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Chlorine in PDB 5x8c: Amppcp and Tmp Bound Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8

Enzymatic activity of Amppcp and Tmp Bound Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8

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

Protein crystallography data

The structure of Amppcp and Tmp Bound Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8, PDB code: 5x8c 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) 50.77 / 2.07
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.100, 47.530, 152.280, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.9

Other elements in 5x8c:

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

Magnesium (Mg) 11 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Amppcp and Tmp Bound Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 (pdb code 5x8c). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Amppcp and Tmp Bound Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8, PDB code: 5x8c:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5x8c

Go back to Chlorine Binding Sites List in 5x8c
Chlorine binding site 1 out of 5 in the Amppcp and Tmp Bound 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 1 of Amppcp and Tmp Bound Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:24.8
occ:1.00
 N A:GLY171 3.2 13.8 1.0
C A:GLU169 3.3 13.7 1.0
N A:ARG172 3.3 12.8 1.0
CA A:GLU169 3.4 13.6 1.0
O A:GLU169 3.5 12.4 1.0
N A:PRO170 3.6 13.9 1.0
CA A:GLY171 3.6 14.4 1.0
CB A:GLU169 3.7 13.5 1.0
CD A:PRO170 3.9 14.5 1.0
C A:GLY171 3.9 13.9 1.0
CB A:ARG172 4.1 12.5 1.0
CG A:GLU169 4.2 13.4 1.0
C A:PRO170 4.2 13.7 1.0
CA A:ARG172 4.3 12.3 1.0
CA A:PRO170 4.5 14.4 1.0
N A:GLU169 4.8 14.2 1.0
OE1 A:GLU169 4.9 13.6 1.0
O A:HOH348 5.0 14.9 1.0

Chlorine binding site 2 out of 5 in 5x8c

Go back to Chlorine Binding Sites List in 5x8c
Chlorine binding site 2 out of 5 in the Amppcp and Tmp Bound 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 Amppcp and Tmp Bound Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:32.1
occ:1.00
 O A:HOH314 2.6 25.3 1.0
N A:PHE5 3.0 10.7 1.0
CB A:PHE5 3.6 9.8 1.0
CA A:LEU4 3.7 13.7 1.0
C A:LEU4 3.8 12.3 1.0
CA A:PHE5 3.8 10.1 1.0
CB A:ARG125 3.9 14.1 1.0
CD1 A:LEU4 3.9 13.3 1.0
O A:HOH388 4.0 31.5 1.0
O A:GLY3 4.1 18.0 1.0
O A:PHE5 4.2 9.9 1.0
O A:HOH391 4.3 34.0 1.0
N A:ARG125 4.3 13.0 1.0
C A:PHE5 4.5 9.8 1.0
N A:LEU4 4.5 15.2 1.0
CA A:ARG125 4.6 13.2 1.0
C A:GLY3 4.7 19.1 1.0
CB A:LEU4 4.7 13.6 1.0
CG A:LEU4 4.8 13.4 1.0
CD2 A:LEU81 4.9 13.1 1.0
CG A:ARG125 4.9 15.4 1.0
O A:LEU4 4.9 11.8 1.0
O A:LYS123 4.9 14.5 1.0

Chlorine binding site 3 out of 5 in 5x8c

Go back to Chlorine Binding Sites List in 5x8c
Chlorine binding site 3 out of 5 in the Amppcp and Tmp Bound 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 Amppcp and Tmp Bound Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl208

b:29.8
occ:1.00
 O B:HOH306 3.0 13.8 1.0
N B:ASP177 3.2 15.7 1.0
CD1 B:LEU180 3.7 23.3 1.0
CA B:LEU176 3.9 13.5 1.0
CB B:ASP177 3.9 18.6 1.0
C B:LEU176 4.0 13.8 1.0
CD2 B:LEU176 4.0 16.1 1.0
CA B:ASP177 4.1 16.8 1.0
CB B:LEU176 4.4 14.6 1.0
O B:VAL175 4.5 11.8 1.0
O B:ASP177 4.7 17.0 1.0
CG B:LEU176 4.8 15.2 1.0
C B:ASP177 4.9 15.6 1.0

Chlorine binding site 4 out of 5 in 5x8c

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Chlorine binding site 4 out of 5 in the Amppcp and Tmp Bound 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 Amppcp and Tmp Bound Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl209

b:26.0
occ:1.00
 O B:HOH318 3.0 15.9 1.0
O B:HOH352 3.0 15.2 1.0
CE B:LYS123 3.5 29.0 1.0
NZ B:LYS123 3.6 29.1 1.0
CD B:PRO124 3.6 15.1 1.0
CZ B:ARG172 3.9 12.5 1.0
NH2 B:ARG172 4.0 12.1 1.0
NH1 B:ARG172 4.0 12.6 1.0
CB B:LYS123 4.1 20.0 1.0
CA B:LYS123 4.2 18.0 1.0
CD2 B:LEU93 4.2 10.3 1.0
CE2 B:TYR92 4.2 8.7 1.0
CG B:LYS123 4.3 23.2 1.0
CB B:LEU93 4.4 10.0 1.0
CD2 B:TYR92 4.4 8.9 1.0
CD B:LYS123 4.5 26.4 1.0
NE B:ARG172 4.5 12.3 1.0
CG B:PRO124 4.5 14.9 1.0
O B:LEU122 4.6 14.5 1.0
OD1 B:ASP94 4.7 11.2 1.0
N B:PRO124 4.7 15.2 1.0
CG B:LEU93 4.8 10.1 1.0
OD2 B:ASP94 4.9 11.5 1.0
C B:LYS123 5.0 16.6 1.0
CG B:ASP94 5.0 10.9 1.0

Chlorine binding site 5 out of 5 in 5x8c

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Chlorine binding site 5 out of 5 in the Amppcp and Tmp Bound 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 Amppcp and Tmp Bound Crystal Structure of Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl210

b:27.5
occ:1.00
 N B:LYS16 3.3 20.6 1.0
N B:GLY13 3.3 17.2 1.0
N B:SER14 3.5 15.8 1.0
N B:GLY15 3.5 16.8 1.0
NZ B:LYS16 3.6 20.4 1.0
CE B:LYS16 3.6 19.5 1.0
CB B:LYS16 3.7 21.2 1.0
CA B:GLY13 3.8 16.7 1.0
O B:HOH363 3.9 18.7 1.0
CA B:LYS16 4.0 20.6 1.0
O B:HOH368 4.0 27.2 1.0
OG B:SER14 4.0 15.0 1.0
C B:GLY13 4.0 16.6 1.0
O B:LEU11 4.0 13.8 1.0
C B:GLY15 4.1 18.8 1.0
CA B:GLY15 4.2 17.5 1.0
N B:THR17 4.2 22.5 1.0
CG B:LYS16 4.2 20.2 1.0
O B:HOH354 4.2 36.2 1.0
C B:ASP12 4.3 18.4 1.0
C B:SER14 4.3 16.6 1.0
CA B:SER14 4.4 16.0 1.0
CD B:LYS16 4.5 20.2 1.0
CA B:ASP12 4.5 20.0 1.0
C B:LYS16 4.6 21.1 1.0
OG1 B:THR17 4.8 27.4 1.0
CB B:SER14 4.8 15.9 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: Fri Jul 26 20:51:30 2024

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