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Magnesium in PDB 3zvt: 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: 3zvt 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) 35.83 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.993, 92.227, 107.044, 90.00, 94.43, 90.00
R / Rfree (%) 20.284 / 25.41

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

Magnesium binding site 1 out of 4 in 3zvt

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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:60.5
occ:1.00
 O A:GLU188 2.2 53.9 1.0
OE2 A:GLU251 2.4 61.9 1.0
NE2 A:HIS247 2.5 54.3 1.0
OE1 A:GLU251 2.8 61.6 1.0
CD A:GLU251 2.9 61.6 1.0
O A:ALA186 3.1 53.1 1.0
C A:GLU188 3.2 53.3 1.0
CD2 A:HIS247 3.4 53.9 1.0
CE1 A:HIS247 3.5 55.0 1.0
CB A:GLU188 3.6 52.4 1.0
N A:GLU188 3.6 52.1 1.0
CA A:GLU188 3.6 52.3 1.0
C A:ALA186 4.2 52.7 1.0
C A:ALA187 4.4 52.2 1.0
N A:GLY189 4.4 53.6 1.0
CG A:GLU251 4.4 60.5 1.0
CD2 A:LEU248 4.6 51.7 1.0
CG A:HIS247 4.6 54.5 1.0
ND1 A:HIS247 4.6 55.6 1.0
O A:GLY185 4.8 53.3 1.0
N A:TYR190 4.9 54.6 1.0
CA A:GLY189 4.9 54.6 1.0
CA A:ALA187 5.0 52.2 1.0
N A:ALA187 5.0 52.2 1.0

Magnesium binding site 2 out of 4 in 3zvt

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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:64.3
occ:1.00
 ND1 A:HIS462 3.0 82.4 1.0
CG2 A:VAL406 3.1 57.9 1.0
CE1 A:HIS462 3.7 83.1 1.0
O A:GLU404 3.8 56.3 1.0
O A:ALA402 3.9 56.1 1.0
CG A:HIS462 4.0 82.2 1.0
O A:GLN463 4.0 85.2 1.0
CB A:HIS462 4.3 81.9 1.0
CB A:VAL406 4.6 56.9 1.0
N A:GLN463 4.8 84.9 1.0
NE2 A:HIS462 4.8 82.8 1.0
C A:ALA402 4.9 56.1 1.0
CD2 A:HIS462 5.0 81.7 1.0
C A:GLU404 5.0 55.8 1.0

Magnesium binding site 3 out of 4 in 3zvt

Go back to Magnesium Binding Sites List in 3zvt
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:69.1
occ:1.00
 O D:GLU188 1.9 68.1 1.0
OE2 D:GLU251 2.0 82.0 1.0
NE2 D:HIS247 2.6 77.2 1.0
CD D:GLU251 3.1 82.4 1.0
C D:GLU188 3.1 66.6 1.0
CD2 D:HIS247 3.6 75.1 1.0
OE1 D:GLU251 3.6 81.7 1.0
CE1 D:HIS247 3.6 77.0 1.0
N D:GLU188 3.9 64.3 1.0
CA D:GLU188 3.9 65.1 1.0
CB D:GLU188 4.1 66.1 1.0
N D:GLY189 4.2 66.3 1.0
CG D:GLU251 4.3 83.6 1.0
CA D:GLY189 4.4 67.8 1.0
C D:ALA187 4.6 63.1 1.0
N D:TYR190 4.7 65.7 1.0
C D:GLY189 4.7 67.2 1.0
CG D:HIS247 4.7 73.6 1.0
ND1 D:HIS247 4.7 75.5 1.0
CG D:GLU188 4.9 66.7 1.0

Magnesium binding site 4 out of 4 in 3zvt

Go back to Magnesium Binding Sites List in 3zvt
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:35.9
occ:1.00
 ND1 D:HIS462 2.4 78.9 1.0
CE1 D:HIS462 3.1 79.1 1.0
CG D:HIS462 3.4 79.0 1.0
CG2 D:VAL406 3.7 65.8 1.0
CB D:HIS462 3.9 79.1 1.0
O D:ALA402 4.1 64.0 1.0
NE2 D:HIS462 4.2 79.2 1.0
CD2 D:HIS462 4.4 79.0 1.0
CA D:HIS462 4.6 80.7 1.0
O D:GLN463 4.8 80.4 1.0
N D:GLN463 4.8 80.7 1.0
O D:GLU404 4.9 64.9 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: Thu Aug 15 14:06:44 2024

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