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Magnesium in PDB 2y59: Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein

Enzymatic activity of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein

All present enzymatic activity of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein:
3.4.16.4;

Protein crystallography data

The structure of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein, PDB code: 2y59 was solved by E.Sauvage, A.Zervosen, R.Herman, F.Kerff, M.Rocaboy, P.Charlier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.880, 91.353, 106.919, 90.00, 94.27, 90.00
R / Rfree (%) 19.5 / 25.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein (pdb code 2y59). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein, PDB code: 2y59:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2y59

Go back to Magnesium Binding Sites List in 2y59
Magnesium binding site 1 out of 4 in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:27.1
occ:1.00
 NE2 A:HIS247 2.1 34.7 1.0
O A:GLU188 2.2 31.8 1.0
OE2 A:GLU251 2.3 41.1 1.0
CD A:GLU251 2.9 40.0 1.0
CE1 A:HIS247 3.0 36.2 1.0
CD2 A:HIS247 3.0 34.1 1.0
OE1 A:GLU251 3.1 39.4 1.0
C A:GLU188 3.4 32.3 1.0
O A:ALA186 3.8 29.1 1.0
ND1 A:HIS247 4.1 35.6 1.0
CG A:HIS247 4.1 33.8 1.0
CG A:GLU251 4.3 38.8 1.0
N A:GLY189 4.3 32.5 1.0
CA A:GLU188 4.3 32.3 1.0
CA A:GLY189 4.4 33.2 1.0
CB A:GLU188 4.4 32.8 1.0
N A:GLU188 4.6 31.2 1.0
C A:GLY189 4.7 33.4 1.0
C A:ALA186 4.8 28.9 1.0
C A:ALA187 4.9 30.6 1.0
N A:TYR190 5.0 33.1 1.0
CD2 A:LEU248 5.0 25.9 1.0

Magnesium binding site 2 out of 4 in 2y59

Go back to Magnesium Binding Sites List in 2y59
Magnesium binding site 2 out of 4 in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg508

b:61.0
occ:1.00
 ND1 A:HIS462 2.9 55.5 1.0
O A:ALA402 3.4 38.7 1.0
CG2 A:VAL406 3.5 37.3 1.0
CG A:HIS462 3.6 53.8 1.0
CE1 A:HIS462 3.6 56.7 1.0
CB A:HIS462 3.8 52.8 1.0
O A:GLN463 3.9 51.6 1.0
O A:GLU404 4.0 37.9 1.0
CB A:VAL406 4.3 37.2 1.0
C A:ALA402 4.4 38.3 1.0
N A:GLN463 4.5 53.6 1.0
CD2 A:HIS462 4.5 54.2 1.0
NE2 A:HIS462 4.5 56.2 1.0
CA A:HIS462 4.7 54.0 1.0
CA A:ALA402 4.8 39.3 1.0
C A:GLN463 4.9 52.1 1.0

Magnesium binding site 3 out of 4 in 2y59

Go back to Magnesium Binding Sites List in 2y59
Magnesium binding site 3 out of 4 in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg508

b:47.8
occ:1.00
 O D:GLU188 2.1 39.4 1.0
OE2 D:GLU251 2.4 49.9 1.0
NE2 D:HIS247 2.5 43.2 1.0
OE1 D:GLU251 2.8 50.3 1.0
CD D:GLU251 2.9 50.8 1.0
CD2 D:HIS247 3.1 41.9 1.0
C D:GLU188 3.3 38.9 1.0
O D:ALA186 3.5 39.0 1.0
CE1 D:HIS247 3.6 43.6 1.0
CA D:GLU188 4.0 38.6 1.0
N D:GLU188 4.1 37.4 1.0
CB D:GLU188 4.1 39.5 1.0
N D:GLY189 4.3 38.4 1.0
CG D:HIS247 4.4 40.9 1.0
CG D:GLU251 4.4 51.5 1.0
ND1 D:HIS247 4.6 41.5 1.0
C D:ALA186 4.6 37.9 1.0
CA D:GLY189 4.6 39.4 1.0
C D:ALA187 4.7 36.8 1.0
C D:GLY189 4.8 39.3 1.0
CD2 D:LEU248 4.8 33.7 1.0

Magnesium binding site 4 out of 4 in 2y59

Go back to Magnesium Binding Sites List in 2y59
Magnesium binding site 4 out of 4 in the Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg509

b:48.7
occ:1.00
 ND1 D:HIS462 2.8 72.1 1.0
CG2 D:VAL406 3.4 54.1 1.0
CG D:HIS462 3.7 71.4 1.0
CB D:HIS462 3.7 70.2 1.0
CE1 D:HIS462 3.9 72.6 1.0
O D:HOH2045 4.3 48.9 1.0
O D:ALA402 4.4 57.0 1.0
CA D:HIS462 4.5 71.8 1.0
CB D:VAL406 4.8 52.9 1.0
CD2 D:HIS462 4.9 71.5 1.0
O D:GLU404 4.9 52.7 1.0
O D:GLN463 4.9 71.5 1.0
N D:GLN463 5.0 71.8 1.0
NE2 D:HIS462 5.0 72.2 1.0

Reference:

A.Zervosen, R.Herman, F.Kerff, A.Herman, A.Bouillez, F.Prati, R.F.Pratt, J.M.Frere, B.Joris, A.Luxen, P.Charlier, E.Sauvage. Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin- Binding Protein. J.Am.Chem.Soc. V. 133 10839 2011.
ISSN: ISSN 0002-7863
PubMed: 21574608
DOI: 10.1021/JA200696Y
Page generated: Wed Aug 14 07:25:59 2024

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