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Magnesium in PDB 5zb0: Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8

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

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

Protein crystallography data

The structure of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8, PDB code: 5zb0 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 / 1.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.871, 47.385, 151.987, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 15.3

Other elements in 5zb0:

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

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8 (pdb code 5zb0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8, PDB code: 5zb0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5zb0

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Magnesium binding site 1 out of 8 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:13.4
occ:1.00
 OG1 A:THR7 2.7 7.1 1.0
OE2 A:GLU9 2.7 6.4 1.0
OD2 A:ASP94 2.7 15.9 1.0
O A:HOH302 2.8 18.4 1.0
CB A:THR7 3.4 6.0 1.0
CG A:GLU9 3.4 5.9 1.0
CD A:GLU9 3.5 5.8 1.0
CB A:TYR92 3.5 6.2 1.0
CG A:ASP94 3.6 9.0 1.0
CB A:ASP94 3.8 6.5 1.0
CG2 A:THR7 3.8 6.7 1.0
CG2 A:THR127 3.8 7.3 1.0
OG1 A:THR127 3.8 7.4 1.0
N A:ASP94 4.0 5.8 1.0
N A:TYR92 4.1 5.3 1.0
CA A:TYR92 4.1 5.6 1.0
CD2 A:TYR92 4.2 6.9 1.0
CG A:PRO124 4.2 13.0 1.0
C A:TYR92 4.2 5.7 1.0
NH1 A:ARG172 4.3 8.7 1.0
N A:LEU93 4.3 5.6 1.0
CG A:TYR92 4.4 6.3 1.0
CB A:THR127 4.4 6.9 1.0
CA A:ASP94 4.5 5.8 1.0
OE1 A:GLU9 4.7 6.0 1.0
OD1 A:ASP94 4.7 9.7 1.0
CA A:THR7 4.8 5.9 1.0
O A:TYR92 4.8 6.0 1.0
CB A:GLU9 4.9 5.6 1.0

Magnesium binding site 2 out of 8 in 5zb0

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Magnesium binding site 2 out of 8 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:7.0
occ:1.00
 O3B A:ADP202 2.0 6.6 1.0
O A:HOH331 2.1 8.4 1.0
OG1 A:THR17 2.1 6.7 1.0
O A:HOH356 2.1 7.2 1.0
O A:HOH317 2.1 8.2 1.0
O A:HOH315 2.1 8.3 1.0
CB A:THR17 3.2 6.6 1.0
PB A:ADP202 3.3 6.5 1.0
O1B A:ADP202 3.5 7.6 1.0
N A:THR17 4.0 5.9 1.0
O A:HOH378 4.0 10.0 1.0
O1A A:ADP202 4.1 8.9 1.0
OD2 A:ASP90 4.1 6.8 1.0
O A:HOH364 4.1 30.2 1.0
CA A:THR17 4.2 6.1 1.0
CG2 A:THR17 4.2 7.7 1.0
O3B A:TYD201 4.2 14.2 1.0
O2A A:TYD201 4.2 10.2 1.0
OD1 A:ASP90 4.3 7.0 1.0
O2B A:ADP202 4.3 6.8 1.0
O3A A:ADP202 4.3 7.1 1.0
O A:HOH370 4.4 10.8 1.0
O1B A:TYD201 4.4 14.1 1.0
O3A A:TYD201 4.5 12.8 1.0
PA A:ADP202 4.6 7.5 1.0
CG A:ASP90 4.6 6.3 1.0
PB A:TYD201 4.7 13.0 1.0
O2A A:ADP202 4.9 8.2 1.0
PA A:TYD201 4.9 10.1 1.0
CE A:LYS16 4.9 6.8 1.0
NZ A:LYS16 5.0 6.3 1.0
CB A:LYS16 5.0 6.2 1.0
O A:HOH395 5.0 12.0 1.0

Magnesium binding site 3 out of 8 in 5zb0

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Magnesium binding site 3 out of 8 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:14.1
occ:1.00
 OD2 A:ASP68 2.8 8.5 1.0
O A:PHE65 3.0 6.2 1.0
CD1 A:PHE65 3.5 6.4 1.0
CA A:PHE65 3.6 5.9 1.0
CA A:PRO40 3.7 6.1 1.0
NH2 A:ARG69 3.7 7.1 1.0
CB A:GLU39 3.7 6.3 1.0
CG A:ASP68 3.7 6.7 1.0
C A:PHE65 3.7 6.0 1.0
CB A:ASP68 3.7 6.5 1.0
CB A:PRO40 3.8 7.3 1.0
CB A:PHE65 3.8 5.8 1.0
OE1 A:GLU39 4.0 7.7 1.0
C5M A:TYD201 4.0 6.1 1.0
CG A:GLU39 4.1 7.1 1.0
CD A:GLU39 4.1 6.7 1.0
CG A:PHE65 4.1 5.9 1.0
N A:ARG69 4.2 5.7 1.0
CZ A:ARG69 4.2 6.8 1.0
N A:PRO40 4.3 6.0 1.0
CA A:GLU39 4.5 6.0 1.0
CE1 A:PHE65 4.5 6.7 1.0
CB A:ARG69 4.6 6.3 1.0
C A:GLU39 4.7 5.8 1.0
O4 A:TYD201 4.7 6.5 1.0
NE A:ARG69 4.7 6.6 1.0
C A:ASP68 4.7 5.8 1.0
CA A:ARG69 4.8 6.0 1.0
CA A:ASP68 4.8 6.1 1.0
C5 A:TYD201 4.8 5.8 1.0
C A:PRO40 4.9 6.5 1.0
OD1 A:ASP68 4.9 8.1 1.0
NH1 A:ARG69 4.9 7.1 1.0
N A:GLY41 4.9 6.7 1.0
OE2 A:GLU39 4.9 7.8 1.0
N A:PHE65 5.0 5.5 1.0
CG A:PRO40 5.0 7.7 1.0
N A:SER66 5.0 6.0 1.0

Magnesium binding site 4 out of 8 in 5zb0

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Magnesium binding site 4 out of 8 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:15.0
occ:1.00
 OG A:SER66 2.9 4.4 0.5
OH A:TYR62 2.9 9.7 1.0
NH1 A:ARG69 3.0 7.1 1.0
CB A:SER66 3.5 7.7 0.5
CZ A:TYR62 3.5 7.9 1.0
CB A:SER66 3.6 5.1 0.5
CD A:ARG69 3.6 6.8 1.0
CD1 A:LEU93 3.7 7.4 1.0
CA A:SER66 3.7 6.8 0.5
CA A:SER66 3.7 6.1 0.5
CE1 A:TYR62 3.7 7.2 1.0
CB A:ALA115 3.7 13.9 1.0
CA A:ALA115 4.0 11.9 1.0
CZ A:ARG69 4.0 6.8 1.0
NE A:ARG69 4.2 6.6 1.0
CB A:ALA118 4.3 16.0 1.0
CB A:ARG69 4.4 6.3 1.0
CG A:ARG69 4.4 6.3 1.0
N A:ALA115 4.5 8.7 1.0
N A:SER66 4.5 6.0 1.0
CE2 A:TYR62 4.5 7.8 1.0
C A:SER66 4.8 5.9 1.0
O A:SER66 4.8 6.3 1.0
CG1 A:VAL114 4.8 8.1 1.0
CD1 A:TYR62 4.8 6.4 1.0
OG A:SER96 4.8 6.7 1.0
OG A:SER66 4.9 10.7 0.5
O A:LEU111 5.0 8.2 1.0

Magnesium binding site 5 out of 8 in 5zb0

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Magnesium binding site 5 out of 8 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:14.3
occ:1.00
 OG1 B:THR7 2.7 7.8 1.0
OE2 B:GLU9 2.7 7.3 1.0
OD2 B:ASP94 2.8 14.8 1.0
O B:HOH365 2.8 14.7 1.0
CB B:THR7 3.4 7.3 1.0
CG B:GLU9 3.4 6.5 1.0
CD B:GLU9 3.5 6.7 1.0
CB B:TYR92 3.6 6.9 1.0
CG B:ASP94 3.6 8.9 1.0
CG2 B:THR127 3.7 8.0 1.0
CB B:ASP94 3.8 7.0 1.0
CG2 B:THR7 3.8 8.0 1.0
OG1 B:THR127 3.8 8.0 1.0
N B:ASP94 4.1 6.0 1.0
N B:TYR92 4.2 6.7 1.0
CA B:TYR92 4.2 6.7 1.0
CG B:PRO124 4.2 13.1 1.0
NH1 B:ARG172 4.3 9.4 1.0
CD2 B:TYR92 4.3 7.5 1.0
C B:TYR92 4.4 6.4 1.0
CB B:THR127 4.4 7.3 1.0
N B:LEU93 4.4 6.5 1.0
CG B:TYR92 4.5 6.7 1.0
CA B:ASP94 4.5 6.1 1.0
OE1 B:GLU9 4.7 7.2 1.0
OD1 B:ASP94 4.7 9.2 1.0
CA B:THR7 4.8 7.4 1.0
CB B:GLU9 4.9 6.4 1.0
O B:TYR92 4.9 6.9 1.0

Magnesium binding site 6 out of 8 in 5zb0

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Magnesium binding site 6 out of 8 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:17.0
occ:1.00
 OD2 B:ASP68 2.8 13.6 1.0
O B:PHE65 3.0 6.2 1.0
CD1 B:PHE65 3.5 9.1 1.0
NH2 B:ARG69 3.6 7.3 1.0
CG B:ASP68 3.7 8.1 1.0
CA B:PHE65 3.7 6.1 1.0
C B:PHE65 3.7 5.7 1.0
CA B:PRO40 3.8 8.1 1.0
CB B:GLU39 3.8 8.1 1.0
CB B:ASP68 3.8 7.0 1.0
CB B:PHE65 3.8 6.5 1.0
C5M B:TYD201 3.9 8.8 1.0
OE1 B:GLU39 3.9 9.3 1.0
CB B:PRO40 3.9 9.3 1.0
CD B:GLU39 4.1 8.7 1.0
CG B:PHE65 4.1 7.3 1.0
N B:ARG69 4.2 5.9 1.0
CZ B:ARG69 4.2 6.7 1.0
CG B:GLU39 4.2 9.5 1.0
N B:PRO40 4.4 8.2 1.0
CE1 B:PHE65 4.5 10.6 1.0
CB B:ARG69 4.6 6.5 1.0
O4 B:TYD201 4.6 7.6 1.0
CA B:GLU39 4.6 8.0 1.0
NE B:ARG69 4.6 7.2 1.0
C5 B:TYD201 4.7 8.0 1.0
CA B:ARG69 4.7 6.3 1.0
OD1 B:ASP68 4.7 8.9 1.0
C B:ASP68 4.8 5.9 1.0
C B:GLU39 4.8 7.7 1.0
CA B:ASP68 4.8 6.1 1.0
OE2 B:GLU39 4.8 9.6 1.0
NH1 B:ARG69 4.9 7.5 1.0
C B:PRO40 4.9 7.9 1.0
N B:GLY41 5.0 8.2 1.0
C4 B:TYD201 5.0 7.0 1.0

Magnesium binding site 7 out of 8 in 5zb0

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Magnesium binding site 7 out of 8 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:13.7
occ:1.00
 OG B:SER66 2.9 3.5 0.5
NH1 B:ARG69 3.0 7.5 1.0
OG B:SER66 3.1 11.6 0.5
OH B:TYR62 3.1 8.8 1.0
CB B:SER66 3.5 8.4 0.5
CB B:SER66 3.6 4.4 0.5
CD1 B:LEU93 3.6 7.9 1.0
CZ B:TYR62 3.7 7.7 1.0
CD B:ARG69 3.7 7.1 1.0
CA B:SER66 3.8 6.5 0.5
CE1 B:TYR62 3.8 7.0 1.0
CA B:SER66 3.8 5.4 0.5
CB B:ALA115 3.8 7.4 1.0
CA B:ALA115 4.0 7.1 1.0
CZ B:ARG69 4.1 6.7 1.0
CB B:ALA118 4.2 10.2 1.0
NE B:ARG69 4.3 7.2 1.0
CB B:ARG69 4.5 6.5 1.0
CG B:ARG69 4.5 7.1 1.0
N B:ALA115 4.5 6.1 1.0
N B:SER66 4.6 5.7 1.0
CE2 B:TYR62 4.7 7.6 1.0
C B:SER66 4.9 5.6 1.0
O B:SER66 4.9 6.5 1.0
CG2 B:THR119 4.9 11.4 1.0
CD1 B:TYR62 4.9 6.0 1.0
CG B:LEU93 5.0 7.1 1.0
OG B:SER96 5.0 7.5 1.0

Magnesium binding site 8 out of 8 in 5zb0

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Magnesium binding site 8 out of 8 in the Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Thymidylate Kinase in Complex with Adp and Tdp From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg206

b:14.4
occ:1.00
 O B:HOH334 2.0 18.6 1.0
O1B B:ADP202 2.0 11.0 1.0
O B:HOH317 2.1 25.4 1.0
OG1 B:THR17 2.1 12.2 1.0
O B:HOH320 2.1 11.8 1.0
O B:HOH381 2.1 18.6 1.0
CB B:THR17 3.2 12.3 1.0
PB B:ADP202 3.2 10.0 1.0
O2B B:ADP202 3.5 10.5 1.0
N B:THR17 4.0 9.4 1.0
O B:HOH388 4.0 27.2 1.0
O1A B:ADP202 4.1 13.9 1.0
OD2 B:ASP90 4.1 13.1 1.0
CA B:THR17 4.2 11.1 1.0
CG2 B:THR17 4.2 13.7 1.0
O3B B:ADP202 4.3 9.7 1.0
O3A B:ADP202 4.3 10.5 1.0
OD1 B:ASP90 4.4 11.0 1.0
PA B:ADP202 4.6 11.3 1.0
CG B:ASP90 4.7 10.7 1.0
O B:HOH341 4.8 20.8 1.0
NZ B:LYS16 4.9 9.8 1.0
OD1 B:ASP12 4.9 17.2 0.5
CB B:LYS16 4.9 8.6 1.0
CE B:LYS16 4.9 9.9 1.0
O2A B:TYD201 5.0 47.7 1.0
O2A B:ADP202 5.0 11.5 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 Sep 30 11:48:09 2024

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