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Potassium in PDB 2c9d: Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Hexane 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)Hexane 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)Hexane 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)Hexane 1-Phosphate, PDB code: 2c9d 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) 12.00 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.955, 79.959, 88.352, 64.27, 64.39, 62.81
R / Rfree (%) 25.9 / 32.6

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

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)Hexane 1-Phosphate (pdb code 2c9d). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 17 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)Hexane 1-Phosphate, PDB code: 2c9d:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 17 in 2c9d

Go back to Potassium Binding Sites List in 2c9d
Potassium binding site 1 out of 17 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Hexane 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)Hexane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1161

b:30.8
occ:1.00
 O A:HIS73 2.7 31.9 1.0
O A:ALA70 2.8 31.9 1.0
OG1 A:THR110 3.0 32.0 1.0
C A:HIS73 3.9 31.9 1.0
C A:ALA70 4.0 31.9 1.0
CB A:THR110 4.3 32.0 1.0
N A:HIS73 4.5 31.9 1.0
CG2 A:THR110 4.5 32.1 1.0
O A:SER108 4.6 31.9 1.0
CA A:ALA70 4.7 31.9 1.0
CA A:ASP74 4.8 31.9 1.0
N A:ASP74 4.8 31.9 1.0
CA A:HIS73 4.9 31.9 1.0
N A:ARG71 5.0 31.9 1.0

Potassium binding site 2 out of 17 in 2c9d

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Potassium binding site 2 out of 17 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Hexane 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)Hexane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1162

b:27.4
occ:1.00
 O H:LEU156 2.7 31.9 1.0
O A:LEU156 2.8 32.0 1.0
O H:HOH2058 2.8 34.6 1.0
O A:HOH2058 2.9 21.2 1.0
O A:ARG157 3.2 31.8 1.0
O H:ARG157 3.2 31.9 1.0
O H:GLU155 3.4 31.9 1.0
C H:LEU156 3.6 31.9 1.0
O A:GLU155 3.7 31.9 1.0
C A:LEU156 3.7 31.9 1.0
C A:ARG157 4.0 31.9 1.0
C H:ARG157 4.0 31.9 1.0
CE1 A:HIS159 4.1 31.5 1.0
CE1 H:HIS159 4.2 32.1 1.0
ND1 A:HIS159 4.2 31.5 1.0
CA H:LEU156 4.3 31.9 1.0
N H:ARG157 4.4 31.9 1.0
ND1 H:HIS159 4.5 32.1 1.0
C H:GLU155 4.5 32.0 1.0
N A:ARG157 4.5 31.9 1.0
CA A:LEU156 4.5 31.9 1.0
CA A:ARG157 4.7 31.8 1.0
CA H:ARG157 4.7 31.8 1.0
NE2 H:HIS159 4.7 32.2 1.0
N A:ALA158 4.7 31.9 1.0
C A:GLU155 4.8 31.9 1.0
O A:HOH2057 4.8 46.0 1.0
N A:HIS159 4.8 31.9 1.0
CA A:ALA158 4.8 31.9 1.0
N H:ALA158 4.9 31.9 1.0
N H:LEU156 4.9 31.9 1.0
NE2 A:HIS159 4.9 32.0 1.0
N H:HIS159 5.0 31.9 1.0

Potassium binding site 3 out of 17 in 2c9d

Go back to Potassium Binding Sites List in 2c9d
Potassium binding site 3 out of 17 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Hexane 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)Hexane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1161

b:32.5
occ:1.00
 O B:HOH2042 2.7 27.3 1.0
O B:ALA70 2.8 31.9 1.0
O F:HOH2010 2.8 28.6 1.0
OG1 B:THR110 3.0 30.9 1.0
O B:HIS73 3.1 31.9 1.0
C B:ALA70 4.0 31.9 1.0
CB B:THR110 4.2 31.7 1.0
O B:SER108 4.3 31.9 1.0
CG2 B:THR110 4.3 31.3 1.0
C B:HIS73 4.3 31.9 1.0
O F:HOH2023 4.4 17.5 1.0
O B:HOH2031 4.6 30.7 1.0
CA B:ALA70 4.7 31.9 1.0
N B:HIS73 4.8 31.9 1.0
O B:HOH2034 4.9 25.2 1.0
O B:HOH2012 4.9 30.7 1.0
CB B:ALA70 5.0 32.1 1.0
N B:ARG71 5.0 31.9 1.0

Potassium binding site 4 out of 17 in 2c9d

Go back to Potassium Binding Sites List in 2c9d
Potassium binding site 4 out of 17 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Hexane 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)Hexane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1162

b:31.8
occ:1.00
 O D:HOH2033 2.6 31.4 1.0
O J:LEU156 2.8 31.9 1.0
O D:LEU156 3.1 31.9 1.0
O D:ARG157 3.4 31.9 1.0
O J:ARG157 3.4 31.9 1.0
O D:HOH2031 3.5 31.7 1.0
O D:GLU155 3.7 32.0 1.0
C J:LEU156 3.8 31.9 1.0
O J:GLU155 3.8 32.0 1.0
C D:LEU156 4.0 31.9 1.0
C J:ARG157 4.1 31.9 1.0
C D:ARG157 4.2 31.9 1.0
CE1 D:HIS159 4.3 32.5 1.0
CE1 J:HIS159 4.4 32.6 1.0
NE2 D:HIS159 4.5 32.5 1.0
CA J:LEU156 4.6 31.9 1.0
N J:ARG157 4.6 31.9 1.0
ND1 D:HIS159 4.6 32.6 1.0
ND1 J:HIS159 4.6 32.7 1.0
CA D:LEU156 4.7 31.9 1.0
N D:ARG157 4.7 31.9 1.0
N D:HIS159 4.8 31.9 1.0
CA J:ARG157 4.8 31.9 1.0
C D:GLU155 4.8 31.9 1.0
N J:ALA158 4.9 31.9 1.0
CD2 D:HIS159 4.9 32.4 1.0
C J:GLU155 4.9 31.9 1.0
N D:ALA158 4.9 31.9 1.0
CA D:ALA158 4.9 31.9 1.0
CA D:ARG157 4.9 31.9 1.0
CA J:ALA158 5.0 31.9 1.0

Potassium binding site 5 out of 17 in 2c9d

Go back to Potassium Binding Sites List in 2c9d
Potassium binding site 5 out of 17 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Hexane 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)Hexane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1163

b:32.7
occ:1.00
 O G:HOH2051 2.7 28.0 1.0
O G:LEU156 2.7 31.9 1.0
O B:LEU156 2.7 31.9 1.0
O B:ARG157 3.3 31.9 1.0
O G:ARG157 3.4 31.9 1.0
C G:LEU156 3.7 31.9 1.0
C B:LEU156 3.7 31.9 1.0
O B:GLU155 3.8 31.9 1.0
O G:GLU155 3.9 32.0 1.0
NE2 B:HIS159 4.0 32.5 1.0
C B:ARG157 4.0 31.9 1.0
C G:ARG157 4.1 31.9 1.0
CE1 B:HIS159 4.2 32.3 1.0
CE1 G:HIS159 4.3 32.0 1.0
CA G:LEU156 4.5 31.9 1.0
CD2 B:HIS159 4.5 32.6 1.0
N B:ARG157 4.5 31.9 1.0
CA B:LEU156 4.5 31.9 1.0
N G:ARG157 4.5 31.9 1.0
ND1 G:HIS159 4.7 31.9 1.0
CA B:ARG157 4.7 31.9 1.0
CA G:ARG157 4.7 31.9 1.0
NE2 G:HIS159 4.7 32.0 1.0
ND1 B:HIS159 4.8 32.4 1.0
N B:ALA158 4.8 31.9 1.0
N G:ALA158 4.8 31.9 1.0
CA B:ALA158 4.9 31.9 1.0
C B:GLU155 4.9 31.9 1.0
C G:GLU155 4.9 31.9 1.0
CG B:HIS159 4.9 32.4 1.0
N B:HIS159 4.9 31.9 1.0
CA G:ALA158 5.0 31.9 1.0

Potassium binding site 6 out of 17 in 2c9d

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Potassium binding site 6 out of 17 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Hexane 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)Hexane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1161

b:29.6
occ:1.00
 OG1 C:THR110 3.0 31.7 1.0
O C:HIS73 3.1 31.9 1.0
O C:ALA70 3.4 31.9 1.0
O C:HOH2040 3.5 24.4 1.0
O C:HOH2029 3.8 21.5 1.0
C C:HIS73 4.3 31.9 1.0
CB C:THR110 4.3 31.9 1.0
O C:SER108 4.4 31.9 1.0
O C:HOH2027 4.4 25.1 1.0
CG2 C:THR110 4.4 31.5 1.0
C C:ALA70 4.6 31.9 1.0
CA C:ASP74 4.8 31.9 1.0
N C:HIS73 5.0 31.9 1.0
N C:ASP74 5.0 32.0 1.0

Potassium binding site 7 out of 17 in 2c9d

Go back to Potassium Binding Sites List in 2c9d
Potassium binding site 7 out of 17 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Hexane 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)Hexane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1162

b:36.2
occ:1.00
 O C:HOH2050 2.7 26.7 1.0
O F:LEU156 2.7 31.9 1.0
O C:LEU156 2.8 31.9 1.0
O F:ARG157 3.2 31.9 1.0
O C:ARG157 3.3 31.9 1.0
O C:GLU155 3.6 31.9 1.0
C F:LEU156 3.6 31.9 1.0
O F:GLU155 3.6 31.9 1.0
C C:LEU156 3.7 31.9 1.0
ND1 C:HIS159 3.8 31.5 1.0
CE1 C:HIS159 3.9 31.3 1.0
C F:ARG157 4.0 31.9 1.0
C C:ARG157 4.0 31.9 1.0
CE1 F:HIS159 4.1 32.6 1.0
NE2 F:HIS159 4.2 32.9 1.0
CA F:LEU156 4.4 31.9 1.0
N F:ARG157 4.4 31.9 1.0
N C:ARG157 4.5 31.9 1.0
CA C:LEU156 4.5 31.9 1.0
ND1 F:HIS159 4.6 32.7 1.0
CA F:ARG157 4.6 31.9 1.0
C C:GLU155 4.7 31.9 1.0
C F:GLU155 4.7 31.9 1.0
CA C:ARG157 4.7 31.9 1.0
N F:ALA158 4.8 31.9 1.0
N C:ALA158 4.8 31.9 1.0
N C:HIS159 4.8 31.9 1.0
CA C:ALA158 4.9 31.9 1.0
CD2 F:HIS159 4.9 33.0 1.0
CA F:ALA158 4.9 31.9 1.0
N F:HIS159 5.0 32.0 1.0

Potassium binding site 8 out of 17 in 2c9d

Go back to Potassium Binding Sites List in 2c9d
Potassium binding site 8 out of 17 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Hexane 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)Hexane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1161

b:30.0
occ:1.00
 O D:HIS73 2.8 31.9 1.0
O D:ALA70 3.0 31.9 1.0
OG1 D:THR110 3.3 31.7 1.0
C D:HIS73 3.9 31.9 1.0
C D:ALA70 4.2 31.9 1.0
N D:HIS73 4.4 31.9 1.0
CB D:THR110 4.5 31.7 1.0
O I:HOH2027 4.5 33.0 1.0
CG2 D:THR110 4.5 31.6 1.0
CA D:ASP74 4.7 31.9 1.0
N D:ASP74 4.7 31.9 1.0
O D:SER108 4.8 31.9 1.0
CA D:HIS73 4.8 31.9 1.0
N D:ASN72 5.0 31.9 1.0

Potassium binding site 9 out of 17 in 2c9d

Go back to Potassium Binding Sites List in 2c9d
Potassium binding site 9 out of 17 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Hexane 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)Hexane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K1161

b:30.7
occ:1.00
 O E:HOH2035 2.6 28.7 1.0
O E:HIS73 2.7 31.9 1.0
O E:ALA70 2.9 31.9 1.0
OG1 E:THR110 3.1 32.5 1.0
O E:HOH2029 3.3 23.4 1.0
O E:HOH2012 3.7 25.5 1.0
C E:HIS73 3.9 31.9 1.0
C E:ALA70 4.1 31.9 1.0
CB E:THR110 4.4 32.1 1.0
CG2 E:THR110 4.5 32.0 1.0
N E:HIS73 4.5 31.9 1.0
O E:SER108 4.7 31.9 1.0
CA E:ASP74 4.7 31.9 1.0
N E:ASP74 4.8 32.0 1.0
OD1 E:ASP74 4.8 33.0 1.0
CA E:ALA70 4.8 31.9 1.0
CA E:HIS73 4.9 31.9 1.0
O E:HOH2047 4.9 13.7 1.0

Potassium binding site 10 out of 17 in 2c9d

Go back to Potassium Binding Sites List in 2c9d
Potassium binding site 10 out of 17 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to 3-(1,3,7- Trihydro-9-D-Ribityl-2,6,8-Purinetrione-7-Yl)Hexane 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)Hexane 1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K1162

b:38.7
occ:1.00
 O E:LEU156 2.8 31.9 1.0
O I:LEU156 3.1 31.9 1.0
O E:ARG157 3.3 31.9 1.0
O I:ARG157 3.5 31.9 1.0
C E:LEU156 3.8 31.9 1.0
O E:GLU155 3.8 32.0 1.0
O I:GLU155 3.9 31.9 1.0
C E:ARG157 4.0 31.9 1.0
C I:LEU156 4.0 31.9 1.0
CE1 I:HIS159 4.1 32.9 1.0
C I:ARG157 4.3 31.9 1.0
NE2 I:HIS159 4.4 32.8 1.0
CE1 E:HIS159 4.4 33.0 1.0
ND1 I:HIS159 4.5 32.7 1.0
N E:ARG157 4.5 31.9 1.0
CA E:LEU156 4.6 31.9 1.0
CA E:ARG157 4.7 31.9 1.0
CA I:LEU156 4.7 31.9 1.0
N E:ALA158 4.7 31.9 1.0
NE2 E:HIS159 4.8 33.1 1.0
CA E:ALA158 4.8 31.9 1.0
N I:ARG157 4.8 31.9 1.0
ND1 E:HIS159 4.8 32.8 1.0
C E:GLU155 4.8 31.9 1.0
N E:HIS159 4.9 31.9 1.0
C I:GLU155 5.0 31.9 1.0
CA I:ARG157 5.0 31.9 1.0
N I:HIS159 5.0 31.9 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 06:12:43 2024

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