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Magnesium in PDB 5x8b: Crystal Structure of Atp-Tmp and Adp Bound Thymidylate Kinase From Thermus Thermophilus HB8

Enzymatic activity of Crystal Structure of Atp-Tmp and Adp Bound Thymidylate Kinase From Thermus Thermophilus HB8

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

Protein crystallography data

The structure of Crystal Structure of Atp-Tmp and Adp Bound Thymidylate Kinase From Thermus Thermophilus HB8, PDB code: 5x8b 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 / 1.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.058, 47.467, 152.453, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 18.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Atp-Tmp and Adp Bound Thymidylate Kinase From Thermus Thermophilus HB8 (pdb code 5x8b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Atp-Tmp and Adp Bound Thymidylate Kinase From Thermus Thermophilus HB8, PDB code: 5x8b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5x8b

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Magnesium binding site 1 out of 7 in the Crystal Structure of Atp-Tmp and Adp Bound Thymidylate Kinase 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 Atp-Tmp and Adp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:14.0
occ:1.00
 O2G A:ATP201 2.0 16.1 1.0
O A:HOH353 2.0 14.6 1.0
O A:HOH331 2.0 15.4 1.0
OG1 A:THR17 2.1 13.2 1.0
O A:HOH325 2.1 16.1 1.0
O1B A:ATP201 2.1 12.5 1.0
CB A:THR17 3.2 10.9 1.0
PG A:ATP201 3.2 23.6 1.0
PB A:ATP201 3.3 13.0 1.0
O3B A:ATP201 3.4 16.8 1.0
NH2 A:ARG38 4.0 15.8 0.5
N A:THR17 4.0 10.9 1.0
O3G A:ATP201 4.1 30.4 1.0
O1A A:ATP201 4.1 16.9 1.0
OD2 A:ASP90 4.1 13.8 1.0
CG2 A:THR17 4.1 13.4 1.0
CA A:THR17 4.2 10.6 1.0
O3P A:TMP202 4.2 20.6 0.5
O1G A:ATP201 4.4 31.2 1.0
O3A A:ATP201 4.4 13.6 1.0
O2B A:ATP201 4.4 14.0 1.0
OD1 A:ASP90 4.4 14.2 1.0
NH1 A:ARG38 4.5 25.0 0.5
PA A:ATP201 4.6 14.7 1.0
CG A:ASP90 4.7 12.1 1.0
CZ A:ARG38 4.7 22.0 0.5
O A:HOH341 4.9 17.4 1.0
CE A:LYS16 4.9 13.5 1.0
O2A A:ATP201 5.0 14.1 1.0

Magnesium binding site 2 out of 7 in 5x8b

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Magnesium binding site 2 out of 7 in the Crystal Structure of Atp-Tmp and Adp Bound Thymidylate Kinase 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 Atp-Tmp and Adp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:18.6
occ:1.00
 OG A:SER66 2.9 14.3 1.0
OH A:TYR62 2.9 12.7 1.0
NH2 A:ARG69 2.9 11.5 1.0
CZ A:TYR62 3.5 11.4 1.0
CB A:SER66 3.5 10.2 1.0
CD1 A:LEU93 3.6 11.0 1.0
CD A:ARG69 3.7 10.7 1.0
CE1 A:TYR62 3.7 11.3 1.0
CA A:SER66 3.7 9.2 1.0
CB A:ALA115 3.8 18.3 1.0
CA A:ALA115 4.0 14.9 1.0
CZ A:ARG69 4.0 10.4 1.0
NE A:ARG69 4.3 10.8 1.0
CB A:ALA118 4.3 21.0 1.0
CB A:ARG69 4.4 10.1 1.0
CG A:ARG69 4.5 10.2 1.0
N A:ALA115 4.5 11.5 1.0
CE2 A:TYR62 4.5 10.6 1.0
N A:SER66 4.5 9.5 1.0
CD1 A:TYR62 4.8 10.6 1.0
CG1 A:VAL114 4.8 11.8 1.0
C A:SER66 4.8 9.1 1.0
O A:SER66 4.9 10.4 1.0
OG A:SER96 4.9 12.2 1.0
CG A:LEU93 5.0 10.2 1.0

Magnesium binding site 3 out of 7 in 5x8b

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Magnesium binding site 3 out of 7 in the Crystal Structure of Atp-Tmp and Adp Bound Thymidylate Kinase 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 Atp-Tmp and Adp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:19.4
occ:1.00
 O A:LEU130 2.7 10.1 1.0
O A:HOH346 3.0 13.3 1.0
N A:LEU11 3.0 10.0 1.0
N A:LEU132 3.2 10.1 1.0
CG A:LEU11 3.4 15.4 1.0
CA A:GLY10 3.5 9.8 1.0
CA A:ASP131 3.6 9.5 1.0
C A:GLY10 3.7 9.8 1.0
C A:LEU130 3.8 9.3 1.0
CB A:LEU11 3.9 12.2 1.0
C A:ASP131 3.9 10.5 1.0
CA A:LEU11 4.0 11.5 1.0
CB A:LEU132 4.1 11.9 1.0
CD2 A:LEU11 4.1 18.2 1.0
N A:ASP131 4.1 10.1 1.0
CA A:LEU132 4.2 11.0 1.0
O A:LEU132 4.2 13.3 1.0
OD1 A:ASP131 4.3 12.0 1.0
CD1 A:LEU129 4.3 10.1 1.0
CD2 A:TYR162 4.4 9.0 1.0
CD1 A:LEU11 4.4 15.1 1.0
CB A:SER14 4.4 11.1 1.0
C A:LEU132 4.7 12.0 1.0
CG A:ARG159 4.7 19.4 1.0
OG A:SER14 4.7 11.5 1.0
CE2 A:TYR162 4.8 8.8 1.0
CB A:ASP131 4.8 10.9 1.0
N A:GLY10 4.8 9.4 1.0
O A:GLY10 4.9 10.8 1.0

Magnesium binding site 4 out of 7 in 5x8b

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Magnesium binding site 4 out of 7 in the Crystal Structure of Atp-Tmp and Adp Bound Thymidylate Kinase 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 Atp-Tmp and Adp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:18.3
occ:1.00
 OD2 A:ASP94 2.7 18.9 1.0
OG1 A:THR7 2.7 10.6 1.0
OE2 A:GLU9 2.7 10.1 1.0
CB A:THR7 3.4 10.1 1.0
CG A:GLU9 3.4 9.4 1.0
CD A:GLU9 3.5 9.8 1.0
CB A:TYR92 3.5 8.4 1.0
CG A:ASP94 3.6 12.2 1.0
CB A:ASP94 3.8 10.0 1.0
CG2 A:THR127 3.8 10.4 1.0
OG1 A:THR127 3.8 11.3 1.0
CG2 A:THR7 3.8 10.9 1.0
N A:ASP94 4.0 9.2 1.0
N A:TYR92 4.1 8.9 1.0
CA A:TYR92 4.1 8.8 1.0
CD2 A:TYR92 4.2 9.8 1.0
C A:TYR92 4.3 8.7 1.0
CG A:PRO124 4.3 17.2 1.0
NH1 A:ARG172 4.3 11.9 1.0
N A:LEU93 4.4 9.2 1.0
CG A:TYR92 4.4 9.5 1.0
CB A:THR127 4.4 10.4 1.0
CA A:ASP94 4.5 8.7 1.0
OD1 A:ASP94 4.7 12.9 1.0
OE1 A:GLU9 4.7 9.6 1.0
CA A:THR7 4.8 9.8 1.0
O A:TYR92 4.8 9.6 1.0
CB A:GLU9 4.9 9.1 1.0

Magnesium binding site 5 out of 7 in 5x8b

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Magnesium binding site 5 out of 7 in the Crystal Structure of Atp-Tmp and Adp Bound Thymidylate Kinase 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 Atp-Tmp and Adp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:17.9
occ:1.00
 OG B:SER66 2.9 6.5 0.5
NH1 B:ARG69 3.0 12.1 1.0
OG B:SER66 3.0 13.6 0.5
OH B:TYR62 3.1 15.0 1.0
CB B:SER66 3.5 11.2 0.5
CB B:SER66 3.6 7.6 0.5
CZ B:TYR62 3.7 12.5 1.0
CB B:ALA115 3.7 11.6 1.0
CD1 B:LEU93 3.7 11.0 1.0
CD B:ARG69 3.7 11.0 1.0
CA B:ALA115 3.8 10.8 1.0
CA B:SER66 3.8 8.3 0.5
CA B:SER66 3.8 9.0 0.5
CE1 B:TYR62 3.9 11.8 1.0
CZ B:ARG69 4.1 12.5 1.0
CB B:ALA118 4.1 13.0 1.0
NE B:ARG69 4.3 11.7 1.0
N B:ALA115 4.4 9.3 1.0
CB B:ARG69 4.6 9.1 1.0
CG B:ARG69 4.6 10.0 1.0
CE2 B:TYR62 4.6 12.8 1.0
N B:SER66 4.7 8.6 1.0
CG2 B:THR119 4.8 14.4 1.0
O B:SER66 4.8 9.8 1.0
C B:SER66 4.9 9.2 1.0
CG1 B:VAL114 5.0 11.5 1.0
CD1 B:TYR62 5.0 10.2 1.0

Magnesium binding site 6 out of 7 in 5x8b

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Magnesium binding site 6 out of 7 in the Crystal Structure of Atp-Tmp and Adp Bound Thymidylate Kinase 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 Atp-Tmp and Adp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:22.9
occ:1.00
 OH B:TYR99 2.8 12.6 1.0
O B:HOH377 2.8 19.4 1.0
OD2 B:ASP12 3.0 29.1 0.5
N B:ASP12 3.1 13.8 0.5
N B:ASP12 3.1 13.5 0.5
CG B:ASP12 3.3 21.4 0.5
CB B:ASP12 3.4 17.8 0.5
CE1 B:PHE155 3.6 18.6 1.0
CZ B:TYR99 3.7 10.1 1.0
CE2 B:TYR99 3.7 12.4 1.0
CD1 B:PHE155 3.8 16.1 1.0
CB B:ASP12 3.8 15.7 0.5
CA B:ASP12 3.8 16.1 0.5
CD2 B:LEU11 3.9 14.2 1.0
CA B:LEU11 3.9 11.1 1.0
CB B:LEU11 3.9 12.2 1.0
C B:LEU11 4.0 12.4 1.0
CA B:ASP12 4.0 15.0 0.5
OD1 B:ASP12 4.2 21.9 0.5
O B:ASP12 4.4 16.1 0.5
O B:ASP12 4.4 15.2 0.5
CG B:LEU11 4.6 13.2 1.0
C B:ASP12 4.7 15.4 0.5
C B:ASP12 4.7 14.8 0.5
CZ B:PHE155 4.8 17.8 1.0
NH1 B:ARG91 4.8 12.2 1.0
CE1 B:TYR99 5.0 10.6 1.0

Magnesium binding site 7 out of 7 in 5x8b

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Magnesium binding site 7 out of 7 in the Crystal Structure of Atp-Tmp and Adp Bound Thymidylate Kinase 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 Atp-Tmp and Adp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:23.2
occ:1.00
 O B:HOH302 2.0 23.0 1.0
O1B B:ADP204 2.0 19.4 1.0
O B:HOH403 2.1 27.5 1.0
O B:HOH360 2.1 25.4 1.0
O B:HOH301 2.1 35.4 1.0
OG1 B:THR17 2.2 21.1 1.0
PB B:ADP204 3.3 15.4 0.7
CB B:THR17 3.3 18.3 1.0
O3B B:ADP204 3.6 22.7 1.0
OD2 B:ASP90 3.9 22.5 1.0
NZ B:LYS16 3.9 17.6 0.5
N B:THR17 4.0 14.6 1.0
O1A B:ADP204 4.1 25.5 1.0
O B:HOH304 4.1 27.3 1.0
O2B B:ADP204 4.2 14.5 1.0
CA B:THR17 4.2 17.6 1.0
CG2 B:THR17 4.3 20.3 1.0
O3A B:ADP204 4.3 20.6 1.0
OD1 B:ASP12 4.4 19.6 0.5
OD1 B:ASP90 4.6 20.1 1.0
PA B:ADP204 4.6 17.5 0.7
CG B:ASP90 4.7 16.4 1.0
CB B:LYS16 4.9 14.2 0.5
CB B:LYS16 4.9 13.4 0.5
O2A B:ADP204 4.9 19.3 1.0
O B:HOH318 5.0 25.8 1.0
CE B:LYS16 5.0 11.8 0.5
NZ B:LYS16 5.0 12.4 0.5

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 09:09:19 2024

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