Sodium in PDB 5x8v: Y92H Mutant of Thermus Thermophilus HB8 Thymidylate Kinase

All present enzymatic activity of Y92H Mutant of Thermus Thermophilus HB8 Thymidylate Kinase:
2.7.4.9;

The structure of Y92H Mutant of Thermus Thermophilus HB8 Thymidylate Kinase, PDB code: 5x8v 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)	50.01 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.540, 47.052, 151.480, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.8

The structure of Y92H Mutant of Thermus Thermophilus HB8 Thymidylate Kinase also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Y92H Mutant of Thermus Thermophilus HB8 Thymidylate Kinase (pdb code 5x8v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Y92H Mutant of Thermus Thermophilus HB8 Thymidylate Kinase, PDB code: 5x8v:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Y92H 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 Y92H Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:28.6 occ:1.00 OD1 B:ASP131 2.8 22.4 1.0 O B:HOH320 3.0 23.6 1.0 O B:ARG159 3.2 19.6 1.0 CB B:TYR162 3.5 18.3 1.0 CG B:ARG159 3.6 22.5 1.0 CG B:ASP131 3.8 21.6 1.0 CA B:ASP131 3.8 20.6 1.0 CA B:ARG159 3.8 19.2 1.0 C B:ARG159 3.9 19.5 1.0 CD2 B:TYR162 4.0 15.6 1.0 CD1 B:LEU129 4.0 17.6 1.0 CB B:ASP131 4.1 20.9 1.0 CG B:TYR162 4.2 15.8 1.0 CB B:ARG159 4.2 20.3 1.0 CD B:ARG159 4.3 23.2 1.0 CD2 B:LEU129 4.3 18.9 1.0 CG B:LEU163 4.3 21.5 1.0 N B:LEU132 4.3 21.8 1.0 CG B:LEU129 4.4 17.2 1.0 NE B:ARG159 4.4 26.2 1.0 CD2 B:LEU163 4.5 22.3 1.0 O B:LEU130 4.5 22.7 1.0 C B:ASP131 4.6 20.3 1.0 N B:LEU163 4.6 18.0 1.0 CA B:TYR162 4.7 16.9 1.0 N B:ASP131 4.8 19.8 1.0 O B:LEU132 4.9 23.8 1.0 C B:TYR162 4.9 19.2 1.0 OD2 B:ASP131 4.9 23.9 1.0 O B:VAL158 5.0 19.0 1.0 C B:LEU130 5.0 19.3 1.0

Sodium binding site 2 out of 4 in the Y92H 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 Y92H Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:25.2 occ:1.00 OG1 A:THR7 2.6 17.7 1.0 OD2 A:ASP94 2.7 17.0 1.0 O A:HOH404 2.7 16.3 1.0 OE2 A:GLU9 2.8 18.4 1.0 CB A:THR7 3.4 17.2 1.0 CG A:GLU9 3.4 17.9 1.0 CG A:ASP94 3.5 18.5 1.0 CD A:GLU9 3.5 16.7 1.0 CB A:ASP94 3.7 17.0 1.0 CG2 A:THR127 3.7 16.9 1.0 OG1 A:THR127 3.7 18.6 1.0 CG2 A:THR7 3.8 17.1 1.0 CB A:HIS92 3.9 16.2 1.0 NH1 A:ARG172 4.1 18.5 1.0 N A:ASP94 4.2 17.3 1.0 CG A:PRO124 4.2 19.6 1.0 N A:HIS92 4.3 15.3 1.0 CB A:THR127 4.3 18.4 1.0 CA A:HIS92 4.4 17.3 1.0 OD1 A:ASP94 4.5 17.9 1.0 C A:HIS92 4.5 17.8 1.0 CA A:ASP94 4.6 18.3 1.0 N A:LEU93 4.7 15.8 1.0 OE1 A:GLU9 4.7 18.2 1.0 CA A:THR7 4.8 16.0 1.0 CG A:HIS92 4.8 16.6 1.0 CB A:GLU9 4.9 15.8 1.0 CD2 A:HIS92 4.9 16.8 1.0

Sodium binding site 3 out of 4 in the Y92H 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 Y92H Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:25.6 occ:1.00 OG A:SER66 2.7 19.7 1.0 NH1 A:ARG69 2.9 16.5 1.0 OH A:TYR62 3.0 17.4 1.0 CB A:SER66 3.5 18.2 1.0 CZ A:TYR62 3.5 17.4 1.0 CD1 A:LEU93 3.7 18.2 1.0 CA A:SER66 3.7 17.2 1.0 CE1 A:TYR62 3.7 18.0 1.0 CB A:ALA115 3.7 18.8 1.0 CD A:ARG69 3.8 18.3 1.0 CA A:ALA115 3.9 18.6 1.0 CZ A:ARG69 4.0 17.1 1.0 NE A:ARG69 4.3 17.4 1.0 N A:ALA115 4.5 17.5 1.0 CB A:ARG69 4.5 17.2 1.0 CE2 A:TYR62 4.5 17.4 1.0 CG A:ARG69 4.5 17.5 1.0 CB A:ALA118 4.5 34.4 1.0 N A:SER66 4.6 17.2 1.0 O A:SER66 4.7 16.3 1.0 C A:SER66 4.8 17.2 1.0 CD1 A:TYR62 4.9 16.7 1.0 CG1 A:VAL114 4.9 17.8 1.0

Sodium binding site 4 out of 4 in the Y92H 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 Y92H Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:26.2 occ:1.00 OE2 A:GLU169 2.5 20.4 1.0 O A:HOH382 2.6 33.4 1.0 O A:LEU165 2.8 16.9 1.0 O A:HOH378 2.9 21.6 1.0 CD A:GLU169 3.4 17.7 1.0 CG A:GLU169 3.4 17.9 1.0 C A:LEU165 3.5 15.7 1.0 CA A:LEU165 3.6 16.9 1.0 NH2 A:ARG112 3.8 24.3 1.0 CB A:LEU165 3.8 17.2 1.0 CB A:GLU169 3.9 17.8 1.0 CB A:ALA168 3.9 19.2 1.0 CE1 A:PHE173 4.0 20.4 1.0 CD2 A:LEU165 4.1 18.2 1.0 N A:GLU169 4.2 17.0 1.0 NH2 A:ARG172 4.2 18.2 1.0 O A:HOH347 4.4 24.0 1.0 C A:ALA168 4.5 18.7 1.0 CG A:LEU165 4.5 18.1 1.0 OE1 A:GLU169 4.6 21.9 1.0 CZ A:PHE173 4.6 19.2 1.0 CA A:ALA168 4.7 18.1 1.0 CA A:GLU169 4.7 17.9 1.0 O A:HOH399 4.8 30.0 1.0 N A:ALA166 4.8 15.3 1.0 CD1 A:PHE173 4.8 19.3 1.0 N A:LEU165 5.0 15.4 1.0

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