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Magnesium in PDB 2y55: 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: 2y55 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) 38.9 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 104.234, 92.284, 107.105, 90.00, 94.20, 90.00
R / Rfree (%) 19.4 / 26.2

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 2y55). 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: 2y55:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2y55

Go back to Magnesium Binding Sites List in 2y55
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:Mg1471

b:49.9
occ:1.00
 O A:GLU188 1.9 50.6 1.0
OE2 A:GLU251 2.0 67.0 1.0
NE2 A:HIS247 2.2 51.1 1.0
CD A:GLU251 3.0 64.8 1.0
C A:GLU188 3.0 51.0 1.0
CE1 A:HIS247 3.1 52.7 1.0
CD2 A:HIS247 3.2 50.3 1.0
OE1 A:GLU251 3.3 64.8 1.0
CA A:GLU188 3.9 50.8 1.0
O A:ALA186 3.9 50.9 1.0
CB A:GLU188 3.9 51.8 1.0
N A:GLY189 4.0 51.3 1.0
N A:GLU188 4.1 50.0 1.0
CA A:GLY189 4.2 52.2 1.0
CG A:GLU251 4.2 62.0 1.0
ND1 A:HIS247 4.2 54.2 1.0
CG A:HIS247 4.4 50.3 1.0
C A:GLY189 4.7 52.4 1.0
N A:TYR190 4.7 51.3 1.0
C A:ALA187 4.8 49.6 1.0
C A:ALA186 5.0 49.1 1.0

Magnesium binding site 2 out of 4 in 2y55

Go back to Magnesium Binding Sites List in 2y55
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:Mg1472

b:60.1
occ:1.00
 ND1 A:HIS462 2.8 84.2 1.0
CE1 A:HIS462 3.3 85.0 1.0
CG2 A:VAL406 3.4 66.0 1.0
CG A:HIS462 3.5 81.8 1.0
CB A:HIS462 4.0 80.8 1.0
NE2 A:HIS462 4.3 83.6 1.0
CD2 A:HIS462 4.4 81.9 1.0
O A:GLU404 4.6 63.9 1.0
O A:ALA402 4.6 63.8 1.0
CB A:VAL406 4.6 63.9 1.0
O A:GLN463 4.7 84.2 1.0
CA A:HIS462 4.9 82.7 1.0

Magnesium binding site 3 out of 4 in 2y55

Go back to Magnesium Binding Sites List in 2y55
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:Mg1471

b:56.6
occ:1.00
 NE2 D:HIS247 2.3 80.2 1.0
O D:GLU188 2.3 69.7 1.0
OE2 D:GLU251 2.4 91.1 1.0
CD D:GLU251 3.0 93.1 1.0
OE1 D:GLU251 3.1 92.1 1.0
CE1 D:HIS247 3.2 81.1 1.0
CD2 D:HIS247 3.3 78.5 1.0
C D:GLU188 3.5 68.5 1.0
O D:ALA186 4.0 62.8 1.0
CA D:GLU188 4.3 66.3 1.0
ND1 D:HIS247 4.3 79.7 1.0
N D:GLU188 4.4 63.5 1.0
CB D:GLU188 4.4 68.0 1.0
CG D:HIS247 4.4 77.3 1.0
CG D:GLU251 4.4 96.6 1.0
N D:GLY189 4.5 69.0 1.0
CA D:GLY189 4.8 71.2 1.0
CD2 D:LEU248 4.8 74.7 1.0
C D:GLY189 4.9 70.7 1.0
C D:ALA186 4.9 61.0 1.0
C D:ALA187 4.9 61.1 1.0

Magnesium binding site 4 out of 4 in 2y55

Go back to Magnesium Binding Sites List in 2y55
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:Mg1472

b:32.2
occ:1.00
 ND1 D:HIS462 2.8 0.1 1.0
CE1 D:HIS462 3.7 0.5 1.0
CG D:HIS462 3.8 0.5 1.0
CG2 D:VAL406 4.0 0.7 1.0
CB D:HIS462 4.1 0.6 1.0
O D:ALA402 4.5 0.4 1.0
CA D:HIS462 4.8 0.0 1.0
NE2 D:HIS462 4.8 0.3 1.0
CD2 D:HIS462 4.9 0.1 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 07:25:57 2024

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