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Calcium in PDB 5zb4: Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8

Enzymatic activity of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8

All present enzymatic activity of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8:
2.7.4.9;

Protein crystallography data

The structure of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8, PDB code: 5zb4 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) 19.74 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.170, 47.474, 152.169, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 23.3

Other elements in 5zb4:

The structure of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8 (pdb code 5zb4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 15 binding sites of Calcium where determined in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8, PDB code: 5zb4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 15 in 5zb4

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Calcium binding site 1 out of 15 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:44.5
occ:1.00
 NH1 A:ARG187 3.1 14.8 1.0
CG A:ARG187 3.7 13.4 1.0
CD A:ARG187 3.8 13.8 1.0
CZ A:ARG187 4.1 14.2 1.0
NE A:ARG187 4.4 14.2 1.0
CB A:GLU183 4.5 13.3 1.0
O A:GLU183 4.5 11.6 1.0

Calcium binding site 2 out of 15 in 5zb4

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Calcium binding site 2 out of 15 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:40.3
occ:1.00
 OE1 A:GLN19 2.8 9.4 1.0
O A:GLN19 2.8 10.2 1.0
O A:HOH374 2.9 11.9 1.0
N A:LEU23 3.5 12.0 1.0
CD1 A:ILE189 3.6 11.8 1.0
C A:GLN19 3.6 9.8 1.0
CA A:GLN19 3.7 9.4 1.0
CB A:LEU23 3.7 12.3 1.0
CA A:ALA186 3.8 10.4 1.0
CB A:ALA186 3.8 10.3 1.0
CB A:GLN19 3.8 9.4 1.0
CB A:ARG22 3.9 12.6 1.0
CD A:GLN19 3.9 9.6 1.0
CA A:LEU23 3.9 12.2 1.0
C A:ARG22 4.2 12.2 1.0
CB A:ILE189 4.3 12.7 1.0
CG2 A:ILE189 4.3 12.9 1.0
CG A:GLN19 4.4 9.2 1.0
CG1 A:ILE189 4.5 12.5 1.0
CA A:ARG22 4.6 12.4 1.0
O A:ALA186 4.6 10.6 1.0
CD1 A:LEU23 4.7 13.0 1.0
C A:ALA186 4.7 10.7 1.0
CG A:LEU23 4.7 12.4 1.0
N A:ALA186 4.7 9.8 1.0
N A:ALA20 4.9 10.2 1.0
O A:ARG22 4.9 11.8 1.0
NE2 A:GLN19 5.0 9.7 1.0
CD A:ARG22 5.0 14.3 1.0

Calcium binding site 3 out of 15 in 5zb4

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Calcium binding site 3 out of 15 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:43.5
occ:1.00
 OE2 A:GLU61 2.8 12.5 1.0
O A:HOH302 2.8 18.2 1.0
CB A:GLU148 3.4 38.5 1.0
NH2 A:ARG104 3.6 14.6 1.0
CA A:GLU148 3.8 38.2 1.0
O A:HOH350 3.8 12.2 1.0
CB A:LEU56 4.0 15.7 1.0
CD A:GLU61 4.1 11.6 1.0
O A:LEU56 4.3 12.2 1.0
OE1 A:GLU148 4.3 43.7 1.0
N A:LEU56 4.5 16.1 1.0
O A:GLU148 4.6 32.5 1.0
O A:HOH379 4.6 26.3 1.0
CZ A:ARG104 4.6 13.8 1.0
O A:LEU51 4.6 14.9 1.0
O A:THR53 4.6 16.1 1.0
CD2 A:LEU56 4.6 16.8 1.0
C A:GLU148 4.7 36.4 1.0
CG A:GLU148 4.7 39.8 1.0
CA A:LEU56 4.8 15.2 1.0
N A:GLU148 4.8 41.3 1.0
CG A:GLU61 4.8 11.4 1.0
CD A:GLU148 4.9 42.0 1.0
C A:LEU56 4.9 12.9 1.0
CG A:LEU56 5.0 17.4 1.0
OE1 A:GLU61 5.0 11.0 1.0

Calcium binding site 4 out of 15 in 5zb4

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Calcium binding site 4 out of 15 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:30.7
occ:1.00
 OG A:SER49 2.8 14.1 1.0
CB A:SER49 3.4 15.3 1.0
OE2 B:GLU46 4.1 15.1 1.0
CA A:SER49 4.6 14.9 1.0

Calcium binding site 5 out of 15 in 5zb4

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Calcium binding site 5 out of 15 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:21.5
occ:1.00
 O A:HOH305 2.1 9.3 1.0
O3B A:ADP201 2.2 9.3 1.0
OG1 A:THR17 2.2 8.4 1.0
O A:HOH366 2.2 8.6 1.0
O A:HOH330 2.2 6.4 1.0
O A:HOH320 2.2 10.7 1.0
CB A:THR17 3.2 8.7 1.0
PB A:ADP201 3.3 10.1 1.0
O1B A:ADP201 3.5 9.5 1.0
O1A A:ADP201 4.0 11.1 1.0
N A:THR17 4.0 8.8 1.0
OD2 A:ASP90 4.1 9.5 1.0
O A:HOH367 4.1 13.1 1.0
CA A:THR17 4.2 8.8 1.0
CG2 A:THR17 4.3 8.5 1.0
O3P A:TMP213 4.3 19.0 1.0
O2B A:ADP201 4.3 9.2 1.0
OD1 A:ASP90 4.4 9.6 1.0
O3A A:ADP201 4.4 10.6 1.0
O A:HOH307 4.5 12.1 1.0
PA A:ADP201 4.6 12.5 1.0
O1P A:TMP213 4.6 22.3 1.0
CG A:ASP90 4.7 8.8 1.0
P A:TMP213 4.8 21.1 1.0
O2A A:ADP201 4.9 10.5 1.0
NZ A:LYS16 5.0 8.3 1.0

Calcium binding site 6 out of 15 in 5zb4

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Calcium binding site 6 out of 15 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca207

b:27.6
occ:1.00
 OH A:TYR62 2.7 9.2 1.0
OG A:SER66 2.7 7.5 1.0
NH2 A:ARG69 3.0 8.5 1.0
CZ A:TYR62 3.4 9.2 1.0
CB A:SER66 3.5 7.7 1.0
CE1 A:TYR62 3.6 9.0 1.0
CD1 A:LEU93 3.6 8.8 1.0
CA A:SER66 3.8 7.7 1.0
CD A:ARG69 3.9 9.1 1.0
CB A:ALA115 4.0 14.5 1.0
CA A:ALA115 4.0 13.8 1.0
CZ A:ARG69 4.1 9.0 1.0
CB A:ALA118 4.4 17.8 1.0
NE A:ARG69 4.4 8.5 1.0
CE2 A:TYR62 4.4 9.3 1.0
N A:ALA115 4.5 12.6 1.0
CB A:ARG69 4.5 8.9 1.0
N A:SER66 4.6 7.6 1.0
CG A:ARG69 4.7 9.0 1.0
CD1 A:TYR62 4.7 9.1 1.0
OG A:SER96 4.7 6.7 1.0
CG1 A:VAL114 4.9 11.4 1.0
O A:LEU111 4.9 10.5 1.0
C A:SER66 5.0 7.9 1.0

Calcium binding site 7 out of 15 in 5zb4

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Calcium binding site 7 out of 15 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca208

b:30.4
occ:1.00
 OD2 A:ASP68 2.7 9.6 1.0
O A:PHE65 3.0 7.5 1.0
CD1 A:PHE65 3.6 7.4 1.0
CA A:PHE65 3.6 7.8 1.0
CG A:ASP68 3.7 10.1 1.0
CB A:GLU39 3.7 9.3 1.0
CA A:PRO40 3.7 9.3 1.0
NH1 A:ARG69 3.7 8.8 1.0
C A:PHE65 3.7 7.7 1.0
CB A:ASP68 3.7 9.6 1.0
CB A:PHE65 3.9 7.8 1.0
CB A:PRO40 3.9 9.0 1.0
OE1 A:GLU39 3.9 8.3 1.0
CG A:GLU39 4.0 8.9 1.0
CD A:GLU39 4.0 8.8 1.0
C5M A:TMP213 4.1 9.0 1.0
N A:ARG69 4.2 8.8 1.0
CZ A:ARG69 4.2 9.0 1.0
CG A:PHE65 4.2 7.6 1.0
N A:PRO40 4.3 9.4 1.0
CA A:GLU39 4.4 9.8 1.0
CE1 A:PHE65 4.6 7.5 1.0
CB A:ARG69 4.6 8.9 1.0
C A:GLU39 4.6 9.9 1.0
NE A:ARG69 4.6 8.5 1.0
C A:ASP68 4.7 8.9 1.0
CA A:ARG69 4.7 9.0 1.0
NH2 A:ARG69 4.7 8.5 1.0
O4 A:TMP213 4.7 9.1 1.0
CA A:ASP68 4.8 9.0 1.0
OE2 A:GLU39 4.8 7.6 1.0
C A:PRO40 4.8 9.9 1.0
OD1 A:ASP68 4.9 10.9 1.0
N A:GLY41 4.9 9.8 1.0
C5 A:TMP213 4.9 8.8 1.0
N A:PHE65 5.0 7.9 1.0

Calcium binding site 8 out of 15 in 5zb4

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Calcium binding site 8 out of 15 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca209

b:27.4
occ:1.00
 OD2 A:ASP94 2.5 12.1 1.0
OG1 A:THR7 2.7 7.8 1.0
OE2 A:GLU9 2.7 7.3 1.0
CB A:THR7 3.4 8.2 1.0
CG A:GLU9 3.4 7.5 1.0
CG A:ASP94 3.5 9.4 1.0
CD A:GLU9 3.5 7.5 1.0
CB A:TYR92 3.5 8.0 1.0
CB A:ASP94 3.8 8.7 1.0
OG1 A:THR127 3.8 8.8 1.0
CG2 A:THR7 3.8 8.5 1.0
CG2 A:THR127 3.8 9.5 1.0
N A:ASP94 4.1 7.9 1.0
N A:TYR92 4.1 7.4 1.0
CA A:TYR92 4.1 7.6 1.0
CD2 A:TYR92 4.2 8.2 1.0
NH1 A:ARG172 4.2 8.9 1.0
CG A:PRO124 4.2 12.5 1.0
C A:TYR92 4.2 7.8 1.0
CG A:TYR92 4.4 8.1 1.0
N A:LEU93 4.4 7.8 1.0
CB A:THR127 4.5 9.1 1.0
CA A:ASP94 4.5 8.1 1.0
OD1 A:ASP94 4.6 9.2 1.0
OE1 A:GLU9 4.7 7.2 1.0
O A:TYR92 4.8 7.6 1.0
CA A:THR7 4.9 8.5 1.0
CB A:GLU9 4.9 7.8 1.0
C A:ARG91 5.0 7.2 1.0

Calcium binding site 9 out of 15 in 5zb4

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Calcium binding site 9 out of 15 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca210

b:32.9
occ:1.00
 O A:LEU130 2.7 7.4 1.0
O A:HOH332 3.0 7.8 1.0
N A:LEU132 3.1 10.1 1.0
N A:LEU11 3.1 10.3 1.0
CA A:GLY10 3.5 9.5 1.0
CG A:LEU11 3.6 11.7 1.0
CA A:ASP131 3.6 8.9 1.0
C A:LEU130 3.7 7.8 1.0
C A:GLY10 3.8 9.8 1.0
C A:ASP131 3.8 9.4 1.0
CB A:LEU11 3.9 11.3 1.0
CB A:LEU132 4.0 10.9 1.0
CA A:LEU132 4.1 11.0 1.0
CA A:LEU11 4.1 11.1 1.0
N A:ASP131 4.1 8.2 1.0
O A:LEU132 4.2 11.2 1.0
OD1 A:ASP131 4.2 8.0 1.0
CD2 A:LEU11 4.3 11.8 1.0
CB A:SER14 4.4 9.6 1.0
CD1 A:LEU129 4.4 7.8 1.0
CD1 A:LEU11 4.5 11.7 1.0
CD2 A:TYR162 4.6 8.6 1.0
C A:LEU132 4.6 11.1 1.0
CG A:ARG159 4.6 14.6 1.0
OG A:SER14 4.7 9.3 1.0
CB A:ASP131 4.7 8.7 1.0
N A:GLY10 4.8 8.8 1.0
CE2 A:TYR162 4.9 8.3 1.0
CG A:ASP131 5.0 8.7 1.0
O A:GLY10 5.0 9.4 1.0

Calcium binding site 10 out of 15 in 5zb4

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Calcium binding site 10 out of 15 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tmp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:28.3
occ:1.00
 O B:HOH341 2.1 21.8 1.0
O1B B:ADP201 2.1 15.3 1.0
O B:HOH332 2.1 20.0 1.0
O B:HOH355 2.2 15.6 1.0
OG1 B:THR17 2.2 15.3 1.0
O B:HOH306 2.2 16.5 1.0
PB B:ADP201 3.2 17.0 1.0
CB B:THR17 3.2 15.9 1.0
O2B B:ADP201 3.5 16.0 1.0
N B:THR17 3.9 15.0 1.0
O1A B:ADP201 4.0 18.3 1.0
OD2 B:ASP90 4.0 14.0 1.0
CA B:THR17 4.2 15.4 1.0
O B:HOH311 4.2 26.8 1.0
CG2 B:THR17 4.3 17.0 1.0
O3A B:ADP201 4.3 16.5 1.0
O3B B:ADP201 4.3 15.8 1.0
OD1 B:ASP90 4.4 14.7 1.0
PA B:ADP201 4.6 16.7 1.0
O B:HOH304 4.6 26.3 1.0
CG B:ASP90 4.6 13.7 1.0
CB B:LYS16 4.8 13.6 1.0
O2A B:ADP201 4.9 17.2 1.0
O B:HOH339 4.9 24.0 1.0
NZ B:LYS16 4.9 13.8 1.0
C B:LYS16 5.0 13.9 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 2018.
ISSN: ISSN 1879-0003
PubMed: 30447376
DOI: 10.1016/J.IJBIOMAC.2018.11.025
Page generated: Mon Jul 15 15:46:06 2024

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