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Sodium in PDB 5x8k: V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase

Enzymatic activity of V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase

All present enzymatic activity of V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase:
2.7.4.9;

Protein crystallography data

The structure of V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase, PDB code: 5x8k was solved by S.K.Chaudhary, J.Jeyakanthan, K.Sekar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.51 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.600, 47.300, 151.410, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.6

Other elements in 5x8k:

The structure of V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase (pdb code 5x8k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase, PDB code: 5x8k:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 5x8k

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Sodium binding site 1 out of 10 in the V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:16.2
occ:1.00
 OG A:SER66 2.8 10.3 1.0
NH2 A:ARG69 2.9 9.1 1.0
OH A:TYR62 2.9 10.9 1.0
CZ A:TYR62 3.5 10.0 1.0
CB A:SER66 3.6 9.0 1.0
CD1 A:LEU93 3.7 8.3 1.0
CE1 A:TYR62 3.7 9.9 1.0
CB A:ALA115 3.7 10.9 1.0
CA A:ALA115 3.8 10.6 1.0
CA A:SER66 3.8 8.2 1.0
CD A:ARG69 3.9 8.3 1.0
CZ A:ARG69 4.0 8.9 1.0
CB A:ALA118 4.3 12.9 1.0
NE A:ARG69 4.4 8.8 1.0
N A:ALA115 4.4 10.0 1.0
CE2 A:TYR62 4.5 9.7 1.0
N A:SER66 4.6 8.1 1.0
CB A:ARG69 4.7 7.6 1.0
CG A:ARG69 4.7 7.9 1.0
CD1 A:TYR62 4.8 9.6 1.0
C A:SER66 4.9 8.1 1.0
O A:SER66 4.9 8.1 1.0
CG1 A:VAL114 4.9 9.8 1.0

Sodium binding site 2 out of 10 in 5x8k

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Sodium binding site 2 out of 10 in the V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:18.8
occ:1.00
 O A:HOH415 2.6 17.8 1.0
O A:HOH370 2.7 14.7 1.0
O A:HOH407 2.8 19.6 1.0
O A:ARG157 2.8 8.8 1.0
C A:ARG157 3.6 9.8 1.0
CA A:ARG157 3.6 10.6 1.0
N A:GLY161 3.7 9.2 1.0
CB A:GLU160 3.8 11.6 1.0
CD1 A:TYR102 3.8 14.1 1.0
CB A:ARG157 3.9 11.1 1.0
CB A:TYR102 4.0 10.6 1.0
C A:GLU160 4.2 8.7 1.0
CA A:GLY161 4.3 9.4 1.0
CG A:ARG157 4.3 11.4 1.0
CG A:TYR102 4.3 11.5 1.0
CA A:GLU160 4.5 10.4 1.0
O A:TYR102 4.5 10.9 1.0
O A:HOH405 4.7 21.5 1.0
CE1 A:TYR102 4.8 14.7 1.0
CA A:TYR102 4.8 10.0 1.0
O A:ARG156 4.8 10.7 1.0
N A:THR158 4.9 9.2 1.0
O A:GLU160 4.9 8.5 1.0
C A:TYR102 4.9 10.2 1.0
N A:ARG157 4.9 9.8 1.0
CG A:GLU160 4.9 12.5 1.0
CD A:ARG157 5.0 12.4 1.0

Sodium binding site 3 out of 10 in 5x8k

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Sodium binding site 3 out of 10 in the V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:18.0
occ:1.00
 OD1 A:ASP131 2.7 10.6 1.0
O A:HOH348 3.0 16.1 1.0
O A:ARG159 3.2 9.4 1.0
CG A:ARG159 3.4 12.6 1.0
CB A:TYR162 3.5 9.3 1.0
CG A:ASP131 3.7 10.3 1.0
CA A:ARG159 3.8 10.6 1.0
CD1 A:LEU129 3.8 9.3 1.0
C A:ARG159 3.9 10.2 1.0
CA A:ASP131 3.9 10.7 1.0
CB A:ASP131 4.0 10.7 1.0
CD2 A:TYR162 4.0 9.4 1.0
CD2 A:LEU129 4.0 9.5 1.0
CB A:ARG159 4.2 11.2 1.0
CG A:TYR162 4.2 9.0 1.0
CG A:LEU129 4.2 9.2 1.0
CG A:LEU163 4.3 9.1 1.0
CD A:ARG159 4.4 14.6 1.0
NE A:ARG159 4.4 12.8 1.0
N A:LEU163 4.6 8.5 1.0
O A:LEU130 4.6 11.0 1.0
N A:LEU132 4.6 11.9 1.0
CD2 A:LEU163 4.7 9.0 1.0
CA A:TYR162 4.8 9.3 1.0
N A:ASP131 4.8 10.2 1.0
C A:ASP131 4.9 10.9 1.0
CD1 A:LEU163 4.9 9.3 1.0
OD2 A:ASP131 4.9 10.4 1.0
C A:TYR162 4.9 8.4 1.0
O A:LEU132 5.0 13.5 1.0

Sodium binding site 4 out of 10 in 5x8k

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Sodium binding site 4 out of 10 in the V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:16.9
occ:1.00
 OG1 A:THR7 2.6 9.1 1.0
OD2 A:ASP94 2.7 12.0 1.0
OE2 A:GLU9 2.8 9.6 1.0
O A:HOH377 2.8 15.6 1.0
CG A:GLU9 3.4 9.5 1.0
CB A:THR7 3.4 9.8 1.0
CD A:GLU9 3.6 9.3 1.0
CG A:ASP94 3.6 10.0 1.0
CG2 A:THR127 3.7 10.9 1.0
OG1 A:THR127 3.7 10.8 1.0
CB A:TYR92 3.7 8.0 1.0
CB A:ASP94 3.8 8.9 1.0
CG2 A:THR7 3.9 10.1 1.0
NH1 A:ARG172 4.1 11.0 1.0
CG A:PRO124 4.2 13.6 1.0
N A:ASP94 4.2 8.1 1.0
CB A:THR127 4.3 10.8 1.0
N A:TYR92 4.3 7.7 1.0
CA A:TYR92 4.4 7.7 1.0
CD2 A:TYR92 4.4 8.7 1.0
C A:TYR92 4.5 7.7 1.0
N A:LEU93 4.6 7.6 1.0
CA A:ASP94 4.6 8.7 1.0
CG A:TYR92 4.6 8.0 1.0
OD1 A:ASP94 4.6 9.4 1.0
OE1 A:GLU9 4.8 9.1 1.0
CA A:THR7 4.8 9.6 1.0
CB A:GLU9 4.9 9.0 1.0

Sodium binding site 5 out of 10 in 5x8k

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Sodium binding site 5 out of 10 in the V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:21.4
occ:1.00
 OE1 A:GLU160 2.7 15.1 1.0
O A:GLU160 2.7 8.5 1.0
NH2 A:ARG167 3.0 14.8 1.0
O A:HOH308 3.3 23.7 1.0
C A:GLU160 3.5 8.7 1.0
CB A:GLU160 3.6 11.6 1.0
CA A:GLU160 3.6 10.4 1.0
NH1 A:ARG167 3.6 17.1 1.0
CZ A:ARG167 3.8 14.3 1.0
CB A:LEU163 3.8 9.1 1.0
CD A:GLU160 3.8 14.4 1.0
N A:ALA164 3.8 8.4 1.0
CG A:GLU160 4.2 12.5 1.0
O A:HOH407 4.3 19.6 1.0
CB A:ALA164 4.3 8.8 1.0
C A:LEU163 4.3 8.7 1.0
CA A:ALA164 4.4 8.3 1.0
CA A:LEU163 4.6 8.8 1.0
N A:GLY161 4.7 9.2 1.0
CD1 A:LEU163 4.7 9.3 1.0
O A:HOH373 4.9 18.8 1.0
OE2 A:GLU160 4.9 17.1 1.0
CG A:LEU163 4.9 9.1 1.0
N A:LEU163 5.0 8.5 1.0

Sodium binding site 6 out of 10 in 5x8k

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Sodium binding site 6 out of 10 in the V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:18.5
occ:1.00
 OG B:SER66 2.8 10.8 1.0
OH B:TYR62 3.0 10.1 1.0
NH1 B:ARG69 3.0 10.0 1.0
CB B:SER66 3.4 9.6 1.0
CZ B:TYR62 3.5 9.3 1.0
CD1 B:LEU93 3.7 8.9 1.0
CE1 B:TYR62 3.7 9.8 1.0
CA B:SER66 3.8 9.4 1.0
CD B:ARG69 3.8 9.4 1.0
CB B:ALA115 3.8 12.2 1.0
CA B:ALA115 4.0 12.4 1.0
CZ B:ARG69 4.0 10.0 1.0
CB B:ALA118 4.3 18.4 1.0
NE B:ARG69 4.3 9.9 1.0
N B:ALA115 4.5 10.9 1.0
CE2 B:TYR62 4.5 9.1 1.0
N B:SER66 4.6 9.8 1.0
CB B:ARG69 4.6 9.2 1.0
CG B:ARG69 4.6 8.9 1.0
CG1 B:VAL114 4.7 9.7 1.0
CD1 B:TYR62 4.8 9.1 1.0
C B:SER66 4.9 9.2 1.0
O B:SER66 4.9 8.2 1.0
O B:LEU111 5.0 10.0 1.0

Sodium binding site 7 out of 10 in 5x8k

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Sodium binding site 7 out of 10 in the V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:20.8
occ:1.00
 OD1 B:ASP131 2.7 13.7 1.0
O B:HOH325 3.1 16.6 1.0
O B:ARG159 3.2 11.0 1.0
CB B:TYR162 3.5 9.2 1.0
CG B:ARG159 3.6 13.7 1.0
CG B:ASP131 3.7 12.6 1.0
CA B:ASP131 3.8 12.0 1.0
C B:ARG159 3.9 11.4 1.0
CA B:ARG159 3.9 11.9 1.0
CD1 B:LEU129 3.9 11.3 1.0
CB B:ASP131 4.0 12.4 1.0
CD2 B:TYR162 4.0 7.9 1.0
CD2 B:LEU129 4.1 11.9 1.0
CG B:TYR162 4.2 8.5 1.0
CD2 B:LEU163 4.2 12.3 1.0
CG B:LEU163 4.2 12.2 1.0
CG B:LEU129 4.3 10.6 1.0
CB B:ARG159 4.3 12.5 1.0
CD B:ARG159 4.3 16.1 1.0
NE B:ARG159 4.4 16.2 1.0
N B:LEU132 4.4 12.9 1.0
N B:LEU163 4.5 10.7 1.0
O B:LEU130 4.6 11.9 1.0
C B:ASP131 4.6 12.6 1.0
CA B:TYR162 4.7 9.2 1.0
N B:ASP131 4.7 11.6 1.0
OD2 B:ASP131 4.8 13.7 1.0
CD1 B:LEU163 4.9 12.7 1.0
C B:TYR162 4.9 10.3 1.0

Sodium binding site 8 out of 10 in 5x8k

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Sodium binding site 8 out of 10 in the V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:21.1
occ:1.00
 O B:HOH356 2.8 20.7 1.0
O B:PRO109 2.8 10.6 1.0
C B:PRO109 3.6 10.1 1.0
CA B:PRO109 3.7 11.2 1.0
N B:GLU113 3.8 11.0 1.0
CB B:ARG112 3.9 12.3 0.5
CB B:ARG112 3.9 11.6 0.5
CB B:PRO109 3.9 11.8 1.0
CB B:GLU113 4.1 16.4 1.0
CA B:GLU113 4.3 13.3 1.0
C B:ARG112 4.3 11.7 1.0
O B:HOH383 4.4 26.1 1.0
NE B:ARG112 4.6 13.9 0.5
CA B:ARG112 4.6 10.9 0.5
CA B:ARG112 4.6 11.2 0.5
OE1 B:GLU113 4.6 25.0 1.0
N B:TRP110 4.8 10.3 1.0
N B:ARG112 5.0 10.3 1.0

Sodium binding site 9 out of 10 in 5x8k

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Sodium binding site 9 out of 10 in the V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:18.3
occ:1.00
 OD2 B:ASP94 2.7 17.5 1.0
OG1 B:THR7 2.7 8.7 1.0
OE2 B:GLU9 2.7 8.9 1.0
O B:HOH301 2.9 38.2 1.0
CB B:THR7 3.4 8.6 1.0
CG B:GLU9 3.5 9.1 1.0
CD B:GLU9 3.5 9.7 1.0
CG B:ASP94 3.6 11.6 1.0
CB B:TYR92 3.6 7.8 1.0
CB B:ASP94 3.7 9.5 1.0
CG2 B:THR127 3.8 10.5 1.0
OG1 B:THR127 3.8 10.2 1.0
CG2 B:THR7 3.8 8.7 1.0
N B:ASP94 4.1 8.8 1.0
N B:TYR92 4.1 7.6 1.0
NH1 B:ARG172 4.1 12.9 1.0
CA B:TYR92 4.2 8.0 1.0
CG B:PRO124 4.3 14.4 1.0
CD2 B:TYR92 4.3 8.8 1.0
C B:TYR92 4.3 7.8 1.0
N B:LEU93 4.4 8.2 1.0
CB B:THR127 4.4 10.1 1.0
CG B:TYR92 4.5 8.2 1.0
CA B:ASP94 4.5 8.9 1.0
OE1 B:GLU9 4.7 8.7 1.0
OD1 B:ASP94 4.7 11.2 1.0
CA B:THR7 4.8 9.5 1.0
O B:TYR92 4.9 7.9 1.0
CB B:GLU9 5.0 9.5 1.0

Sodium binding site 10 out of 10 in 5x8k

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Sodium binding site 10 out of 10 in the V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of V158T Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:22.0
occ:1.00
 OE2 B:GLU169 2.7 19.4 1.0
O B:HOH327 2.7 17.0 1.0
O B:LEU165 2.8 13.4 1.0
O B:HOH377 2.8 25.7 1.0
CD B:GLU169 3.5 17.0 1.0
C B:LEU165 3.5 13.0 1.0
CG B:GLU169 3.5 16.0 1.0
CA B:LEU165 3.5 12.1 1.0
CB B:ALA168 3.7 17.7 1.0
CD2 B:LEU165 3.8 12.7 1.0
CB B:LEU165 3.8 12.6 1.0
NH2 B:ARG112 3.8 14.2 0.5
CB B:GLU169 3.8 15.9 1.0
CE1 B:PHE173 4.1 13.5 1.0
N B:GLU169 4.2 15.3 1.0
CG B:LEU165 4.4 11.9 1.0
NH2 B:ARG172 4.4 13.6 1.0
C B:ALA168 4.4 18.1 1.0
CA B:ALA168 4.6 18.3 1.0
OE1 B:GLU169 4.6 18.7 1.0
CA B:GLU169 4.7 16.2 1.0
N B:ALA166 4.8 13.9 1.0
CD1 B:PHE173 4.9 13.8 1.0
N B:LEU165 4.9 12.4 1.0
CZ B:PHE173 4.9 13.3 1.0
N B:ALA168 4.9 17.3 1.0
O B:ALA164 5.0 13.8 1.0

Reference:

S.K.Chaudhary, J.Jeyakanthan, K.Sekar. Structural and Functional Roles of Dynamically Correlated Residues in Thymidylate Kinase. Acta Crystallogr D Struct V. 74 341 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 29652261
DOI: 10.1107/S2059798318002267
Page generated: Tue Oct 8 01:10:25 2024

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