
CD A:GLU184 4.7 33.6 1.0
CA A:THR187 4.8 15.1 1.0
CB A:GLU184 4.9 19.1 1.0
CA A:ILE183 5.0 17.6 1.0
CG A:GLU184 5.0 25.3 1.0

Sodium binding site 2 out of 15 in 3b1q

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Sodium binding site 2 out of 15 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na333

b:18.8
occ:1.00
 O F:HOH988 2.1 31.4 1.0
O A:HOH785 2.3 25.4 1.0
O A:HOH422 2.4 22.2 1.0
O A:HOH421 2.4 25.9 1.0
O A:HOH786 2.4 30.9 1.0
O A:HOH784 2.5 29.8 1.0
NH2 A:ARG256 4.0 19.5 1.0
OE1 A:GLN169 4.2 27.3 1.0
OE2 A:GLU195 4.3 21.0 1.0
ND2 F:ASN34 4.3 61.3 1.0
CZ A:ARG256 4.3 20.6 1.0
O A:HOH416 4.4 26.1 1.0
O A:HOH406 4.4 24.0 1.0
CA A:GLY168 4.4 17.9 1.0
OE1 A:GLU195 4.5 20.4 1.0
O A:HOH368 4.5 19.1 1.0
OD1 A:ASP166 4.7 21.4 1.0
CD A:GLN169 4.7 27.5 1.0
NH1 A:ARG256 4.7 16.8 1.0
NE2 A:GLN169 4.8 26.5 1.0
O5' A:NOS401 4.8 17.6 1.0
NE A:ARG256 4.8 21.8 1.0
CD A:GLU195 4.9 23.0 1.0
OD1 A:ASP253 4.9 16.0 1.0
O A:HOH384 4.9 21.4 1.0

Sodium binding site 3 out of 15 in 3b1q

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Sodium binding site 3 out of 15 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na334

b:29.4
occ:1.00
 O A:HOH788 2.2 37.3 1.0
O A:HOH787 2.3 36.2 1.0
O A:GLY204 2.4 24.9 1.0
O A:HOH984 2.5 41.0 1.0
O A:HOH362 2.8 30.2 1.0
C A:GLY204 3.6 22.8 1.0
CA A:GLY204 4.3 22.8 1.0
OE2 A:GLU209 4.5 30.9 1.0
CD1 A:TRP205 4.5 28.0 1.0
N A:TRP205 4.6 20.7 1.0
OE1 A:GLU209 4.8 41.6 1.0
CA A:TRP205 4.8 22.4 1.0

Sodium binding site 4 out of 15 in 3b1q

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Sodium binding site 4 out of 15 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na330

b:22.4
occ:1.00
 O B:ARG213 2.3 24.8 1.0
O B:HOH601 2.3 31.3 1.0
O B:ALA186 2.3 20.4 1.0
O B:GLU184 2.4 22.7 1.0
O B:ILE183 2.5 19.8 1.0
C B:GLU184 3.0 22.4 1.0
C B:ALA186 3.5 18.7 1.0
C B:ARG213 3.5 23.5 1.0
CA B:GLU184 3.6 22.2 1.0
N B:ALA186 3.6 19.3 1.0
C B:ILE183 3.6 20.0 1.0
CG1 B:VAL214 3.7 20.6 1.0
C B:LEU185 3.9 21.5 1.0
N B:LEU185 3.9 20.6 1.0
CA B:ALA186 4.1 18.7 1.0
N B:GLU184 4.1 20.1 1.0
O B:HOH602 4.1 34.1 1.0
CA B:VAL214 4.2 19.6 1.0
N B:VAL214 4.3 21.8 1.0
CA B:LEU185 4.4 21.4 1.0
O B:LEU185 4.4 21.9 1.0
CB B:VAL214 4.6 18.1 1.0
N B:THR187 4.6 16.2 1.0
CA B:ARG213 4.6 25.5 1.0
CB B:ALA186 4.6 19.1 1.0
CB B:ARG213 4.6 25.8 1.0
CA B:THR187 4.9 17.2 1.0
CB B:GLU184 4.9 22.8 1.0
CA B:ILE183 4.9 19.2 1.0

Sodium binding site 5 out of 15 in 3b1q

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Sodium binding site 5 out of 15 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na331

b:18.0
occ:1.00
 O B:HOH599 2.2 41.9 1.0
O B:HOH600 2.3 34.8 1.0
O B:HOH596 2.3 28.3 1.0
O B:GLY204 2.3 26.2 1.0
O B:HOH597 2.4 32.5 1.0
O B:HOH598 2.5 39.1 1.0
C B:GLY204 3.5 25.2 1.0
CA B:GLY204 4.2 26.2 1.0
OE2 B:GLU209 4.5 29.4 1.0
O B:HOH861 4.5 36.9 1.0
N B:TRP205 4.5 24.6 1.0
OE1 B:GLU209 4.7 37.1 1.0
CD1 B:TRP205 4.8 27.6 1.0
CA B:TRP205 4.8 25.5 1.0

Sodium binding site 6 out of 15 in 3b1q

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Sodium binding site 6 out of 15 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na332

b:21.8
occ:1.00
 O B:HOH782 1.9 37.6 1.0
O B:HOH607 2.1 37.5 1.0
O B:ARG231 2.3 35.8 1.0
O C:GLY204 2.3 29.8 1.0
O B:HOH608 2.4 31.9 1.0
O B:HOH378 2.7 24.6 1.0
C B:ARG231 3.5 35.1 1.0
C C:GLY204 3.5 27.3 1.0
CA B:ARG231 4.1 35.4 1.0
CA C:GLY204 4.2 28.2 1.0
OE2 C:GLU209 4.4 33.1 1.0
O C:HOH926 4.4 35.1 1.0
OE1 C:GLU209 4.5 35.7 1.0
N B:ASP232 4.5 34.4 1.0
N C:TRP205 4.5 26.4 1.0
OD2 B:ASP208 4.5 39.9 1.0
CD1 C:TRP205 4.6 30.6 1.0
OD1 B:ASP208 4.6 38.2 1.0
CB B:ARG231 4.7 37.0 1.0
CA B:ASP232 4.8 35.8 1.0
CA C:TRP205 4.8 25.7 1.0
CD C:GLU209 4.9 35.0 1.0
O B:HIS230 4.9 31.8 1.0
CG B:ASP208 5.0 35.9 1.0

Sodium binding site 7 out of 15 in 3b1q

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Sodium binding site 7 out of 15 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na332

b:26.4
occ:1.00
 O C:HOH779 2.0 38.2 1.0
O C:ALA186 2.4 17.8 1.0
O C:GLU184 2.4 21.8 1.0
O C:ARG213 2.5 26.0 1.0
O C:ILE183 2.6 20.1 1.0
O C:HOH519 2.9 27.6 1.0
C C:GLU184 2.9 20.7 1.0
O C:HOH1059 3.5 37.8 1.0
CA C:GLU184 3.5 21.3 1.0
C C:ALA186 3.5 15.7 1.0
N C:ALA186 3.7 17.3 1.0
C C:ARG213 3.7 24.5 1.0
C C:ILE183 3.7 19.6 1.0
CG1 C:VAL214 3.8 21.8 1.0
N C:LEU185 3.9 20.2 1.0
C C:LEU185 4.0 20.1 1.0
N C:GLU184 4.1 19.5 1.0
CA C:ALA186 4.1 15.7 1.0
CA C:VAL214 4.2 19.9 1.0
N C:VAL214 4.4 21.9 1.0
O C:LEU185 4.4 20.2 1.0
CA C:LEU185 4.4 20.8 1.0
N C:THR187 4.6 15.6 1.0
CB C:VAL214 4.7 19.9 1.0
CB C:ALA186 4.7 16.4 1.0
CA C:ARG213 4.8 26.2 1.0
CB C:GLU184 4.8 23.4 1.0
O C:HOH1060 4.9 42.5 1.0
CA C:THR187 4.9 15.8 1.0
CB C:ARG213 4.9 27.7 1.0

Sodium binding site 8 out of 15 in 3b1q

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Sodium binding site 8 out of 15 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na333

b:17.7
occ:1.00
 O C:HOH634 2.2 37.1 1.0
O C:HOH632 2.3 28.1 1.0
O C:HOH631 2.3 27.9 1.0
O C:HOH1039 2.4 40.0 1.0
O C:HOH464 2.4 29.1 1.0
O C:HOH633 2.4 40.1 1.0
O C:HOH454 2.5 25.6 1.0
NH2 C:ARG256 4.1 21.4 1.0
OE2 C:GLU195 4.2 24.6 1.0
OE1 C:GLN169 4.2 25.5 1.0
CA C:GLY168 4.2 14.4 1.0
CZ C:ARG256 4.4 19.6 1.0
OE1 C:GLU195 4.4 21.2 1.0
O C:HOH630 4.4 24.1 1.0
O C:HOH374 4.4 21.7 1.0
O C:HOH357 4.6 16.3 1.0
OD1 C:ASP166 4.6 22.5 1.0
NH1 C:ARG256 4.7 18.2 1.0
CD C:GLN169 4.7 24.7 1.0
O C:HOH375 4.7 20.4 1.0
CD C:GLU195 4.7 22.6 1.0
O5' C:NOS401 4.8 15.3 1.0
NE C:ARG256 4.9 20.2 1.0
NE2 C:GLN169 4.9 25.1 1.0

Sodium binding site 9 out of 15 in 3b1q

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Sodium binding site 9 out of 15 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na328

b:31.7
occ:1.00
 O D:HOH486 2.1 34.3 1.0
O D:ALA186 2.3 23.9 1.0
O D:ARG213 2.3 29.4 1.0
O D:GLU184 2.3 29.1 1.0
O D:ILE183 2.7 27.3 1.0
C D:GLU184 3.0 28.5 1.0
C D:ALA186 3.4 23.3 1.0
N D:ALA186 3.5 22.1 1.0
C D:ARG213 3.5 30.0 1.0
CA D:GLU184 3.6 28.7 1.0
C D:ILE183 3.7 25.4 1.0
C D:LEU185 3.8 25.0 1.0
CG1 D:VAL214 3.8 27.4 1.0
N D:LEU185 3.9 26.3 1.0
CA D:ALA186 3.9 22.4 1.0
N D:GLU184 4.1 26.9 1.0
O D:LEU185 4.2 26.2 1.0
CA D:VAL214 4.3 25.8 1.0
CA D:LEU185 4.3 26.2 1.0
N D:VAL214 4.3 29.0 1.0
CB D:ARG213 4.5 30.4 1.0
CA D:ARG213 4.5 31.4 1.0
N D:THR187 4.5 22.6 1.0
CB D:ALA186 4.5 21.0 1.0
CB D:VAL214 4.7 26.0 1.0
CB D:GLU184 4.9 29.7 1.0
CA D:THR187 4.9 23.7 1.0

Sodium binding site 10 out of 15 in 3b1q

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Sodium binding site 10 out of 15 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Inosine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na333

b:26.7
occ:1.00
 O E:ALA186 2.2 18.5 1.0
O E:HOH416 2.3 29.9 1.0
O E:ARG213 2.4 27.3 1.0
O E:GLU184 2.6 19.8 1.0
O E:ILE183 2.7 19.1 1.0
C E:GLU184 3.1 19.0 1.0
CG1 E:VAL214 3.2 25.1 1.0
C E:ALA186 3.3 17.2 1.0
CA E:GLU184 3.5 19.2 1.0
C E:ARG213 3.5 25.3 1.0
N E:ALA186 3.5 17.7 1.0
CA E:VAL214 3.7 23.5 1.0
C E:ILE183 3.7 18.7 1.0
CA E:ALA186 3.9 17.4 1.0
CB E:VAL214 4.0 21.1 1.0
C E:LEU185 4.0 19.8 1.0
N E:LEU185 4.0 17.6 1.0
N E:VAL214 4.1 22.9 1.0
N E:GLU184 4.1 17.8 1.0
N E:THR187 4.4 15.9 1.0
CB E:ALA186 4.5 16.3 1.0
O E:LEU185 4.5 19.9 1.0
CA E:LEU185 4.5 18.8 1.0
CA E:THR187 4.8 17.5 1.0
CA E:ARG213 4.8 24.5 1.0
CB E:GLU184 4.8 19.6 1.0
C E:VAL214 5.0 23.1 1.0

Reference:

Y.Yasutake, H.Ota, E.Hino, S.Sakasegawa, T.Tamura. Structures of Burkholderia Thailandensis Nucleoside Kinase: Implications For the Catalytic Mechanism and Nucleoside Selectivity Acta Crystallogr.,Sect.D V. 67 945 2011.
ISSN: ISSN 0907-4449
PubMed: 22101821
DOI: 10.1107/S0907444911038777
Page generated: Sun Aug 17 12:45:47 2025

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