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Potassium in PDB 1w19: Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate

Enzymatic activity of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate

All present enzymatic activity of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate:
2.5.1.9;

Protein crystallography data

The structure of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate, PDB code: 1w19 was solved by E.Morgunova, W.Meining, B.Illarionov, I.Haase, M.Fischer, M.Cushman, A.Bacher, R.Ladenstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.54 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 131.267, 80.688, 86.188, 90.00, 120.29, 90.00
R / Rfree (%) 14.9 / 19.4

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Potassium atom in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate (pdb code 1w19). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 13 binding sites of Potassium where determined in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate, PDB code: 1w19:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 13 in 1w19

Go back to Potassium Binding Sites List in 1w19
Potassium binding site 1 out of 13 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1164

b:16.1
occ:1.00
 O A:ALA70 2.6 13.8 1.0
O A:HIS73 2.6 10.8 1.0
O A:HOH2092 2.7 21.0 1.0
O A:HOH2033 2.7 37.5 1.0
O A:HOH2056 2.7 34.4 1.0
OG1 A:THR110 2.8 13.5 1.0
O A:HOH2093 3.5 26.9 1.0
C A:ALA70 3.8 13.1 1.0
C A:HIS73 3.8 11.4 1.0
CG2 A:THR110 4.0 13.3 1.0
CB A:THR110 4.0 11.8 1.0
O A:HOH2128 4.0 28.0 1.0
O A:HOH2031 4.2 21.1 1.0
O A:SER108 4.3 9.5 1.0
N A:HIS73 4.4 11.8 1.0
O A:ARG71 4.4 17.8 1.0
C A:ARG71 4.5 16.2 1.0
CA A:ALA70 4.6 12.5 1.0
O A:HOH2059 4.6 35.8 1.0
N A:ASP74 4.6 10.8 1.0
O A:HOH2061 4.6 47.0 1.0
CA A:ASP74 4.7 10.4 1.0
N A:ARG71 4.7 14.2 1.0
N A:ASN72 4.8 15.3 1.0
CA A:HIS73 4.8 11.3 1.0
CA A:ARG71 4.8 15.5 1.0
CB A:ALA70 4.9 12.4 1.0

Potassium binding site 2 out of 13 in 1w19

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Potassium binding site 2 out of 13 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1165

b:22.0
occ:1.00
 O A:ALA34 2.6 10.7 1.0
O A:HOH2021 2.7 24.9 1.0
O A:GLY130 2.7 10.5 1.0
OD2 A:ASP137 2.7 15.2 1.0
O A:ALA129 3.0 10.9 1.0
C A:GLY130 3.3 10.4 1.0
C A:ALA34 3.5 10.7 1.0
CA A:GLY130 3.5 10.0 1.0
N A:GLY38 3.7 9.8 1.0
CG A:ASP137 3.7 13.5 1.0
O A:HOH2117 3.7 29.6 1.0
CA A:GLY38 3.9 9.9 1.0
C A:ALA129 4.0 10.2 1.0
CA A:ALA34 4.0 10.6 1.0
CB A:ALA34 4.1 10.6 1.0
OD1 A:ASP137 4.2 13.7 1.0
N A:GLY130 4.2 9.8 1.0
N A:LEU131 4.3 10.5 1.0
N A:LEU35 4.4 10.6 1.0
CB A:ASP37 4.5 11.3 1.0
OD1 A:ASP37 4.5 12.5 1.0
O A:HOH2107 4.5 32.6 1.0
C A:ASP37 4.5 10.4 1.0
CB A:ASP137 4.7 13.2 1.0
CA A:LEU35 4.8 10.4 1.0

Potassium binding site 3 out of 13 in 1w19

Go back to Potassium Binding Sites List in 1w19
Potassium binding site 3 out of 13 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1166

b:25.4
occ:0.50
 O A:LEU156 3.3 12.8 1.0
O A:ARG157 3.3 13.0 1.0
C A:ARG157 4.0 13.4 1.0
C A:LEU156 4.0 12.8 1.0
ND1 A:HIS159 4.0 29.7 1.0
CE1 A:HIS159 4.1 30.9 1.0
O A:GLU155 4.3 15.0 1.0
N A:ARG157 4.5 12.6 1.0
CA A:ARG157 4.6 12.7 1.0
N A:ALA158 4.6 15.1 1.0
CA A:ALA158 4.7 16.4 1.0
N A:HIS159 4.8 19.5 1.0
O A:HIS159 4.8 21.8 1.0
CA A:LEU156 4.8 13.2 1.0

Potassium binding site 4 out of 13 in 1w19

Go back to Potassium Binding Sites List in 1w19
Potassium binding site 4 out of 13 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1164

b:19.3
occ:1.00
 O B:ALA70 2.6 13.4 1.0
O B:HIS73 2.7 11.2 1.0
OG1 B:THR110 2.7 11.9 1.0
O B:HOH2044 2.7 41.7 1.0
O B:HOH2086 2.8 26.2 1.0
O B:HOH2058 2.8 37.6 1.0
O B:HOH2087 3.2 35.2 1.0
C B:ALA70 3.8 13.2 1.0
C B:HIS73 3.8 11.7 1.0
CB B:THR110 3.9 11.9 1.0
CG2 B:THR110 4.0 11.6 1.0
O B:HOH2024 4.1 24.7 1.0
O B:HOH2090 4.2 26.9 1.0
O B:SER108 4.3 10.6 1.0
N B:HIS73 4.4 12.6 1.0
CA B:ALA70 4.6 12.5 1.0
C B:ARG71 4.6 14.7 1.0
O B:HOH2063 4.7 33.9 1.0
N B:ASP74 4.7 11.6 1.0
CA B:ASP74 4.7 11.3 1.0
O B:ARG71 4.8 14.6 1.0
N B:ARG71 4.8 13.2 1.0
CA B:HIS73 4.8 11.6 1.0
CA B:ARG71 4.9 14.0 1.0
N B:ASN72 4.9 13.9 1.0
CB B:ALA70 5.0 12.8 1.0
O B:HOH2018 5.0 26.9 1.0

Potassium binding site 5 out of 13 in 1w19

Go back to Potassium Binding Sites List in 1w19
Potassium binding site 5 out of 13 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1165

b:23.2
occ:1.00
 O B:HOH2015 2.6 25.5 1.0
O B:HOH2017 2.7 24.2 1.0
OD2 B:ASP137 2.7 15.1 1.0
O B:ALA34 2.8 12.4 1.0
O B:GLY130 2.9 10.1 1.0
O B:ALA129 2.9 9.8 1.0
C B:GLY130 3.4 10.8 1.0
CA B:GLY130 3.6 10.1 1.0
C B:ALA34 3.6 12.4 1.0
CG B:ASP137 3.7 12.5 1.0
N B:GLY38 3.7 10.1 1.0
C B:ALA129 3.9 10.2 1.0
CA B:GLY38 3.9 10.7 1.0
OD1 B:ASP137 4.1 10.5 1.0
N B:GLY130 4.2 10.4 1.0
CA B:ALA34 4.2 13.3 1.0
OD1 B:ASP37 4.2 14.1 1.0
O B:HOH2115 4.3 31.7 1.0
CB B:ALA34 4.3 13.2 1.0
CB B:ASP37 4.4 10.6 1.0
N B:LEU131 4.4 10.9 1.0
O B:HOH2104 4.4 44.9 1.0
N B:LEU35 4.6 11.8 1.0
C B:ASP37 4.6 10.7 1.0
CB B:ASP137 4.7 12.2 1.0
CG B:ASP37 4.8 12.0 1.0
CA B:LEU35 4.9 11.1 1.0
CA B:ASP37 5.0 11.0 1.0

Potassium binding site 6 out of 13 in 1w19

Go back to Potassium Binding Sites List in 1w19
Potassium binding site 6 out of 13 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1166

b:29.2
occ:1.00
 O B:HOH2126 2.7 37.2 1.0
O B:LEU156 2.7 11.7 1.0
O B:ARG157 2.9 12.8 1.0
O B:GLU155 3.3 13.1 1.0
C B:LEU156 3.3 11.7 1.0
C B:ARG157 3.6 13.1 1.0
CE1 B:HIS159 3.7 26.7 1.0
ND1 B:HIS159 3.9 26.0 1.0
N B:ARG157 3.9 11.9 1.0
CA B:LEU156 4.1 11.9 1.0
CA B:ARG157 4.2 12.1 1.0
C B:GLU155 4.3 13.5 1.0
N B:ALA158 4.4 14.1 1.0
CA B:ALA158 4.7 14.9 1.0
N B:LEU156 4.7 12.7 1.0
N B:HIS159 4.8 17.3 1.0
NE2 B:HIS159 4.9 28.0 1.0
O A:HOH2054 5.0 45.4 1.0

Potassium binding site 7 out of 13 in 1w19

Go back to Potassium Binding Sites List in 1w19
Potassium binding site 7 out of 13 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1163

b:19.7
occ:1.00
 O C:ALA70 2.6 14.9 1.0
O C:HOH2039 2.6 40.0 1.0
O C:HIS73 2.7 9.4 1.0
O C:HOH2067 2.7 24.4 1.0
OG1 C:THR110 2.7 11.2 1.0
O C:HOH2036 2.8 40.6 1.0
O C:HOH2066 3.3 48.6 1.0
C C:ALA70 3.8 14.0 1.0
C C:HIS73 3.8 10.7 1.0
CB C:THR110 4.0 11.3 1.0
CG2 C:THR110 4.0 11.4 1.0
O C:HOH2100 4.0 29.3 1.0
O C:HOH2016 4.1 40.9 1.0
O C:SER108 4.3 10.7 1.0
O C:HOH2041 4.4 35.4 1.0
N C:HIS73 4.5 11.7 1.0
CA C:ALA70 4.5 13.0 1.0
N C:ASP74 4.7 10.6 1.0
C C:ARG71 4.7 15.6 1.0
CA C:ASP74 4.7 10.5 1.0
O C:ARG71 4.7 17.2 1.0
CA C:HIS73 4.8 11.1 1.0
N C:ARG71 4.8 14.4 1.0
CB C:ALA70 4.9 12.9 1.0
CA C:ARG71 4.9 15.3 1.0

Potassium binding site 8 out of 13 in 1w19

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Potassium binding site 8 out of 13 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1164

b:39.9
occ:1.00
 O C:HOH2091 2.5 38.6 1.0
O C:ALA34 2.8 12.8 1.0
O C:ALA129 2.8 13.6 1.0
OD2 C:ASP137 2.9 20.0 1.0
O C:GLY130 3.0 14.3 1.0
O C:HOH2010 3.0 35.8 1.0
C C:GLY130 3.5 14.6 1.0
C C:ALA34 3.6 13.4 1.0
N C:GLY38 3.7 12.0 1.0
CA C:GLY130 3.8 14.4 1.0
CG C:ASP137 3.8 17.8 1.0
C C:ALA129 3.9 13.8 1.0
CA C:GLY38 4.0 11.4 1.0
O C:HOH2084 4.1 36.7 1.0
OD1 C:ASP37 4.1 20.0 1.0
CA C:ALA34 4.1 13.8 1.0
OD1 C:ASP137 4.1 21.4 1.0
CB C:ALA34 4.2 13.6 1.0
N C:GLY130 4.3 13.7 1.0
N C:LEU131 4.4 15.4 1.0
CB C:ASP37 4.4 13.8 1.0
N C:LEU35 4.5 13.1 1.0
C C:ASP37 4.6 12.8 1.0
CG C:ASP37 4.7 16.1 1.0
CB C:ASP137 4.9 16.7 1.0
CA C:LEU35 4.9 12.8 1.0
CA C:ASP37 5.0 13.4 1.0

Potassium binding site 9 out of 13 in 1w19

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Potassium binding site 9 out of 13 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1165

b:29.5
occ:1.00
 O C:LEU156 2.8 14.8 1.0
O C:ARG157 2.9 13.5 1.0
C C:LEU156 3.4 14.7 1.0
C C:ARG157 3.6 14.6 1.0
CE1 C:HIS159 3.7 24.2 1.0
O C:GLU155 3.8 16.0 1.0
N C:ARG157 4.0 14.4 1.0
ND1 C:HIS159 4.0 23.5 1.0
CA C:ARG157 4.2 14.4 1.0
CA C:LEU156 4.3 14.6 1.0
N C:ALA158 4.5 15.4 1.0
NE2 C:HIS159 4.7 23.4 1.0
CA C:ALA158 4.7 16.5 1.0
C C:GLU155 4.7 16.0 1.0
N C:HIS159 5.0 18.9 1.0
N C:LEU156 5.0 15.2 1.0

Potassium binding site 10 out of 13 in 1w19

Go back to Potassium Binding Sites List in 1w19
Potassium binding site 10 out of 13 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Propane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1164

b:17.5
occ:1.00
 O D:HIS73 2.6 12.1 1.0
O D:ALA70 2.6 14.0 1.0
O D:HOH2027 2.7 36.4 1.0
O D:HOH2052 2.7 35.4 1.0
OG1 D:THR110 2.7 11.1 1.0
O D:HOH2085 2.8 23.7 1.0
C D:HIS73 3.8 12.0 1.0
C D:ALA70 3.8 13.5 1.0
O D:HOH2117 3.9 21.9 1.0
CB D:THR110 4.0 11.1 1.0
CG2 D:THR110 4.0 10.8 1.0
O D:SER108 4.3 7.7 1.0
N D:HIS73 4.5 12.2 1.0
CA D:ALA70 4.6 12.8 1.0
O D:HOH2055 4.6 28.8 1.0
CA D:ASP74 4.6 12.5 1.0
N D:ASP74 4.6 12.4 1.0
C D:ARG71 4.7 15.2 1.0
CA D:HIS73 4.8 11.7 1.0
N D:ARG71 4.8 14.4 1.0
N D:ASN72 4.9 14.4 1.0
CA D:ARG71 4.9 15.1 1.0
CB D:ALA70 5.0 12.7 1.0
O D:ARG71 5.0 16.1 1.0

Reference:

E.Morgunova, W.Meining, B.Illarionov, I.Haase, G.Jin, A.Bacher, M.Cushman, M.Fischer, R.Ladenstein. Crystal Structure of Lumazine Synthase From Mycobacterium Tuberculosis As A Target For Rational Drug Design: Binding Mode of A New Class of Purinetrione Inhibitors(,) Biochemistry V. 44 2746 2005.
ISSN: ISSN 0006-2960
PubMed: 15723519
DOI: 10.1021/BI047848A
Page generated: Mon Aug 12 05:40:04 2024

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