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Potassium in PDB 2vi5: Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide

Enzymatic activity of Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide

All present enzymatic activity of Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide:
2.5.1.9;

Protein crystallography data

The structure of Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide, PDB code: 2vi5 was solved by E.Morgunova, Y.Zhang, G.Jin, B.Illarionov, A.Bacher, M.Fischer, M.Cushman, R.Ladenstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 77.033, 76.692, 86.254, 64.32, 64.41, 63.60
R / Rfree (%) 26 / 29.9

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Potassium atom in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide (pdb code 2vi5). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 15 binding sites of Potassium where determined in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide, PDB code: 2vi5:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 15 in 2vi5

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Potassium binding site 1 out of 15 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide


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 N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K601

b:26.7
occ:1.00
 O A:HOH2064 2.6 24.6 1.0
O A:ALA70 2.7 38.5 1.0
O A:HOH2036 2.8 27.8 1.0
O A:HIS73 2.9 37.8 1.0
OG1 A:THR110 2.9 37.6 1.0
C A:ALA70 3.9 38.4 1.0
O A:HOH2030 3.9 28.4 1.0
C A:HIS73 4.0 37.7 1.0
O A:HOH2042 4.2 58.9 1.0
CB A:THR110 4.2 37.6 1.0
O A:SER108 4.3 37.2 1.0
N A:HIS73 4.4 38.1 1.0
CG2 A:THR110 4.5 37.5 1.0
C A:ARG71 4.6 38.8 1.0
CA A:ALA70 4.7 38.3 1.0
O A:ARG71 4.8 38.9 1.0
N A:ARG71 4.8 38.6 1.0
N A:ASP74 4.8 37.6 1.0
CA A:ASP74 4.8 37.4 1.0
CA A:ARG71 4.8 38.8 1.0
N A:ASN72 4.9 38.8 1.0
CA A:HIS73 4.9 37.9 1.0
O I:HOH2030 4.9 29.7 1.0

Potassium binding site 2 out of 15 in 2vi5

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Potassium binding site 2 out of 15 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide


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 N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:43.2
occ:1.00
 O A:HOH2085 3.0 36.2 1.0
O A:ARG157 3.3 42.2 1.0
O J:ARG157 3.3 42.2 1.0
O J:LEU156 3.4 41.7 1.0
O A:LEU156 3.5 41.7 1.0
O A:GLU155 3.7 41.6 1.0
O J:GLU155 3.7 41.6 1.0
C J:LEU156 3.9 41.7 1.0
C A:LEU156 4.0 41.7 1.0
CE1 A:HIS159 4.0 44.4 1.0
C A:ARG157 4.0 42.3 1.0
C J:ARG157 4.1 42.3 1.0
CE1 J:HIS159 4.3 44.4 1.0
ND1 A:HIS159 4.3 44.3 1.0
N J:ARG157 4.5 41.9 1.0
N A:ARG157 4.5 41.9 1.0
CA J:LEU156 4.6 41.6 1.0
CA A:LEU156 4.6 41.6 1.0
NE2 A:HIS159 4.6 44.4 1.0
CA J:ARG157 4.7 42.1 1.0
ND1 J:HIS159 4.7 44.3 1.0
CA A:ARG157 4.7 42.1 1.0
C A:GLU155 4.7 41.5 1.0
C J:GLU155 4.7 41.5 1.0
N A:ALA158 4.8 42.6 1.0
N J:ALA158 4.8 42.6 1.0
N A:HIS159 4.8 43.5 1.0
NE2 J:HIS159 4.8 44.5 1.0
CA A:ALA158 4.9 43.0 1.0
CA J:ALA158 5.0 43.0 1.0

Potassium binding site 3 out of 15 in 2vi5

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Potassium binding site 3 out of 15 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide


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 N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K601

b:31.5
occ:1.00
 O B:HOH2058 2.6 29.1 1.0
O B:ALA70 2.7 38.5 1.0
OG1 B:THR110 2.8 37.3 1.0
O B:HIS73 2.9 37.8 1.0
O B:HOH2022 3.0 26.5 1.0
C B:ALA70 3.9 38.4 1.0
C B:HIS73 4.0 37.7 1.0
O B:HOH2033 4.0 27.7 1.0
O B:HOH2078 4.1 20.4 1.0
CB B:THR110 4.1 37.6 1.0
O B:HOH2046 4.2 43.1 1.0
O B:SER108 4.3 37.1 1.0
CG2 B:THR110 4.4 37.5 1.0
N B:HIS73 4.5 38.2 1.0
C B:ARG71 4.7 38.8 1.0
CA B:ALA70 4.8 38.4 1.0
CA B:ASP74 4.8 37.4 1.0
N B:ASP74 4.8 37.6 1.0
N B:ARG71 4.8 38.6 1.0
CA B:ARG71 4.8 38.8 1.0
N B:ASN72 4.9 38.8 1.0
O B:ARG71 4.9 39.0 1.0
CA B:HIS73 4.9 37.9 1.0

Potassium binding site 4 out of 15 in 2vi5

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Potassium binding site 4 out of 15 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide


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 N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K603

b:39.8
occ:1.00
 O B:HOH2079 2.8 24.3 1.0
O B:ARG157 3.3 42.2 1.0
O I:ARG157 3.3 42.2 1.0
O I:LEU156 3.4 41.7 1.0
O B:LEU156 3.5 41.7 1.0
O B:GLU155 3.5 41.5 1.0
O I:GLU155 3.7 41.5 1.0
C I:LEU156 3.9 41.7 1.0
C B:LEU156 3.9 41.7 1.0
CD2 I:HIS159 3.9 44.7 1.0
C B:ARG157 4.0 42.3 1.0
C I:ARG157 4.0 42.3 1.0
CE1 B:HIS159 4.2 44.4 1.0
NE2 I:HIS159 4.4 44.8 1.0
N B:ARG157 4.4 41.9 1.0
N I:ARG157 4.4 41.9 1.0
ND1 B:HIS159 4.4 44.3 1.0
CA B:LEU156 4.5 41.6 1.0
CA I:LEU156 4.5 41.6 1.0
C B:GLU155 4.5 41.5 1.0
CA I:ARG157 4.7 42.1 1.0
CA B:ARG157 4.7 42.1 1.0
C I:GLU155 4.7 41.5 1.0
NE2 B:HIS159 4.7 44.4 1.0
N I:ALA158 4.8 42.6 1.0
N B:ALA158 4.8 42.6 1.0
N B:HIS159 4.9 43.5 1.0
CA I:ALA158 5.0 43.0 1.0
CA B:ALA158 5.0 43.0 1.0
N B:LEU156 5.0 41.5 1.0

Potassium binding site 5 out of 15 in 2vi5

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Potassium binding site 5 out of 15 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide


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 N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K601

b:32.5
occ:1.00
 O C:ALA70 2.7 38.5 1.0
O C:HIS73 2.8 37.7 1.0
O C:HOH2027 2.8 32.7 1.0
OG1 C:THR110 2.8 37.2 1.0
C C:HIS73 3.9 37.8 1.0
C C:ALA70 3.9 38.4 1.0
CB C:THR110 4.2 37.6 1.0
O C:SER108 4.4 37.2 1.0
CG2 C:THR110 4.4 37.7 1.0
N C:HIS73 4.4 38.1 1.0
O G:HOH2021 4.7 34.5 1.0
CA C:ASP74 4.7 37.4 1.0
N C:ASP74 4.7 37.6 1.0
C C:ARG71 4.7 38.8 1.0
CA C:ALA70 4.7 38.3 1.0
CA C:HIS73 4.8 37.8 1.0
N C:ARG71 4.9 38.6 1.0
N C:ASN72 4.9 38.8 1.0
O C:HOH2001 4.9 37.6 1.0
O C:ARG71 4.9 38.9 1.0
CA C:ARG71 4.9 38.8 1.0

Potassium binding site 6 out of 15 in 2vi5

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Potassium binding site 6 out of 15 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide


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 N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K603

b:46.7
occ:1.00
 O C:HOH2055 3.2 45.8 1.0
O H:ARG157 3.2 42.2 1.0
O C:ARG157 3.3 42.2 1.0
O C:LEU156 3.4 41.7 1.0
O C:GLU155 3.4 41.5 1.0
O H:LEU156 3.5 41.7 1.0
O H:GLU155 3.7 41.6 1.0
C C:LEU156 3.8 41.7 1.0
C H:LEU156 4.0 41.7 1.0
CE1 H:HIS159 4.0 44.5 1.0
C H:ARG157 4.0 42.3 1.0
CE1 C:HIS159 4.0 44.5 1.0
C C:ARG157 4.0 42.2 1.0
ND1 H:HIS159 4.3 44.2 1.0
ND1 C:HIS159 4.3 44.3 1.0
N C:ARG157 4.3 41.9 1.0
CA C:LEU156 4.4 41.6 1.0
C C:GLU155 4.5 41.5 1.0
N H:ARG157 4.5 41.9 1.0
NE2 H:HIS159 4.5 44.4 1.0
CA H:LEU156 4.6 41.6 1.0
CA C:ARG157 4.6 42.0 1.0
CA H:ARG157 4.7 42.1 1.0
C H:GLU155 4.7 41.5 1.0
NE2 C:HIS159 4.7 44.4 1.0
N H:ALA158 4.7 42.6 1.0
N H:HIS159 4.8 43.5 1.0
CA H:ALA158 4.8 43.0 1.0
N C:ALA158 4.9 42.6 1.0
N C:LEU156 4.9 41.5 1.0
CG H:HIS159 5.0 44.2 1.0

Potassium binding site 7 out of 15 in 2vi5

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Potassium binding site 7 out of 15 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide


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 N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K601

b:27.6
occ:1.00
 O D:ALA70 2.6 38.6 1.0
OG1 D:THR110 2.9 37.6 1.0
O D:HIS73 2.9 37.7 1.0
O D:HOH2051 2.9 23.3 1.0
O D:HOH2052 3.4 46.6 1.0
O D:HOH2026 3.8 23.8 1.0
C D:ALA70 3.8 38.4 1.0
C D:HIS73 4.0 37.8 1.0
CB D:THR110 4.1 37.6 1.0
CG2 D:THR110 4.2 37.5 1.0
O D:SER108 4.3 37.1 1.0
N D:HIS73 4.5 38.2 1.0
CA D:ALA70 4.7 38.3 1.0
C D:ARG71 4.7 38.8 1.0
CA D:ASP74 4.8 37.4 1.0
N D:ASP74 4.8 37.6 1.0
N D:ARG71 4.8 38.6 1.0
CA D:ARG71 4.9 38.7 1.0
N D:ASN72 4.9 38.8 1.0
CA D:HIS73 4.9 37.9 1.0
O D:ARG71 4.9 38.9 1.0

Potassium binding site 8 out of 15 in 2vi5

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Potassium binding site 8 out of 15 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide


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 N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K603

b:52.7
occ:1.00
 O G:HOH2050 2.7 37.8 1.0
O D:ARG157 3.4 42.2 1.0
O G:ARG157 3.4 42.2 1.0
O D:LEU156 3.4 41.7 1.0
O D:GLU155 3.5 41.6 1.0
O G:LEU156 3.5 41.7 1.0
O G:GLU155 3.7 41.6 1.0
C D:LEU156 3.8 41.7 1.0
C G:LEU156 4.0 41.7 1.0
CE1 G:HIS159 4.1 44.4 1.0
CE1 D:HIS159 4.1 44.5 1.0
C D:ARG157 4.1 42.3 1.0
C G:ARG157 4.1 42.3 1.0
ND1 G:HIS159 4.2 44.3 1.0
N D:ARG157 4.4 41.9 1.0
CA D:LEU156 4.4 41.6 1.0
NE2 D:HIS159 4.5 44.3 1.0
C D:GLU155 4.5 41.5 1.0
N G:ARG157 4.5 41.9 1.0
ND1 D:HIS159 4.6 44.3 1.0
CA G:LEU156 4.6 41.6 1.0
CA D:ARG157 4.7 42.1 1.0
C G:GLU155 4.7 41.5 1.0
CA G:ARG157 4.8 42.1 1.0
N G:ALA158 4.9 42.6 1.0
N D:ALA158 4.9 42.6 1.0
N D:LEU156 4.9 41.5 1.0
N G:HIS159 5.0 43.5 1.0

Potassium binding site 9 out of 15 in 2vi5

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Potassium binding site 9 out of 15 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide


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 N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K601

b:27.6
occ:1.00
 O E:ALA70 2.6 38.6 1.0
O E:HOH2065 2.7 20.4 1.0
OG1 E:THR110 2.9 38.0 1.0
O E:HIS73 2.9 37.7 1.0
C E:ALA70 3.8 38.5 1.0
O E:HOH2078 4.0 23.0 1.0
C E:HIS73 4.0 37.7 1.0
O E:HOH2031 4.0 29.9 1.0
CB E:THR110 4.1 37.7 1.0
O E:SER108 4.2 37.1 1.0
CG2 E:THR110 4.3 37.3 1.0
O E:HOH2046 4.5 25.9 1.0
N E:HIS73 4.5 38.1 1.0
O J:HOH2050 4.6 27.3 1.0
CA E:ALA70 4.6 38.3 1.0
C E:ARG71 4.7 38.8 1.0
CA E:ASP74 4.8 37.4 1.0
N E:ARG71 4.8 38.5 1.0
N E:ASP74 4.8 37.6 1.0
O E:ARG71 4.9 39.0 1.0
CA E:ARG71 4.9 38.8 1.0
CA E:HIS73 4.9 37.8 1.0
N E:ASN72 5.0 38.8 1.0

Potassium binding site 10 out of 15 in 2vi5

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Potassium binding site 10 out of 15 in the Lumazine Synthase From Mycobacterium Tuberculosis Bound to N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide


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 N-6- (Ribitylamino)Pyrimidine-2,4(1H,3H)-Dione-5-Yl-Propionamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K603

b:64.0
occ:1.00
 O F:HOH2071 2.9 25.8 1.0
O F:ARG157 3.3 42.2 1.0
O F:GLU155 3.4 41.6 1.0
O E:LEU156 3.5 41.7 1.0
O E:ARG157 3.5 42.2 1.0
O E:GLU155 3.6 41.6 1.0
O E:HOH2041 3.7 31.6 1.0
O F:LEU156 3.8 41.7 1.0
C E:LEU156 4.0 41.7 1.0
O E:HOH2077 4.0 45.5 1.0
CE1 F:HIS159 4.0 44.3 1.0
C F:LEU156 4.1 41.7 1.0
CE1 E:HIS159 4.2 44.4 1.0
C F:ARG157 4.2 42.3 1.0
C E:ARG157 4.3 42.3 1.0
ND1 F:HIS159 4.3 44.3 1.0
NE2 F:HIS159 4.4 44.3 1.0
C F:GLU155 4.5 41.5 1.0
ND1 E:HIS159 4.5 44.2 1.0
CA E:LEU156 4.5 41.6 1.0
N F:ARG157 4.6 41.9 1.0
N E:ARG157 4.6 41.9 1.0
CA F:LEU156 4.6 41.6 1.0
C E:GLU155 4.6 41.4 1.0
NE2 E:HIS159 4.8 44.5 1.0
N F:HIS159 4.8 43.5 1.0
CA E:ARG157 4.9 42.1 1.0
CA F:ARG157 4.9 42.1 1.0
CG F:HIS159 4.9 44.1 1.0

Reference:

Y.Zhang, B.Illarionov, E.Morgunova, A.Bacher, M.Fischer, R.Ladenstein, M.Cushman. A New Series of N-[2,4-Dioxo-6-D-Ribitylamino-1,2, 3,4-Tetrahydropyrimidin-5-Yl]Oxalamic Acid Derivatives As Inhibitors of Lumazine Syntase and Riboflavin Synthase: Design, Synthesis, Biochemical Evaluation, Crystallography and Mechanistic Implications. J.Org.Chem. V. 73 2715 2008.
ISSN: ISSN 0022-3263
PubMed: 18331058
DOI: 10.1021/JO702631A
Page generated: Mon Aug 12 07:13:37 2024

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