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Magnesium in PDB 2y4a: 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: 2y4a 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) 46.10 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.308, 91.568, 106.871, 90.00, 94.37, 90.00
R / Rfree (%) 18.7 / 22.5

Other elements in 2y4a:

The structure of Unexpected Tricovalent Binding Mode of Boronic Acids Within the Active Site of A Penicillin Binding Protein also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

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 2y4a). 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: 2y4a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2y4a

Go back to Magnesium Binding Sites List in 2y4a
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:Mg610

b:28.3
occ:1.00
 NE2 A:HIS247 2.2 41.7 1.0
O A:GLU188 2.2 36.7 1.0
OE2 A:GLU251 2.3 48.5 1.0
OE1 A:GLU251 2.8 43.1 1.0
CD A:GLU251 2.9 45.4 1.0
CD2 A:HIS247 3.0 41.1 1.0
CE1 A:HIS247 3.3 42.6 1.0
C A:GLU188 3.3 37.0 1.0
O A:ALA186 3.5 36.6 1.0
CB A:GLU188 4.0 37.7 1.0
CA A:GLU188 4.0 36.7 1.0
N A:GLU188 4.2 36.0 1.0
CG A:HIS247 4.2 40.3 1.0
ND1 A:HIS247 4.3 41.3 1.0
CG A:GLU251 4.4 44.4 1.0
N A:GLY189 4.4 37.2 1.0
CD2 A:LEU248 4.4 38.2 1.0
C A:ALA186 4.6 36.2 1.0
C A:ALA187 4.7 35.6 1.0
CA A:GLY189 4.7 37.7 1.0
C A:GLY189 5.0 37.8 1.0

Magnesium binding site 2 out of 4 in 2y4a

Go back to Magnesium Binding Sites List in 2y4a
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:Mg611

b:66.0
occ:1.00
 ND1 A:HIS462 2.9 69.1 1.0
O A:ALA402 3.0 52.4 1.0
CG A:HIS462 3.5 68.2 1.0
O A:GLU404 3.6 50.5 1.0
CE1 A:HIS462 3.7 69.6 1.0
CG2 A:VAL406 3.7 48.4 1.0
CB A:HIS462 3.8 67.8 1.0
O A:GLN463 3.9 66.9 1.0
CB A:VAL406 3.9 48.3 1.0
C A:ALA402 4.0 52.4 1.0
CD2 A:HIS462 4.5 69.3 1.0
CA A:ALA402 4.5 53.6 1.0
NE2 A:HIS462 4.5 70.0 1.0
N A:GLN463 4.6 69.7 1.0
CG1 A:VAL406 4.7 49.4 1.0
C A:GLU404 4.7 49.9 1.0
CA A:HIS462 4.7 69.8 1.0
C A:GLN463 4.9 67.8 1.0
N A:VAL406 5.0 48.1 1.0
N A:GLU404 5.0 50.1 1.0

Magnesium binding site 3 out of 4 in 2y4a

Go back to Magnesium Binding Sites List in 2y4a
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:Mg610

b:26.7
occ:1.00
 O D:GLU188 2.1 44.8 1.0
NE2 D:HIS247 2.2 43.4 1.0
OE2 D:GLU251 2.3 54.9 1.0
CD2 D:HIS247 3.0 43.5 1.0
CD D:GLU251 3.0 55.3 1.0
OE1 D:GLU251 3.2 52.4 1.0
CE1 D:HIS247 3.3 44.8 1.0
C D:GLU188 3.3 44.2 1.0
O D:ALA186 3.8 44.4 1.0
CG D:HIS247 4.2 43.5 1.0
N D:GLY189 4.2 44.2 1.0
CA D:GLY189 4.3 45.1 1.0
CA D:GLU188 4.3 43.5 1.0
ND1 D:HIS247 4.3 43.7 1.0
CB D:GLU188 4.4 44.5 1.0
CG D:GLU251 4.4 57.5 1.0
N D:GLU188 4.5 42.2 1.0
C D:GLY189 4.5 44.7 1.0
N D:TYR190 4.8 43.5 1.0
C D:ALA187 4.9 41.6 1.0
O D:GLY189 4.9 45.2 1.0
CG D:GLU188 4.9 48.0 1.0
C D:ALA186 5.0 43.2 1.0

Magnesium binding site 4 out of 4 in 2y4a

Go back to Magnesium Binding Sites List in 2y4a
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:Mg611

b:51.1
occ:1.00
 ND1 D:HIS462 3.7 97.7 1.0
CG2 D:VAL406 3.7 76.5 1.0
CE1 D:HIS462 4.4 97.6 1.0
CG D:HIS462 4.8 98.0 1.0
CB D:HIS462 5.0 98.3 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 07:24:16 2024

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