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Chlorine in PDB 5x7j: Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8

Enzymatic activity of Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8

All present enzymatic activity of Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8:
2.7.4.9;

Protein crystallography data

The structure of Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8, PDB code: 5x7j 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) 40.88 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.470, 80.210, 122.630, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22

Other elements in 5x7j:

The structure of Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 also contains other interesting chemical elements:

Calcium (Ca) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 (pdb code 5x7j). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8, PDB code: 5x7j:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 5x7j

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Chlorine binding site 1 out of 10 in the Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:17.4
occ:1.00
 O A:HOH326 3.1 17.8 1.0
N A:GLY171 3.2 15.7 1.0
C A:GLU169 3.4 16.1 1.0
CA A:GLU169 3.4 15.0 1.0
N A:ARG172 3.5 14.6 1.0
CA A:GLY171 3.6 17.4 1.0
N A:PRO170 3.6 14.9 1.0
CB A:GLU169 3.7 16.3 1.0
O A:GLU169 3.8 13.6 1.0
CD A:PRO170 4.0 16.2 1.0
C A:GLY171 4.0 19.4 1.0
C A:PRO170 4.2 15.6 1.0
CB A:ARG172 4.3 14.5 1.0
CG A:GLU169 4.3 15.3 1.0
CA A:PRO170 4.5 15.7 1.0
CA A:ARG172 4.5 13.4 1.0
N A:GLU169 4.8 15.9 1.0
CG A:PRO170 4.9 17.1 1.0
O A:ALA168 4.9 16.0 1.0
OE2 A:GLU169 5.0 16.6 1.0

Chlorine binding site 2 out of 10 in 5x7j

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Chlorine binding site 2 out of 10 in the Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:22.9
occ:1.00
 O A:HOH364 3.1 15.5 1.0
NZ A:LYS123 3.2 21.2 1.0
O A:HOH335 3.2 19.9 1.0
O A:HOH315 3.3 20.1 1.0
CZ A:ARG172 3.8 12.4 1.0
CD A:PRO124 3.8 14.9 1.0
NH2 A:ARG172 3.8 14.1 1.0
CG A:LYS123 3.9 23.5 1.0
NH1 A:ARG172 3.9 13.2 1.0
CB A:LYS123 4.1 19.3 1.0
CE A:LYS123 4.1 22.9 1.0
NE A:ARG172 4.2 12.8 1.0
CA A:LYS123 4.2 16.1 1.0
CD2 A:LEU93 4.3 15.4 1.0
CE2 A:TYR92 4.4 11.7 1.0
OD1 A:ASP94 4.5 15.2 1.0
CD A:LYS123 4.5 22.9 1.0
CD2 A:TYR92 4.5 10.9 1.0
CB A:LEU93 4.5 14.0 1.0
O A:HOH337 4.6 29.1 1.0
CG A:PRO124 4.7 15.0 1.0
O A:LEU122 4.7 15.1 1.0
N A:PRO124 4.8 14.2 1.0
CD A:ARG172 4.8 13.8 1.0
CG A:LEU93 4.9 14.8 1.0
CG A:ASP94 5.0 13.5 1.0

Chlorine binding site 3 out of 10 in 5x7j

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Chlorine binding site 3 out of 10 in the Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:20.5
occ:1.00
 CA A:CA205 3.2 38.7 1.0
N A:GLY13 3.4 20.6 1.0
N A:LYS16 3.5 17.3 1.0
N A:THR17 3.5 16.7 1.0
N A:GLY15 3.6 16.8 1.0
NZ A:LYS16 3.8 18.8 1.0
OG1 A:THR17 3.9 16.7 1.0
N A:SER14 3.9 16.5 1.0
CB A:LYS16 4.0 21.7 1.0
O A:LEU11 4.1 15.6 1.0
CE A:LYS16 4.1 21.7 1.0
CB A:THR17 4.1 16.9 1.0
OG A:SER14 4.1 16.1 1.0
C A:GLY15 4.1 18.2 1.0
CA A:GLY13 4.1 20.2 1.0
CA A:LYS16 4.1 18.3 1.0
CA A:ASP12 4.2 23.6 1.0
CA A:GLY15 4.2 18.0 1.0
C A:ASP12 4.3 21.2 1.0
C A:GLY13 4.4 20.9 1.0
C A:LYS16 4.4 17.9 1.0
CA A:THR17 4.5 15.9 1.0
C A:SER14 4.6 16.8 1.0
CA A:SER14 4.7 16.5 1.0
OD1 A:ASP12 4.7 35.3 1.0
CG A:LYS16 4.7 22.0 1.0
CD A:LYS16 4.9 23.9 1.0
CB A:SER14 5.0 16.1 1.0
C A:LEU11 5.0 17.2 1.0

Chlorine binding site 4 out of 10 in 5x7j

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Chlorine binding site 4 out of 10 in the Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:24.5
occ:1.00
 O A:HOH310 2.9 33.7 1.0
O A:HOH377 3.1 35.5 1.0
N A:PHE5 3.1 13.4 1.0
CB A:ARG125 3.7 16.0 1.0
CA A:LEU4 3.8 14.5 1.0
CB A:PHE5 3.9 13.7 1.0
C A:LEU4 4.0 13.4 1.0
CA A:PHE5 4.0 13.3 1.0
CD1 A:LEU4 4.1 18.1 1.0
O A:PHE5 4.3 12.6 1.0
O A:GLY3 4.3 17.5 1.0
N A:ARG125 4.4 13.2 1.0
CG A:ARG125 4.6 17.2 1.0
CA A:ARG125 4.6 14.8 1.0
C A:PHE5 4.7 13.0 1.0
N A:LEU4 4.7 15.4 1.0
C A:GLY3 4.8 18.6 1.0
CB A:LEU4 4.9 16.4 1.0
CG A:LEU4 5.0 16.9 1.0

Chlorine binding site 5 out of 10 in 5x7j

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Chlorine binding site 5 out of 10 in the Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:21.8
occ:1.00
 O B:HOH384 3.1 13.3 1.0
O B:HOH357 3.1 14.4 1.0
O B:HOH355 3.1 20.3 1.0
NZ B:LYS123 3.3 21.3 1.0
CD B:PRO124 3.7 13.2 1.0
NH2 B:ARG172 3.7 12.5 1.0
CZ B:ARG172 3.8 12.2 1.0
CG B:LYS123 3.9 22.5 1.0
NH1 B:ARG172 4.0 11.3 1.0
CB B:LYS123 4.1 17.6 1.0
NE B:ARG172 4.1 12.1 1.0
CE B:LYS123 4.2 22.7 1.0
CA B:LYS123 4.2 16.0 1.0
CD2 B:LEU93 4.3 11.6 1.0
CE2 B:TYR92 4.4 12.2 1.0
CB B:LEU93 4.4 10.4 1.0
CD2 B:TYR92 4.5 11.5 1.0
CD B:LYS123 4.6 24.4 1.0
CG B:PRO124 4.6 13.4 1.0
OD1 B:ASP94 4.6 11.6 1.0
O B:HOH322 4.7 25.9 1.0
O B:LEU122 4.7 12.4 1.0
CD B:ARG172 4.8 12.1 1.0
N B:PRO124 4.8 12.2 1.0
CG B:LEU93 4.8 10.7 1.0
OD2 B:ASP94 5.0 16.4 1.0

Chlorine binding site 6 out of 10 in 5x7j

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Chlorine binding site 6 out of 10 in the Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:17.2
occ:1.00
 O B:HOH400 2.9 28.8 1.0
O B:HOH324 3.1 13.9 1.0
N B:GLY171 3.2 12.8 1.0
CA B:GLU169 3.4 12.6 1.0
C B:GLU169 3.4 13.2 1.0
N B:ARG172 3.5 12.1 1.0
CA B:GLY171 3.6 13.1 1.0
CB B:GLU169 3.6 12.5 1.0
N B:PRO170 3.7 13.4 1.0
O B:GLU169 3.8 11.2 1.0
C B:GLY171 3.9 13.9 1.0
CD B:PRO170 4.0 14.6 1.0
CG B:GLU169 4.3 12.0 1.0
C B:PRO170 4.3 13.8 1.0
CB B:ARG172 4.4 11.2 1.0
CA B:ARG172 4.6 11.1 1.0
CA B:PRO170 4.6 14.0 1.0
N B:GLU169 4.8 12.6 1.0
OE1 B:GLU169 4.8 13.8 1.0
O B:ALA168 4.9 12.2 1.0
CG B:PRO170 5.0 15.6 1.0

Chlorine binding site 7 out of 10 in 5x7j

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Chlorine binding site 7 out of 10 in the Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:19.8
occ:1.00
 OG B:SER66 3.0 18.6 1.0
OH B:TYR62 3.1 21.6 1.0
NH1 B:ARG69 3.1 18.5 1.0
CB B:SER66 3.6 17.4 1.0
CA B:ALA115 3.7 19.0 1.0
CB B:ALA115 3.7 18.8 1.0
CD B:ARG69 3.8 16.7 1.0
CB B:ALA118 3.8 15.0 1.0
CD1 B:LEU93 3.9 10.8 1.0
CZ B:TYR62 3.9 19.1 1.0
CA B:SER66 3.9 16.3 1.0
CE1 B:TYR62 4.0 16.8 1.0
CZ B:ARG69 4.1 17.6 1.0
N B:ALA115 4.4 18.9 1.0
NE B:ARG69 4.4 20.0 1.0
CG B:ARG69 4.5 15.7 1.0
CG2 B:THR119 4.6 15.0 1.0
CB B:ARG69 4.6 15.2 1.0
O B:SER66 4.8 14.7 1.0
N B:SER66 4.8 16.0 1.0
C B:ALA115 4.8 20.4 1.0
C B:SER66 4.9 15.3 1.0
O B:ALA115 4.9 18.4 1.0
CE2 B:TYR62 5.0 16.6 1.0
C B:VAL114 5.0 18.0 1.0
CG1 B:VAL114 5.0 19.0 1.0

Chlorine binding site 8 out of 10 in 5x7j

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Chlorine binding site 8 out of 10 in the Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:16.0
occ:1.00
 CA B:CA207 3.1 35.9 1.0
N B:GLY13 3.3 15.6 1.0
N B:GLY15 3.4 11.6 1.0
N B:LYS16 3.6 12.6 1.0
N B:THR17 3.7 13.8 1.0
NZ B:LYS16 3.8 16.3 1.0
OG1 B:THR17 3.8 13.2 1.0
N B:SER14 3.8 12.6 1.0
CG B:LYS16 3.9 16.8 1.0
CA B:GLY15 3.9 13.0 1.0
C B:GLY15 4.0 13.2 1.0
CB B:THR17 4.0 13.7 1.0
O B:LEU11 4.0 13.5 1.0
CA B:ASP12 4.0 15.6 1.0
CA B:GLY13 4.0 13.8 1.0
OG B:SER14 4.1 12.1 1.0
C B:ASP12 4.1 15.7 1.0
C B:GLY13 4.2 13.3 1.0
CE B:LYS16 4.2 17.2 1.0
O B:HOH387 4.5 29.6 1.0
CA B:LYS16 4.5 13.5 1.0
C B:SER14 4.5 13.0 1.0
CA B:THR17 4.5 13.3 1.0
C B:LYS16 4.6 13.9 1.0
CA B:SER14 4.6 12.5 1.0
CD B:LYS16 4.7 19.8 1.0
O B:HOH396 4.8 27.0 1.0
OD1 B:ASP12 4.8 18.4 1.0
CB B:LYS16 4.8 16.3 1.0
C B:LEU11 4.9 12.7 1.0
O B:GLY15 4.9 13.3 1.0
CB B:ASP12 4.9 18.8 1.0
O B:GLY13 4.9 13.5 1.0
CB B:SER14 5.0 12.1 1.0
N B:ASP12 5.0 15.0 1.0

Chlorine binding site 9 out of 10 in 5x7j

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Chlorine binding site 9 out of 10 in the Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl205

b:17.7
occ:1.00
 O B:HOH345 3.1 13.8 1.0
NH2 B:ARG22 3.3 16.1 1.0
NE B:ARG22 3.3 13.8 1.0
NE2 B:GLN190 3.4 22.4 1.0
OE1 B:GLN190 3.6 25.1 1.0
CZ B:ARG22 3.8 15.6 1.0
CD B:GLN190 3.9 24.9 1.0
CB B:ALA186 4.1 12.4 1.0
CB B:ARG22 4.1 13.6 1.0
O B:ARG22 4.3 15.0 1.0
CD B:ARG22 4.4 15.0 1.0
CG B:ARG22 4.6 13.8 1.0
C B:ARG22 4.7 14.2 1.0
CB B:PHE26 4.8 15.4 1.0
CA B:ARG22 4.8 11.9 1.0

Chlorine binding site 10 out of 10 in 5x7j

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Chlorine binding site 10 out of 10 in the Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl206

b:34.0
occ:1.00
 NE B:ARG140 2.8 14.0 1.0
O B:ALA136 3.0 17.3 1.0
CG B:ARG140 3.5 16.1 1.0
CD B:ARG140 3.5 14.8 1.0
C B:ALA136 3.7 16.9 1.0
CB B:ALA136 3.7 17.3 1.0
CZ B:ARG140 3.7 15.5 1.0
CA B:ALA136 3.9 16.8 1.0
NH2 B:ARG140 3.9 13.9 1.0
NH2 B:ARG139 4.5 21.4 1.0
CD1 B:LEU132 4.6 21.0 1.0
N B:ALA137 4.7 15.5 1.0
CB B:ARG140 4.8 17.6 1.0
NH1 B:ARG140 5.0 16.1 1.0

Reference:

S.K.Chaudhary, Y.Iyyappan, M.Elayappan, J.Jeyakanthan, K.Sekar. Insights Into Product Release Dynamics Through Structural Analyses of Thymidylate Kinase. Int. J. Biol. Macromol. V. 123 637 2019.
ISSN: ISSN 1879-0003
PubMed: 30447376
DOI: 10.1016/J.IJBIOMAC.2018.11.025
Page generated: Fri Jul 26 20:51:05 2024

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