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Caesium in PDB 5xak: Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8

Enzymatic activity of Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8

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

Protein crystallography data

The structure of Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8, PDB code: 5xak 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) 25.16 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.160, 47.090, 150.940, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 18.9

Other elements in 5xak:

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

Chlorine (Cl) 2 atoms

Caesium Binding Sites:

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

Caesium binding site 1 out of 6 in 5xak

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Caesium binding site 1 out of 6 in the Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs202

b:41.9
occ:0.45
 O A:GLY171 3.0 35.3 1.0
O A:PRO170 3.1 34.9 1.0
O A:PHE173 3.2 22.1 1.0
C A:GLY171 3.7 27.0 1.0
CG2 A:VAL174 4.1 21.4 1.0
C A:PHE173 4.1 18.2 1.0
O A:HOH313 4.1 31.7 1.0
C A:PRO170 4.2 27.8 1.0
CA A:GLY171 4.2 30.1 1.0
CD2 A:LEU126 4.3 21.2 1.0
N A:ARG172 4.5 20.1 1.0
C A:ARG172 4.5 17.5 1.0
N A:PHE173 4.6 18.9 1.0
N A:GLY171 4.7 25.6 1.0
O A:ARG172 4.7 17.2 1.0
N A:VAL174 4.7 16.7 1.0
CA A:VAL174 4.8 18.6 1.0
CA A:ARG172 4.9 18.1 1.0
CA A:PHE173 5.0 18.2 1.0

Caesium binding site 2 out of 6 in 5xak

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Caesium binding site 2 out of 6 in the Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs203

b:50.3
occ:0.51
 O A:LEU180 2.8 30.1 1.0
O A:ALA178 3.2 25.2 1.0
O A:HOH310 3.3 33.8 1.0
C A:LEU180 4.0 25.9 1.0
N A:GLU182 4.2 27.6 1.0
O A:HOH337 4.3 28.2 1.0
C A:ALA178 4.4 24.0 1.0
C A:THR179 4.4 27.1 1.0
O A:THR179 4.4 34.8 1.0
C A:PRO181 4.5 28.5 1.0
CA A:PRO181 4.5 33.6 1.0
CD1 A:ILE185 4.6 24.9 1.0
N A:PRO181 4.7 27.9 1.0
CA A:THR179 4.7 27.3 1.0
N A:LEU180 4.7 24.5 1.0
CA A:GLU182 4.8 25.9 1.0

Caesium binding site 3 out of 6 in 5xak

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Caesium binding site 3 out of 6 in the Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs202

b:29.8
occ:0.44
 O B:ARG120 3.0 23.4 1.0
O B:HOH383 3.6 52.6 1.0
C B:ARG120 4.0 19.1 1.0
CA B:GLY121 4.8 20.5 1.0
N B:GLY121 4.8 19.2 1.0
CA B:ARG120 4.9 19.4 1.0
CB B:ARG120 4.9 24.3 1.0

Caesium binding site 4 out of 6 in 5xak

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Caesium binding site 4 out of 6 in the Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs203

b:19.6
occ:0.20
 OG B:SER66 3.0 15.9 0.5
OH B:TYR62 3.1 27.7 1.0
NH2 B:ARG69 3.1 16.6 1.0
OG B:SER66 3.2 13.6 0.5
CB B:SER66 3.5 14.2 0.5
CB B:ALA115 3.6 15.8 1.0
CB B:SER66 3.6 12.3 0.5
CA B:ALA115 3.7 14.5 1.0
CD B:ARG69 3.8 17.8 1.0
CZ B:TYR62 3.8 18.9 1.0
CA B:SER66 3.8 11.8 0.5
CA B:SER66 3.8 11.6 0.5
CD1 B:LEU93 3.9 18.5 1.0
CB B:ALA118 4.0 17.1 1.0
CE1 B:TYR62 4.1 16.5 1.0
CZ B:ARG69 4.2 15.6 1.0
N B:ALA115 4.3 11.3 1.0
NE B:ARG69 4.4 15.9 1.0
CG B:ARG69 4.6 14.9 1.0
CB B:ARG69 4.6 13.1 1.0
CG2 B:THR119 4.7 19.1 1.0
O B:SER66 4.7 11.2 1.0
N B:SER66 4.8 11.5 1.0
C B:SER66 4.8 10.3 1.0
CE2 B:TYR62 4.9 17.9 1.0
C B:ALA115 4.9 15.0 1.0
C B:VAL114 4.9 12.7 1.0
CG1 B:VAL114 4.9 16.3 1.0
O B:ALA115 4.9 16.8 1.0

Caesium binding site 5 out of 6 in 5xak

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Caesium binding site 5 out of 6 in the Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 5 of Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs204

b:36.6
occ:0.43
 O B:LEU180 2.8 23.9 1.0
O B:HOH366 3.1 36.3 1.0
O B:ALA178 3.2 22.1 1.0
O B:HOH313 3.5 31.4 1.0
O B:HOH351 3.8 23.4 1.0
C B:LEU180 3.9 24.1 1.0
N B:GLU182 4.2 25.1 1.0
CD1 B:ILE185 4.3 19.8 1.0
C B:THR179 4.3 20.9 1.0
C B:ALA178 4.3 18.1 1.0
O B:THR179 4.4 28.4 1.0
C B:PRO181 4.5 25.7 1.0
CA B:PRO181 4.6 28.3 1.0
N B:LEU180 4.6 23.2 1.0
CA B:THR179 4.7 22.5 1.0
N B:PRO181 4.7 26.7 1.0
CA B:GLU182 4.7 25.7 1.0
CA B:LEU180 4.9 23.9 1.0
CB B:GLU182 5.0 28.4 1.0

Caesium binding site 6 out of 6 in 5xak

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Caesium binding site 6 out of 6 in the Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 6 of Crystal Structure (Form II) of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs205

b:29.5
occ:0.34
 O B:PRO170 3.1 22.4 1.0
O B:PHE173 3.3 18.8 1.0
O B:GLY171 3.5 25.8 1.0
C B:GLY171 3.8 20.0 1.0
CG2 B:VAL174 3.9 19.9 1.0
C B:PHE173 4.1 14.4 1.0
CA B:GLY171 4.2 19.2 1.0
CD2 B:LEU126 4.2 21.4 1.0
C B:PRO170 4.2 18.7 1.0
O B:HOH303 4.3 24.1 1.0
N B:ARG172 4.4 15.3 1.0
C B:ARG172 4.5 15.1 1.0
N B:PHE173 4.6 14.6 1.0
O B:ARG172 4.7 16.6 1.0
N B:VAL174 4.7 13.4 1.0
N B:GLY171 4.7 17.8 1.0
CA B:VAL174 4.9 14.6 1.0
CA B:ARG172 4.9 15.0 1.0
CA B:PHE173 5.0 12.9 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 Jul 30 20:45:59 2024

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