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Potassium in PDB 2c97: Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate

Enzymatic activity of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate

All present enzymatic activity of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate:
2.5.1.9;

Protein crystallography data

The structure of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate, PDB code: 2c97 was solved by E.Morgunova, B.Illarionov, G.Jin, 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) 15.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 131.640, 82.244, 86.346, 90.00, 120.53, 90.00
R / Rfree (%) 14.6 / 21.5

Other elements in 2c97:

The structure of Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Potassium atom in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate (pdb code 2c97). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 16 binding sites of Potassium where determined in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate, PDB code: 2c97:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 16 in 2c97

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Potassium binding site 1 out of 16 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl 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 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1161

b:30.6
occ:1.00
 O A:HOH2081 2.7 13.2 1.0
O A:ALA70 2.7 28.6 1.0
O A:HOH2049 2.8 26.9 1.0
O A:HIS73 2.8 24.3 1.0
OG1 A:THR110 2.8 27.3 1.0
O A:HOH2056 3.5 30.8 1.0
O A:HOH2082 3.9 28.8 1.0
C A:ALA70 3.9 27.7 1.0
O A:HOH2031 4.0 16.5 1.0
C A:HIS73 4.0 24.5 1.0
CB A:THR110 4.1 26.6 1.0
O A:HOH2054 4.2 21.6 1.0
CG2 A:THR110 4.2 26.3 1.0
O A:SER108 4.3 23.4 1.0
N A:HIS73 4.4 25.6 1.0
O A:ARG71 4.5 30.2 1.0
C A:ARG71 4.5 29.1 1.0
CA A:ALA70 4.7 26.9 1.0
N A:ASN72 4.8 28.7 1.0
CA A:ARG71 4.9 28.7 1.0
CA A:HIS73 4.9 25.1 1.0
N A:ASP74 4.9 23.9 1.0
CA A:ASP74 4.9 23.8 1.0
N A:ARG71 4.9 27.8 1.0
O A:HOH2024 5.0 25.5 1.0

Potassium binding site 2 out of 16 in 2c97

Go back to Potassium Binding Sites List in 2c97
Potassium binding site 2 out of 16 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl 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 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1162

b:36.9
occ:1.00
 O A:ALA34 2.7 23.3 1.0
O A:GLY130 2.7 23.1 1.0
O A:HOH2019 2.7 23.7 1.0
OD2 A:ASP137 2.9 29.6 1.0
O A:ALA129 3.1 24.4 1.0
C A:GLY130 3.4 23.1 1.0
C A:ALA34 3.6 24.1 1.0
O A:HOH2109 3.7 25.4 1.0
CA A:GLY130 3.7 23.1 1.0
CG A:ASP137 3.7 29.9 1.0
N A:GLY38 3.8 23.1 1.0
CA A:GLY38 4.0 23.4 1.0
C A:ALA129 4.1 24.0 1.0
OD1 A:ASP137 4.1 29.5 1.0
CA A:ALA34 4.2 24.7 1.0
CB A:ALA34 4.2 24.4 1.0
N A:GLY130 4.4 23.6 1.0
N A:LEU131 4.4 22.6 1.0
CB A:ASP37 4.4 23.8 1.0
N A:LEU35 4.5 23.2 1.0
C A:ASP37 4.6 23.6 1.0
OD1 A:ASP37 4.8 28.1 1.0
CB A:ASP137 4.8 27.9 1.0
CA A:LEU35 5.0 22.8 1.0

Potassium binding site 3 out of 16 in 2c97

Go back to Potassium Binding Sites List in 2c97
Potassium binding site 3 out of 16 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl 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 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1163

b:22.3
occ:0.50
 O A:HOH2117 2.8 30.2 1.0
O A:LEU156 3.0 25.5 1.0
O A:ARG157 3.0 26.5 1.0
O A:GLU155 3.6 27.3 1.0
C A:LEU156 3.6 26.0 1.0
C A:ARG157 3.8 26.9 1.0
CE1 A:HIS159 4.0 35.9 1.0
NE2 A:HIS159 4.0 35.7 1.0
N A:ARG157 4.2 26.5 1.0
CA A:ARG157 4.4 26.6 1.0
CA A:LEU156 4.4 25.6 1.0
N A:ALA158 4.6 28.1 1.0
ND1 A:HIS159 4.6 34.7 1.0
O A:HOH2115 4.6 49.7 1.0
C A:GLU155 4.6 27.1 1.0
CD2 A:HIS159 4.7 35.4 1.0
CA A:ALA158 4.8 29.2 1.0
N A:HIS159 5.0 31.4 1.0

Potassium binding site 4 out of 16 in 2c97

Go back to Potassium Binding Sites List in 2c97
Potassium binding site 4 out of 16 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl 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 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1164

b:28.4
occ:1.00
 O A:ARG84 2.6 18.8 1.0
O A:ASN120 2.7 23.0 1.0
O A:HOH2092 2.8 28.4 1.0
O A:HOH2062 2.9 27.1 1.0
O A:HOH2095 3.6 32.5 1.0
C A:ARG84 3.8 19.2 1.0
C A:ASN120 3.9 23.1 1.0
CG2 A:ILE83 4.2 16.6 1.0
CA A:THR121 4.4 24.2 1.0
CA A:ARG84 4.6 19.3 1.0
CB A:ARG84 4.6 19.4 1.0
N A:ARG84 4.6 19.2 1.0
N A:THR121 4.6 23.5 1.0
N A:GLY85 4.7 19.1 1.0
CG2 A:THR121 4.8 22.0 1.0
CA A:GLY85 4.8 18.4 1.0
CA A:ASN120 5.0 22.8 1.0

Potassium binding site 5 out of 16 in 2c97

Go back to Potassium Binding Sites List in 2c97
Potassium binding site 5 out of 16 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl 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 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1161

b:27.4
occ:1.00
 O B:ALA70 2.7 27.2 1.0
O B:HIS73 2.8 25.5 1.0
OG1 B:THR110 2.8 26.7 1.0
O B:HOH2068 2.8 16.9 1.0
C B:ALA70 3.9 26.8 1.0
C B:HIS73 3.9 25.3 1.0
CB B:THR110 4.0 26.6 1.0
CG2 B:THR110 4.1 25.4 1.0
O B:SER108 4.3 24.6 1.0
N B:HIS73 4.4 25.9 1.0
O B:HOH2046 4.5 23.3 1.0
CA B:ALA70 4.7 26.2 1.0
C B:ARG71 4.7 28.2 1.0
N B:ASN72 4.7 28.1 1.0
CA B:ASP74 4.8 24.7 1.0
N B:ASP74 4.8 25.1 1.0
CA B:HIS73 4.8 25.4 1.0
N B:ARG71 4.9 27.1 1.0
CA B:ARG71 4.9 27.8 1.0

Potassium binding site 6 out of 16 in 2c97

Go back to Potassium Binding Sites List in 2c97
Potassium binding site 6 out of 16 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl 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 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1162

b:33.8
occ:1.00
 O B:HOH2082 2.5 34.8 1.0
O B:ALA34 2.8 27.1 1.0
O B:HOH2015 2.8 34.2 1.0
O B:GLY130 2.9 21.1 1.0
O B:ALA129 3.1 20.8 1.0
OD2 B:ASP137 3.3 32.8 1.0
C B:GLY130 3.4 21.2 1.0
CA B:GLY130 3.6 20.5 1.0
C B:ALA34 3.7 27.1 1.0
N B:GLY38 3.7 23.4 1.0
CG B:ASP137 3.9 31.4 1.0
OD1 B:ASP137 4.0 32.2 1.0
CA B:GLY38 4.0 23.0 1.0
C B:ALA129 4.1 20.8 1.0
CA B:ALA34 4.2 27.5 1.0
CB B:ASP37 4.2 24.5 1.0
OD1 B:ASP37 4.3 29.1 1.0
CB B:ALA34 4.3 27.5 1.0
N B:GLY130 4.3 20.8 1.0
N B:LEU131 4.4 21.5 1.0
C B:ASP37 4.6 24.0 1.0
O B:HOH2081 4.6 25.6 1.0
N B:LEU35 4.7 26.4 1.0
CG B:ASP37 4.7 26.2 1.0
CA B:ASP37 4.9 24.4 1.0

Potassium binding site 7 out of 16 in 2c97

Go back to Potassium Binding Sites List in 2c97
Potassium binding site 7 out of 16 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl 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 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1163

b:22.2
occ:1.00
 O B:LEU156 2.7 25.4 1.0
O B:HOH2095 2.9 26.0 1.0
O B:ARG157 3.0 24.6 1.0
C B:LEU156 3.5 25.9 1.0
O B:GLU155 3.5 28.7 1.0
C B:ARG157 3.7 25.5 1.0
CE1 B:HIS159 4.0 32.0 1.0
NE2 B:HIS159 4.1 32.1 1.0
N B:ARG157 4.2 25.5 1.0
CA B:LEU156 4.3 26.2 1.0
CA B:ARG157 4.3 25.3 1.0
N B:ALA158 4.5 26.2 1.0
C B:GLU155 4.5 28.4 1.0
ND1 B:HIS159 4.6 31.4 1.0
CA B:ALA158 4.7 27.3 1.0
CD2 B:HIS159 4.8 31.3 1.0
N B:LEU156 4.9 27.2 1.0
N B:HIS159 5.0 28.9 1.0

Potassium binding site 8 out of 16 in 2c97

Go back to Potassium Binding Sites List in 2c97
Potassium binding site 8 out of 16 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl 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 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1164

b:32.2
occ:1.00
 O B:ARG84 2.5 21.8 1.0
O B:ASN120 2.8 24.2 1.0
C B:ARG84 3.7 21.6 1.0
C B:ASN120 4.0 23.7 1.0
CG2 B:ILE83 4.3 22.7 1.0
CA B:THR121 4.5 24.2 1.0
CA B:ARG84 4.5 22.0 1.0
N B:GLY85 4.6 21.2 1.0
O B:HOH2049 4.6 35.7 1.0
CA B:GLY85 4.6 20.9 1.0
N B:ARG84 4.7 22.3 1.0
CB B:ARG84 4.7 21.7 1.0
N B:THR121 4.8 24.1 1.0
O B:GLY85 5.0 21.0 1.0

Potassium binding site 9 out of 16 in 2c97

Go back to Potassium Binding Sites List in 2c97
Potassium binding site 9 out of 16 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl 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 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1161

b:26.1
occ:1.00
 O C:ALA70 2.6 26.9 1.0
OG1 C:THR110 2.6 25.7 1.0
O C:HIS73 2.7 24.3 1.0
O C:HOH2061 3.0 21.2 1.0
C C:ALA70 3.8 26.3 1.0
CB C:THR110 3.9 25.4 1.0
C C:HIS73 3.9 24.9 1.0
CG2 C:THR110 4.1 24.9 1.0
O C:HOH2077 4.1 24.0 1.0
O C:HOH2029 4.2 12.5 0.5
O C:SER108 4.3 25.8 1.0
N C:HIS73 4.4 25.1 1.0
CA C:ALA70 4.6 25.6 1.0
O C:HOH2041 4.7 19.1 1.0
C C:ARG71 4.7 26.3 1.0
N C:ARG71 4.8 26.5 1.0
CA C:HIS73 4.8 24.7 1.0
CA C:ARG71 4.8 26.4 1.0
N C:ASP74 4.8 25.1 1.0
CA C:ASP74 4.9 25.1 1.0
N C:ASN72 4.9 26.1 1.0
O C:HOH2011 4.9 16.5 1.0
CB C:ALA70 5.0 25.5 1.0

Potassium binding site 10 out of 16 in 2c97

Go back to Potassium Binding Sites List in 2c97
Potassium binding site 10 out of 16 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl 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 4-(6- Chloro-2,4-Dioxo-1,2,3,4-Tetrahydropyrimidin-5-Yl)Butyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1162

b:20.9
occ:1.00
 O C:LEU156 2.7 25.5 1.0
O C:ARG157 2.9 25.0 1.0
C C:LEU156 3.6 25.4 1.0
C C:ARG157 3.7 25.9 1.0
O C:GLU155 3.7 26.4 1.0
N C:ARG157 4.2 25.3 1.0
CE1 C:HIS159 4.3 34.1 1.0
CA C:ARG157 4.3 25.6 1.0
CA C:LEU156 4.4 25.2 1.0
N C:ALA158 4.4 26.6 1.0
CA C:ALA158 4.6 27.6 1.0
NE2 C:HIS159 4.6 34.3 1.0
C C:GLU155 4.7 26.6 1.0
ND1 C:HIS159 4.7 33.0 1.0

Reference:

E.Morgunova, B.Illarionov, T.Sambaiah, I.Haase, A.Bacher, M.Cushman, M.Fischer, R.Ladenstein. Structural and Thermodynamic Insights Into the Binding Mode of Five Novel Inhibitors of Lumazine Synthase From Mycobacterium Tuberculosis. Febs J. V. 273 4790 2006.
ISSN: ISSN 1742-464X
PubMed: 16984393
DOI: 10.1111/J.1742-4658.2006.05481.X
Page generated: Mon Aug 12 06:09:42 2024

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