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Magnesium in PDB 5xal: Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase

Enzymatic activity of Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase

All present enzymatic activity of Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase:
2.7.4.9;

Protein crystallography data

The structure of Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase, PDB code: 5xal 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) 47.56 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.879, 47.560, 151.509, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 26.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase (pdb code 5xal). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase, PDB code: 5xal:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5xal

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Magnesium binding site 1 out of 8 in the Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:23.9
occ:1.00
 OH A:TYR62 2.8 11.4 1.0
NH1 A:ARG69 2.9 9.8 1.0
OG A:SER66 2.9 12.6 1.0
CZ A:TYR62 3.4 12.5 1.0
CD1 A:LEU93 3.5 12.2 1.0
CB A:SER66 3.6 11.9 1.0
CE1 A:TYR62 3.6 12.1 1.0
CB A:ALA115 3.7 13.6 1.0
CA A:ALA115 3.8 13.6 1.0
CA A:SER66 3.9 11.8 1.0
CD A:ARG69 3.9 10.6 1.0
CZ A:ARG69 4.0 10.5 1.0
N A:ALA115 4.2 13.2 1.0
CB A:ALA118 4.3 17.0 1.0
CE2 A:TYR62 4.4 12.2 1.0
NE A:ARG69 4.4 10.5 1.0
N A:SER66 4.7 11.4 1.0
CG1 A:VAL114 4.7 12.9 1.0
CD1 A:TYR62 4.7 12.4 1.0
CG A:ARG69 4.8 10.7 1.0
C A:VAL114 4.9 13.3 1.0
O A:LEU111 4.9 12.1 1.0
CB A:ARG69 4.9 10.5 1.0
CG A:LEU93 4.9 11.8 1.0

Magnesium binding site 2 out of 8 in 5xal

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Magnesium binding site 2 out of 8 in the Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:20.0
occ:1.00
 OD2 A:ASP94 2.7 12.8 1.0
OG1 A:THR7 2.7 14.5 1.0
OE2 A:GLU9 2.7 10.3 1.0
O A:HOH377 2.8 20.8 1.0
CG A:GLU9 3.4 10.9 1.0
CD A:GLU9 3.4 11.3 1.0
CB A:THR7 3.4 14.8 1.0
CG A:ASP94 3.4 11.4 1.0
CB A:ASP94 3.6 11.6 1.0
CG2 A:THR127 3.7 12.9 1.0
CB A:TYR92 3.7 13.1 1.0
OG1 A:THR127 3.8 13.2 1.0
CG2 A:THR7 3.9 15.5 1.0
N A:ASP94 4.1 11.3 1.0
NH1 A:ARG172 4.1 18.6 1.0
CG A:PRO124 4.2 18.6 1.0
N A:TYR92 4.4 12.0 1.0
CB A:THR127 4.4 13.0 1.0
CA A:TYR92 4.4 12.7 1.0
CD2 A:TYR92 4.4 13.6 1.0
CA A:ASP94 4.5 12.0 1.0
C A:TYR92 4.5 12.7 1.0
OD1 A:ASP94 4.5 11.2 1.0
CG A:TYR92 4.6 13.8 1.0
N A:LEU93 4.6 12.4 1.0
OE1 A:GLU9 4.6 11.0 1.0
CA A:THR7 4.8 14.4 1.0
CB A:GLU9 4.9 12.0 1.0
O A:TYR92 5.0 12.8 1.0

Magnesium binding site 3 out of 8 in 5xal

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Magnesium binding site 3 out of 8 in the Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:22.1
occ:1.00
 O B:PRO109 2.7 12.4 1.0
C B:PRO109 3.5 12.5 1.0
CA B:PRO109 3.7 13.4 1.0
N B:GLU113 3.7 14.4 1.0
CB B:ARG112 3.8 16.9 1.0
CB B:PRO109 4.0 12.9 1.0
CB B:GLU113 4.1 19.7 1.0
CA B:GLU113 4.2 16.7 1.0
C B:ARG112 4.3 14.8 1.0
O A:HOH364 4.4 16.4 1.0
CD B:GLU113 4.5 28.6 1.0
OE1 B:GLU113 4.5 33.0 1.0
CA B:ARG112 4.6 14.1 1.0
OE2 B:GLU113 4.6 32.9 1.0
N B:TRP110 4.8 12.4 1.0
CG B:GLU113 4.9 24.9 1.0
N B:ARG112 5.0 12.7 1.0

Magnesium binding site 4 out of 8 in 5xal

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Magnesium binding site 4 out of 8 in the Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:25.3
occ:1.00
 OG B:SER66 2.7 11.3 0.5
OH B:TYR62 2.9 13.8 1.0
NH1 B:ARG69 2.9 10.6 1.0
CB B:SER66 3.3 12.8 0.5
CB B:SER66 3.4 11.9 0.5
CZ B:TYR62 3.5 12.3 1.0
CA B:SER66 3.7 12.6 0.5
CA B:SER66 3.7 12.1 0.5
CD1 B:LEU93 3.7 10.8 1.0
CE1 B:TYR62 3.7 11.8 1.0
CD B:ARG69 3.8 11.2 1.0
CB B:ALA115 3.9 17.7 1.0
CZ B:ARG69 4.0 10.7 1.0
CA B:ALA115 4.0 17.3 1.0
CB B:ALA118 4.2 21.9 1.0
NE B:ARG69 4.3 10.7 1.0
CB B:ARG69 4.4 10.9 1.0
CG B:ARG69 4.4 11.0 1.0
CE2 B:TYR62 4.4 11.8 1.0
N B:SER66 4.5 12.1 1.0
N B:ALA115 4.5 15.7 1.0
OG B:SER66 4.6 13.7 0.5
CG1 B:VAL114 4.7 13.6 1.0
C B:SER66 4.8 12.2 1.0
CD1 B:TYR62 4.8 11.3 1.0
O B:SER66 4.8 12.1 1.0
CG2 B:THR119 5.0 21.1 1.0

Magnesium binding site 5 out of 8 in 5xal

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Magnesium binding site 5 out of 8 in the Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:19.6
occ:1.00
 OG1 B:THR7 2.6 9.9 1.0
OD2 B:ASP94 2.6 14.9 1.0
OE2 B:GLU9 2.8 11.3 1.0
CB B:THR7 3.3 10.6 1.0
CG B:GLU9 3.5 11.8 1.0
CG2 B:THR127 3.5 11.8 1.0
CD B:GLU9 3.5 12.1 1.0
CG B:ASP94 3.6 13.2 1.0
CB B:TYR92 3.6 11.3 1.0
OG1 B:THR127 3.7 11.9 1.0
CG2 B:THR7 3.8 10.9 1.0
CB B:ASP94 3.9 11.4 1.0
NH1 B:ARG172 4.1 14.4 1.0
N B:TYR92 4.1 10.8 1.0
N B:ASP94 4.2 10.2 1.0
CG B:PRO124 4.2 16.6 1.0
CA B:TYR92 4.2 10.6 1.0
CB B:THR127 4.3 11.8 1.0
CD2 B:TYR92 4.3 13.6 1.0
C B:TYR92 4.4 10.6 1.0
N B:LEU93 4.5 10.2 1.0
CG B:TYR92 4.5 12.1 1.0
CA B:ASP94 4.6 10.8 1.0
CA B:THR7 4.7 10.8 1.0
OE1 B:GLU9 4.7 12.8 1.0
OD1 B:ASP94 4.8 13.8 1.0
O B:HOH366 4.9 29.5 1.0
CB B:GLU9 5.0 11.4 1.0
C B:THR7 5.0 10.8 1.0

Magnesium binding site 6 out of 8 in 5xal

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Magnesium binding site 6 out of 8 in the Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:29.1
occ:1.00
 OD1 B:ASP131 2.8 17.4 1.0
O B:HOH319 2.9 24.3 1.0
O B:ARG159 2.9 12.8 1.0
CB B:TYR162 3.4 11.1 1.0
C B:ARG159 3.7 13.7 1.0
CA B:ARG159 3.7 15.0 1.0
CG B:ARG159 3.7 19.1 1.0
CG B:ASP131 3.8 16.4 1.0
CD1 B:LEU129 3.9 14.7 1.0
CA B:ASP131 4.0 16.1 1.0
CD2 B:TYR162 4.0 10.0 1.0
CG B:TYR162 4.1 10.6 1.0
CB B:ASP131 4.1 15.9 1.0
CD2 B:LEU129 4.1 14.3 1.0
CD B:ARG159 4.2 20.1 1.0
CG B:LEU163 4.2 13.6 1.0
CD2 B:LEU163 4.2 13.2 1.0
CB B:ARG159 4.3 16.4 1.0
NE B:ARG159 4.3 21.0 1.0
CG B:LEU129 4.3 14.1 1.0
N B:LEU163 4.3 12.8 1.0
CA B:TYR162 4.5 11.4 1.0
N B:LEU132 4.6 18.3 1.0
C B:TYR162 4.7 12.3 1.0
O B:LEU130 4.8 12.4 1.0
C B:ASP131 4.8 17.5 1.0
OD2 B:ASP131 4.8 17.0 1.0
O B:VAL158 4.8 14.7 1.0
N B:ARG159 4.9 14.3 1.0
N B:GLU160 4.9 13.2 1.0
N B:ASP131 5.0 14.7 1.0
N B:TYR162 5.0 10.8 1.0

Magnesium binding site 7 out of 8 in 5xal

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Magnesium binding site 7 out of 8 in the Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:26.6
occ:1.00
 OE1 B:GLU39 2.7 12.2 1.0
O B:TYR92 2.7 9.3 1.0
NH2 B:ARG69 3.0 10.5 1.0
CB B:GLU39 3.3 12.8 1.0
C B:TYR92 3.4 10.6 1.0
N B:TYR92 3.5 10.8 1.0
CA B:TYR92 3.5 10.6 1.0
CB B:ARG91 3.6 12.7 1.0
C B:ARG91 3.6 11.2 1.0
CB B:SER95 3.7 10.1 1.0
CD B:GLU39 3.7 12.7 1.0
O B:ARG91 3.9 10.1 1.0
CZ B:ARG69 4.0 10.7 1.0
OG B:SER95 4.0 11.5 1.0
NE B:ARG69 4.1 10.7 1.0
CG B:GLU39 4.1 12.5 1.0
O B:HOH313 4.1 14.7 1.0
CA B:ARG91 4.2 11.6 1.0
C B:GLU39 4.5 14.4 1.0
CA B:GLU39 4.5 13.5 1.0
O B:GLU39 4.5 13.9 1.0
N B:LEU93 4.5 10.2 1.0
CD B:ARG91 4.6 14.0 1.0
CG B:ARG91 4.7 13.9 1.0
CA B:SER95 4.8 10.0 1.0
O B:HOH360 4.8 20.4 1.0
OE2 B:GLU39 4.8 13.0 1.0
N B:SER95 4.9 9.6 1.0
N B:SER96 5.0 10.6 1.0

Magnesium binding site 8 out of 8 in 5xal

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Magnesium binding site 8 out of 8 in the Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Y99F Mutant of Thermus Thermophilus HB8 Thymidylate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg206

b:23.3
occ:1.00
 OE2 B:GLU169 2.5 21.6 1.0
O B:HOH328 2.6 13.7 1.0
O B:LEU165 2.7 14.5 1.0
O B:HOH343 2.8 27.5 1.0
CD B:GLU169 3.4 20.9 1.0
C B:LEU165 3.4 15.1 1.0
CA B:LEU165 3.4 14.6 1.0
CG B:GLU169 3.6 20.7 1.0
CB B:ALA168 3.7 22.3 1.0
CB B:LEU165 3.7 14.1 1.0
NH2 B:ARG112 3.7 26.3 1.0
CD2 B:LEU165 3.9 13.7 1.0
CB B:GLU169 3.9 20.2 1.0
N B:GLU169 4.2 21.2 1.0
CE1 B:PHE173 4.2 13.6 1.0
NH2 B:ARG172 4.3 15.4 1.0
CG B:LEU165 4.4 13.9 1.0
C B:ALA168 4.4 22.6 1.0
CA B:ALA168 4.5 21.5 1.0
OE1 B:GLU169 4.5 20.1 1.0
N B:ALA166 4.7 15.5 1.0
CA B:GLU169 4.7 21.3 1.0
N B:LEU165 4.8 15.7 1.0
N B:ALA168 4.9 21.7 1.0
CZ B:PHE173 4.9 13.4 1.0
O B:HOH325 4.9 27.1 1.0
O B:ALA164 4.9 19.0 1.0
CD1 B:PHE173 4.9 14.3 1.0
CZ B:ARG112 4.9 26.9 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: Mon Sep 30 09:15:33 2024

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