Atomistry » Magnesium » PDB 5x86-5xf5 » 5x86
Atomistry »
  Magnesium »
    PDB 5x86-5xf5 »
      5x86 »

Magnesium in PDB 5x86: Crystal Structure of Tmp Bound Thymidylate Kinase From Thermus Thermophilus HB8

Enzymatic activity of Crystal Structure of Tmp Bound Thymidylate Kinase From Thermus Thermophilus HB8

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

Protein crystallography data

The structure of Crystal Structure of Tmp Bound Thymidylate Kinase From Thermus Thermophilus HB8, PDB code: 5x86 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 (°) 46.901, 47.435, 152.062, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 16.8

Other elements in 5x86:

The structure of Crystal Structure of Tmp Bound Thymidylate Kinase From Thermus Thermophilus HB8 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Tmp Bound Thymidylate Kinase From Thermus Thermophilus HB8 (pdb code 5x86). 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 Tmp Bound Thymidylate Kinase From Thermus Thermophilus HB8, PDB code: 5x86:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5x86

Go back to Magnesium Binding Sites List in 5x86
Magnesium binding site 1 out of 8 in the Crystal Structure of Tmp 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 Tmp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:14.3
occ:1.00
 OG B:SER66 2.9 9.0 1.0
NH2 B:ARG69 3.0 7.8 1.0
OH B:TYR62 3.0 9.8 1.0
CB B:SER66 3.5 8.2 1.0
CZ B:TYR62 3.6 8.2 1.0
CB B:ALA115 3.7 8.3 1.0
CD B:ARG69 3.7 7.8 1.0
CD1 B:LEU93 3.7 8.0 1.0
CE1 B:TYR62 3.7 7.7 1.0
CA B:SER66 3.8 7.4 1.0
CA B:ALA115 3.9 8.2 1.0
CZ B:ARG69 4.0 7.7 1.0
NE B:ARG69 4.3 7.9 1.0
CB B:ALA118 4.3 11.6 1.0
N B:ALA115 4.5 7.1 1.0
CB B:ARG69 4.5 7.5 1.0
CG B:ARG69 4.5 8.1 1.0
N B:SER66 4.6 6.8 1.0
CE2 B:TYR62 4.7 7.8 1.0
CD1 B:TYR62 4.9 7.2 1.0
OG B:SER96 4.9 8.3 1.0
C B:SER66 4.9 6.3 1.0
O B:SER66 4.9 7.5 1.0

Magnesium binding site 2 out of 8 in 5x86

Go back to Magnesium Binding Sites List in 5x86
Magnesium binding site 2 out of 8 in the Crystal Structure of Tmp 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 Tmp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:15.4
occ:1.00
 O B:HOH429 2.7 16.2 1.0
O B:HOH376 2.7 13.5 1.0
O B:HOH454 2.8 14.1 1.0
O B:ARG157 2.8 7.5 1.0
CA B:ARG157 3.5 7.9 1.0
C B:ARG157 3.5 7.2 1.0
N B:GLY161 3.6 6.7 1.0
CB B:GLU160 3.8 8.3 1.0
CD1 B:TYR102 3.8 12.4 1.0
CB B:ARG157 3.8 8.7 1.0
CB B:TYR102 3.9 9.1 1.0
CA B:GLY161 4.1 6.5 1.0
C B:GLU160 4.1 6.7 1.0
CG B:ARG157 4.3 9.7 1.0
CG B:TYR102 4.3 9.9 1.0
O B:HOH456 4.4 28.0 1.0
CA B:GLU160 4.5 7.1 1.0
O B:TYR102 4.5 9.5 1.0
O B:HOH439 4.7 16.2 1.0
O B:ARG156 4.7 8.1 1.0
CE1 B:TYR102 4.8 13.1 1.0
CA B:TYR102 4.8 7.6 1.0
N B:ARG157 4.8 7.5 1.0
N B:VAL158 4.8 7.4 1.0
O B:GLU160 4.8 7.1 1.0
O B:HOH428 4.8 16.4 1.0
C B:TYR102 4.8 7.8 1.0
N B:GLU160 4.9 7.1 1.0
CG B:GLU160 4.9 9.7 1.0
CD B:ARG157 5.0 10.1 1.0

Magnesium binding site 3 out of 8 in 5x86

Go back to Magnesium Binding Sites List in 5x86
Magnesium binding site 3 out of 8 in the Crystal Structure of Tmp 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 Tmp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:14.9
occ:1.00
 OG1 B:THR7 2.7 8.4 1.0
OE2 B:GLU9 2.7 7.7 1.0
OD2 B:ASP94 2.8 12.3 1.0
O B:HOH383 2.8 11.1 1.0
CB B:THR7 3.4 8.2 1.0
CG B:GLU9 3.4 6.9 1.0
CD B:GLU9 3.5 7.1 1.0
CG B:ASP94 3.5 8.3 1.0
CB B:TYR92 3.7 8.3 1.0
CB B:ASP94 3.7 6.9 1.0
CG2 B:THR127 3.7 8.1 1.0
OG1 B:THR127 3.8 8.3 1.0
CG2 B:THR7 3.8 8.3 1.0
N B:ASP94 4.1 6.3 1.0
NH1 B:ARG172 4.1 9.7 1.0
N B:TYR92 4.2 7.1 1.0
CG B:PRO124 4.3 12.8 1.0
CA B:TYR92 4.3 7.3 1.0
CB B:THR127 4.4 7.8 1.0
CD2 B:TYR92 4.4 7.6 1.0
C B:TYR92 4.5 6.9 1.0
CA B:ASP94 4.5 6.5 1.0
N B:LEU93 4.6 6.9 1.0
CG B:TYR92 4.6 7.7 1.0
OD1 B:ASP94 4.6 8.9 1.0
OE1 B:GLU9 4.7 7.8 1.0
CA B:THR7 4.8 8.4 1.0
CB B:GLU9 4.9 6.7 1.0

Magnesium binding site 4 out of 8 in 5x86

Go back to Magnesium Binding Sites List in 5x86
Magnesium binding site 4 out of 8 in the Crystal Structure of Tmp 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 Tmp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:16.6
occ:1.00
 O B:HOH439 2.7 16.2 1.0
O B:GLU160 2.7 7.1 1.0
OE1 B:GLU160 2.8 12.6 1.0
NH2 B:ARG167 3.0 12.3 1.0
O B:HOH334 3.3 15.8 1.0
C B:GLU160 3.5 6.7 1.0
CA B:GLU160 3.6 7.1 1.0
CB B:GLU160 3.6 8.3 1.0
NH1 B:ARG167 3.6 13.4 1.0
N B:ALA164 3.7 6.5 1.0
CZ B:ARG167 3.8 12.6 1.0
CB B:LEU163 3.8 7.1 1.0
CD B:GLU160 3.8 11.9 1.0
CB B:ALA164 4.2 7.3 1.0
C B:LEU163 4.2 6.3 1.0
CA B:ALA164 4.3 6.7 1.0
CG B:GLU160 4.3 9.7 1.0
O B:HOH429 4.3 16.2 1.0
CA B:LEU163 4.5 6.4 1.0
N B:GLY161 4.7 6.7 1.0
O B:HOH456 4.8 28.0 1.0
O B:HOH395 4.8 16.9 1.0
CD1 B:LEU163 4.8 9.3 1.0
CG B:LEU163 4.9 7.9 1.0
N B:LEU163 4.9 6.4 1.0
OE2 B:GLU160 4.9 17.5 1.0
O B:LEU163 4.9 6.7 1.0

Magnesium binding site 5 out of 8 in 5x86

Go back to Magnesium Binding Sites List in 5x86
Magnesium binding site 5 out of 8 in the Crystal Structure of Tmp 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 Tmp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg206

b:18.0
occ:1.00
 OH B:TYR99 2.7 9.4 1.0
O B:HOH312 2.7 23.2 1.0
O B:HOH373 2.8 16.6 1.0
N B:ASP12 3.1 9.8 1.0
CB B:ASP12 3.5 12.9 0.5
CE1 B:PHE155 3.6 14.4 1.0
CZ B:TYR99 3.6 8.1 1.0
CG B:ASP12 3.7 15.9 0.5
CE2 B:TYR99 3.7 8.8 1.0
CB B:ASP12 3.7 11.2 0.5
CD1 B:PHE155 3.8 14.1 1.0
CD2 B:LEU11 3.8 11.7 1.0
CA B:ASP12 3.9 11.1 0.5
CA B:LEU11 3.9 8.5 1.0
OD2 B:ASP12 3.9 22.3 0.5
CA B:ASP12 3.9 10.4 0.5
C B:LEU11 3.9 9.0 1.0
CB B:LEU11 4.0 8.8 1.0
OD1 B:ASP12 4.3 16.8 0.5
O B:ASP12 4.5 12.5 1.0
CG B:LEU11 4.5 9.8 1.0
O3' B:TMP207 4.5 21.1 0.5
C B:ASP12 4.7 10.9 1.0
NH1 B:ARG91 4.8 9.3 1.0
CZ B:PHE155 4.8 16.4 1.0
O3' B:TMP207 4.9 17.0 0.5
CE1 B:TYR99 5.0 8.1 1.0

Magnesium binding site 6 out of 8 in 5x86

Go back to Magnesium Binding Sites List in 5x86
Magnesium binding site 6 out of 8 in the Crystal Structure of Tmp 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 Tmp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:15.2
occ:1.00
 OG A:SER66 2.9 9.5 1.0
OH A:TYR62 2.9 9.3 1.0
NH1 A:ARG69 3.0 7.0 1.0
CB A:SER66 3.5 7.2 1.0
CZ A:TYR62 3.5 8.1 1.0
CD1 A:LEU93 3.6 8.3 1.0
CE1 A:TYR62 3.7 7.4 1.0
CD A:ARG69 3.7 7.2 1.0
CA A:SER66 3.7 7.0 1.0
CB A:ALA115 3.9 13.3 1.0
CZ A:ARG69 4.0 6.5 1.0
CA A:ALA115 4.0 10.9 1.0
NE A:ARG69 4.3 6.7 1.0
CB A:ALA118 4.4 14.6 1.0
CB A:ARG69 4.5 7.4 1.0
N A:SER66 4.5 6.4 1.0
CG A:ARG69 4.5 7.3 1.0
CE2 A:TYR62 4.5 8.4 1.0
N A:ALA115 4.5 8.4 1.0
OG A:SER96 4.8 7.2 1.0
CD1 A:TYR62 4.8 7.4 1.0
CG1 A:VAL114 4.8 9.4 1.0
C A:SER66 4.8 6.6 1.0
O A:SER66 4.9 7.4 1.0

Magnesium binding site 7 out of 8 in 5x86

Go back to Magnesium Binding Sites List in 5x86
Magnesium binding site 7 out of 8 in the Crystal Structure of Tmp 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 Tmp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:15.9
occ:1.00
 O A:PRO109 2.7 9.2 1.0
O A:HOH420 2.8 21.2 1.0
C A:PRO109 3.5 8.6 1.0
CA A:PRO109 3.5 9.0 1.0
N A:GLU113 3.8 8.8 1.0
CB A:PRO109 3.9 9.9 1.0
CB A:ARG112 3.9 9.7 1.0
CB A:GLU113 4.3 11.6 1.0
O A:HOH326 4.3 20.7 1.0
C A:ARG112 4.4 8.8 1.0
CA A:GLU113 4.4 9.1 1.0
O A:HOH435 4.5 16.2 1.0
CA A:ARG112 4.6 9.2 1.0
OE1 A:GLU113 4.7 23.3 1.0
N A:TRP110 4.7 9.0 1.0
O A:HOH331 4.9 19.3 1.0
N A:PRO109 4.9 9.1 1.0
N A:ARG112 5.0 8.4 1.0

Magnesium binding site 8 out of 8 in 5x86

Go back to Magnesium Binding Sites List in 5x86
Magnesium binding site 8 out of 8 in the Crystal Structure of Tmp 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 8 of Crystal Structure of Tmp Bound Thymidylate Kinase From Thermus Thermophilus HB8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:13.9
occ:1.00
 OG1 A:THR7 2.7 7.7 1.0
OD2 A:ASP94 2.7 16.2 1.0
OE2 A:GLU9 2.7 6.9 1.0
O A:HOH355 2.8 14.6 1.0
CB A:THR7 3.4 7.0 1.0
CG A:GLU9 3.4 6.8 1.0
CD A:GLU9 3.5 6.8 1.0
CG A:ASP94 3.5 9.2 1.0
CB A:TYR92 3.6 6.5 1.0
CB A:ASP94 3.7 7.3 1.0
CG2 A:THR127 3.8 7.8 1.0
OG1 A:THR127 3.8 8.2 1.0
CG2 A:THR7 3.9 7.2 1.0
N A:ASP94 4.1 6.0 1.0
N A:TYR92 4.1 6.2 1.0
CA A:TYR92 4.1 6.2 1.0
NH1 A:ARG172 4.3 9.1 1.0
C A:TYR92 4.3 6.1 1.0
CD2 A:TYR92 4.3 7.4 1.0
CG A:PRO124 4.4 13.5 1.0
CB A:THR127 4.4 7.2 1.0
N A:LEU93 4.4 6.1 1.0
CG A:TYR92 4.5 7.2 1.0
CA A:ASP94 4.5 6.2 1.0
OD1 A:ASP94 4.6 9.8 1.0
OE1 A:GLU9 4.7 7.4 1.0
CA A:THR7 4.8 6.8 1.0
O A:TYR92 4.9 6.6 1.0
CB A:GLU9 4.9 6.6 1.0
C A:ARG91 4.9 6.2 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 09:09:19 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy