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Magnesium in PDB 5xt8: Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8

Enzymatic activity of Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8

All present enzymatic activity of Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8:
2.7.4.9;

Protein crystallography data

The structure of Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8, PDB code: 5xt8 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) 48.87 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.620, 80.720, 122.790, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.2

Other elements in 5xt8:

The structure of Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8 also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8 (pdb code 5xt8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8, PDB code: 5xt8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5xt8

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Magnesium binding site 1 out of 10 in the Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) 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 Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:25.0
occ:1.00
 CE1 A:HIS192 2.8 12.9 1.0
NE2 A:HIS192 3.4 13.1 1.0
CD2 A:LEU176 3.8 15.3 1.0
ND1 A:HIS192 3.9 13.8 1.0
C2 A:EDO211 4.0 23.7 1.0
CG1 A:VAL174 4.5 14.2 1.0
O A:HOH325 4.6 14.7 1.0
CD2 A:HIS192 4.7 11.3 1.0
O A:VAL175 4.8 11.5 1.0
O2 A:EDO211 4.9 31.3 1.0
CB A:ALA188 4.9 14.4 1.0
CG A:HIS192 5.0 12.1 1.0

Magnesium binding site 2 out of 10 in 5xt8

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Magnesium binding site 2 out of 10 in the Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) 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 Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:25.0
occ:1.00
 OG A:SER66 2.9 21.0 1.0
OH A:TYR62 3.0 23.6 1.0
NH1 A:ARG69 3.0 17.5 1.0
CB A:SER66 3.6 20.7 1.0
CZ A:TYR62 3.6 19.0 1.0
CA A:ALA115 3.8 20.7 1.0
CD A:ARG69 3.8 16.5 1.0
CD1 A:LEU93 3.8 12.7 1.0
CB A:ALA115 3.8 20.2 1.0
CA A:SER66 3.9 17.9 1.0
CE1 A:TYR62 3.9 18.6 1.0
CB A:ALA118 4.1 17.7 1.0
CZ A:ARG69 4.1 17.6 1.0
N A:ALA115 4.3 19.5 1.0
NE A:ARG69 4.4 17.1 1.0
CE2 A:TYR62 4.5 18.6 1.0
CG A:ARG69 4.7 15.8 1.0
N A:SER66 4.7 18.0 1.0
CB A:ARG69 4.7 15.7 1.0
CG1 A:VAL114 4.8 17.7 1.0
CG2 A:THR119 4.8 17.8 1.0
C A:VAL114 4.9 19.9 1.0
O A:SER66 4.9 16.2 1.0
C A:SER66 4.9 16.7 1.0

Magnesium binding site 3 out of 10 in 5xt8

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Magnesium binding site 3 out of 10 in the Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) 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 Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:21.8
occ:1.00
 OG1 A:THR7 2.6 10.6 1.0
OE2 A:GLU9 2.7 11.9 1.0
OD2 A:ASP94 2.8 16.8 1.0
O A:HOH400 3.1 18.6 1.0
CG A:GLU9 3.4 12.1 1.0
CB A:THR7 3.4 10.4 1.0
CD A:GLU9 3.5 13.0 1.0
CG A:ASP94 3.6 13.7 1.0
CB A:TYR92 3.6 12.8 1.0
CG2 A:THR127 3.7 10.2 1.0
CB A:ASP94 3.7 12.5 1.0
OG1 A:THR127 3.7 9.6 1.0
CG2 A:THR7 3.9 10.2 1.0
NH1 A:ARG172 4.1 13.2 1.0
N A:TYR92 4.2 12.4 1.0
N A:ASP94 4.2 11.0 1.0
CA A:TYR92 4.3 13.1 1.0
CB A:THR127 4.3 10.0 1.0
CG A:PRO124 4.4 14.1 1.0
CD2 A:TYR92 4.4 12.3 1.0
C A:TYR92 4.5 12.9 1.0
CG A:TYR92 4.5 12.8 1.0
CA A:ASP94 4.6 11.5 1.0
OD1 A:ASP94 4.6 12.9 1.0
N A:LEU93 4.7 12.8 1.0
OE1 A:GLU9 4.7 11.7 1.0
CA A:THR7 4.8 10.3 1.0
CB A:GLU9 4.9 12.2 1.0

Magnesium binding site 4 out of 10 in 5xt8

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Magnesium binding site 4 out of 10 in the Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) 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 Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:23.9
occ:1.00
 OE1 A:GLN19 2.7 11.8 1.0
O A:GLN19 2.9 9.7 1.0
O A:HOH301 3.0 21.6 1.0
N A:LEU23 3.6 13.7 1.0
C A:GLN19 3.6 9.6 1.0
CA A:GLN19 3.7 9.9 1.0
CB A:LEU23 3.8 13.7 1.0
CD1 A:ILE189 3.8 12.1 1.0
CB A:GLN19 3.8 9.9 1.0
CB A:ARG22 3.9 13.8 1.0
CD A:GLN19 3.9 10.6 1.0
CA A:LEU23 3.9 13.6 1.0
CA A:ALA186 4.0 12.3 1.0
CB A:ALA186 4.1 12.3 1.0
CG2 A:ILE189 4.1 13.8 1.0
C A:ARG22 4.2 14.2 1.0
CB A:ILE189 4.2 13.9 1.0
CG A:GLN19 4.5 10.3 1.0
O A:ALA186 4.6 12.6 1.0
CA A:ARG22 4.6 13.4 1.0
CG1 A:ILE189 4.6 12.8 1.0
C A:ALA186 4.8 12.8 1.0
N A:ALA20 4.9 10.2 1.0
CG A:LEU23 4.9 14.2 1.0
NE2 A:GLN190 4.9 21.1 1.0
CD1 A:LEU23 4.9 13.6 1.0
N A:ARG22 5.0 12.1 1.0
O A:ARG22 5.0 14.2 1.0
N A:ALA186 5.0 12.2 1.0

Magnesium binding site 5 out of 10 in 5xt8

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Magnesium binding site 5 out of 10 in the Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) 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 Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:28.0
occ:1.00
 CL A:CL209 3.0 20.0 1.0
N A:THR18 3.1 14.4 1.0
OG1 A:THR18 3.2 15.1 1.0
O A:HOH397 3.4 26.5 1.0
CB A:THR17 3.4 14.8 1.0
CA A:GLY15 3.4 13.5 1.0
N A:THR17 3.5 14.9 1.0
C A:GLY15 3.5 14.7 1.0
O A:HOH379 3.6 23.4 1.0
CB A:THR18 3.7 12.8 1.0
CA A:THR17 3.7 13.9 1.0
O A:GLY15 3.8 14.8 1.0
N A:GLY15 3.8 13.5 1.0
C A:THR17 3.9 15.0 1.0
CA A:THR18 4.0 12.5 1.0
N A:LYS16 4.1 14.7 1.0
CG2 A:THR17 4.3 15.8 1.0
OG1 A:THR17 4.3 14.5 1.0
C A:LYS16 4.5 15.3 1.0
CA A:LYS16 4.9 15.4 1.0

Magnesium binding site 6 out of 10 in 5xt8

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Magnesium binding site 6 out of 10 in the Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) 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 Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:23.9
occ:1.00
 O B:ALA83 2.7 16.8 1.0
C B:ALA83 3.6 17.4 1.0
O B:HOH341 3.7 26.5 1.0
CB B:ALA83 3.8 18.3 1.0
CA B:ALA83 3.8 17.2 1.0
O B:HOH389 4.7 15.2 1.0
N B:GLY84 4.8 16.2 1.0
O B:HOH368 4.9 24.6 1.0

Magnesium binding site 7 out of 10 in 5xt8

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Magnesium binding site 7 out of 10 in the Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) 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 Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:26.6
occ:1.00
 OE1 B:GLU169 2.6 16.5 1.0
CL B:CL206 3.1 15.4 1.0
CD B:GLU169 3.5 16.1 1.0
CG B:GLU169 3.6 15.5 1.0
CE B:LYS123 3.7 24.8 1.0
CB B:GLU169 3.7 14.7 1.0
CB B:ARG172 3.9 12.2 1.0
NE B:ARG172 4.1 12.9 1.0
CD B:ARG172 4.3 13.2 1.0
NZ B:LYS123 4.5 22.7 1.0
CA B:GLU169 4.6 13.8 1.0
OE2 B:GLU169 4.7 15.4 1.0
CG B:ARG172 4.7 12.7 1.0
CD B:LYS123 4.9 24.4 1.0
N B:ARG172 5.0 12.3 1.0

Magnesium binding site 8 out of 10 in 5xt8

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Magnesium binding site 8 out of 10 in the Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) 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 Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:21.8
occ:1.00
 OE2 B:GLU9 2.7 12.6 1.0
OG1 B:THR7 2.7 12.3 1.0
OD2 B:ASP94 2.8 18.4 1.0
O B:HOH370 3.0 19.0 1.0
CG B:GLU9 3.3 12.0 1.0
CB B:THR7 3.4 12.2 1.0
CD B:GLU9 3.4 11.9 1.0
CG B:ASP94 3.6 14.9 1.0
CB B:TYR92 3.6 12.1 1.0
CG2 B:THR127 3.7 13.4 1.0
CB B:ASP94 3.8 14.3 1.0
CG2 B:THR7 3.8 12.5 1.0
OG1 B:THR127 3.8 11.8 1.0
N B:TYR92 4.1 13.9 1.0
NH1 B:ARG172 4.1 11.7 1.0
CA B:TYR92 4.2 12.5 1.0
N B:ASP94 4.2 12.4 1.0
CG B:PRO124 4.2 16.6 1.0
C B:TYR92 4.4 12.8 1.0
CB B:THR127 4.4 12.3 1.0
CD2 B:TYR92 4.4 12.3 1.0
N B:LEU93 4.5 12.2 1.0
CG B:TYR92 4.5 12.0 1.0
OE1 B:GLU9 4.6 12.3 1.0
CA B:ASP94 4.6 13.3 1.0
OD1 B:ASP94 4.6 17.0 1.0
CB B:GLU9 4.8 13.2 1.0
CA B:THR7 4.8 12.7 1.0
O B:TYR92 4.9 13.1 1.0
C B:ARG91 5.0 13.9 1.0

Magnesium binding site 9 out of 10 in 5xt8

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Magnesium binding site 9 out of 10 in the Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:23.5
occ:1.00
 OG B:SER66 2.9 22.5 1.0
NH2 B:ARG69 3.0 16.9 1.0
OH B:TYR62 3.1 16.9 1.0
CB B:SER66 3.6 20.1 1.0
CD1 B:LEU93 3.6 15.0 1.0
CZ B:TYR62 3.6 15.5 1.0
CA B:ALA115 3.8 22.4 1.0
CD B:ARG69 3.8 16.2 1.0
CB B:ALA115 3.8 20.8 1.0
CE1 B:TYR62 3.9 15.2 1.0
CA B:SER66 4.0 18.6 1.0
CB B:ALA118 4.0 20.7 1.0
CZ B:ARG69 4.0 16.8 1.0
N B:ALA115 4.3 21.3 1.0
NE B:ARG69 4.3 16.5 1.0
CE2 B:TYR62 4.6 14.8 1.0
CG B:ARG69 4.7 16.0 1.0
CG1 B:VAL114 4.7 22.3 1.0
CB B:ARG69 4.8 16.2 1.0
N B:SER66 4.8 19.5 1.0
C B:VAL114 4.8 22.6 1.0
CD1 B:TYR62 4.9 15.7 1.0
O B:SER66 5.0 15.3 1.0
C B:ALA115 5.0 22.4 1.0

Magnesium binding site 10 out of 10 in 5xt8

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Magnesium binding site 10 out of 10 in the Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Magnesium Bound Apo Structure of Thymidylate Kinase (Form I) From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:37.0
occ:1.00
 OD1 B:ASP131 2.8 17.6 1.0
O B:HOH357 3.2 29.2 1.0
O B:ARG159 3.2 18.9 1.0
CG B:ARG159 3.4 21.7 1.0
CB B:TYR162 3.4 13.6 1.0
CG B:ASP131 3.7 18.0 1.0
CA B:ARG159 3.8 19.7 1.0
CD1 B:LEU129 3.8 14.7 1.0
C B:ARG159 3.9 21.0 1.0
CB B:ASP131 3.9 17.4 1.0
CA B:ASP131 3.9 16.8 1.0
CD2 B:TYR162 4.0 13.7 1.0
CB B:ARG159 4.1 21.9 1.0
CG B:TYR162 4.1 13.7 1.0
CD2 B:LEU129 4.2 14.0 1.0
CG B:LEU163 4.2 20.3 1.0
CG B:LEU129 4.2 14.2 1.0
CD2 B:LEU163 4.4 19.2 1.0
NE B:ARG159 4.5 23.4 1.0
CD B:ARG159 4.6 23.5 1.0
N B:LEU163 4.6 15.1 1.0
N B:LEU132 4.6 22.7 1.0
CA B:TYR162 4.6 14.8 1.0
O B:LEU130 4.8 16.3 1.0
CD1 B:LEU163 4.8 22.7 1.0
C B:ASP131 4.8 18.7 1.0
C B:TYR162 4.9 15.2 1.0
OD2 B:ASP131 4.9 15.7 1.0
N B:ASP131 4.9 15.0 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: Mon Sep 30 09:42:41 2024

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