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Chlorine 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:

Magnesium (Mg) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2y4a

Go back to Chlorine Binding Sites List in 2y4a
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl500

b:58.0
occ:1.00
 CL A:BH6500 0.0 58.0 1.0
C14 A:BH6500 1.8 53.2 1.0
C13 A:BH6500 2.8 52.2 1.0
O6 A:BH6500 2.8 48.2 1.0
C7 A:BH6500 2.8 51.2 1.0
C5 A:BH6500 3.1 48.5 1.0
CG A:TYR147 3.7 32.6 1.0
CD2 A:TYR147 3.8 32.9 1.0
CB A:TYR147 4.0 32.9 1.0
C12 A:BH6500 4.1 52.5 1.0
C8 A:BH6500 4.1 51.6 1.0
CD1 A:TYR147 4.2 32.5 1.0
CE2 A:TYR147 4.4 32.8 1.0
N4 A:BH6500 4.4 44.3 1.0
O2 A:BH6500 4.4 38.0 1.0
C11 A:BH6500 4.6 52.9 1.0
CE1 A:TYR147 4.7 33.4 1.0
CZ A:TYR147 4.8 34.0 1.0

Chlorine binding site 2 out of 4 in 2y4a

Go back to Chlorine Binding Sites List in 2y4a
Chlorine 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 Chlorine with other atoms in the Cl 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
B:Cl500

b:67.5
occ:1.00
 CL B:BH6500 0.0 67.5 1.0
C14 B:BH6500 1.8 61.9 1.0
C13 B:BH6500 2.8 61.4 1.0
C7 B:BH6500 2.8 57.9 1.0
C5 B:BH6500 3.2 52.4 1.0
O6 B:BH6500 3.6 52.8 1.0
CB B:SER49 3.6 29.6 1.0
N B:SER49 3.6 29.8 1.0
O B:THR413 3.7 36.5 1.0
N4 B:BH6500 3.8 44.0 1.0
CA B:SER49 4.0 30.0 1.0
C12 B:BH6500 4.1 60.8 1.0
C8 B:BH6500 4.1 59.3 1.0
CB B:ALA48 4.2 29.7 1.0
SD B:MET414 4.4 41.4 1.0
N B:THR413 4.4 34.4 1.0
C B:ALA48 4.4 30.1 1.0
C B:THR413 4.4 36.0 1.0
OG B:SER49 4.5 33.0 1.0
CA B:ALA48 4.5 30.0 1.0
C11 B:BH6500 4.6 60.6 1.0
O B:GLY348 4.8 31.8 1.0
CG B:MET414 4.8 38.5 1.0
CB B:MET414 4.8 37.5 1.0
C3 B:BH6500 4.8 35.6 1.0
CA B:GLY412 5.0 33.5 1.0

Chlorine binding site 3 out of 4 in 2y4a

Go back to Chlorine Binding Sites List in 2y4a
Chlorine 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 Chlorine with other atoms in the Cl 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
C:Cl500

b:66.7
occ:1.00
 CL C:BH6500 0.0 66.7 1.0
C14 C:BH6500 1.8 62.0 1.0
C13 C:BH6500 2.8 61.9 1.0
C7 C:BH6500 2.8 58.2 1.0
C5 C:BH6500 3.2 51.0 1.0
N C:SER49 3.3 30.3 1.0
CB C:SER49 3.4 30.3 1.0
N4 C:BH6500 3.6 42.7 1.0
O C:THR413 3.7 36.2 1.0
O6 C:BH6500 3.7 49.6 1.0
CA C:SER49 3.8 30.2 1.0
C12 C:BH6500 4.1 61.6 1.0
C8 C:BH6500 4.1 59.9 1.0
CB C:ALA48 4.2 30.8 1.0
N C:THR413 4.2 34.3 1.0
C C:ALA48 4.3 30.7 1.0
OG C:SER49 4.3 32.5 1.0
C C:THR413 4.5 36.4 1.0
CA C:ALA48 4.5 30.8 1.0
C3 C:BH6500 4.6 36.7 1.0
C11 C:BH6500 4.6 61.1 1.0
O C:GLY348 4.6 31.4 1.0
CA C:GLY412 4.7 32.7 1.0
SD C:MET414 4.7 46.3 1.0
C C:GLY412 4.9 33.6 1.0
CA C:THR413 5.0 35.1 1.0

Chlorine binding site 4 out of 4 in 2y4a

Go back to Chlorine Binding Sites List in 2y4a
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl500

b:60.9
occ:1.00
 CL D:BH6500 0.0 60.9 1.0
C14 D:BH6500 1.8 55.4 1.0
O6 D:BH6500 2.7 52.1 1.0
C7 D:BH6500 2.8 54.0 1.0
C13 D:BH6500 2.8 54.5 1.0
C5 D:BH6500 3.1 53.0 1.0
CG D:TYR147 3.5 31.9 1.0
CD1 D:TYR147 3.8 32.5 1.0
CB D:TYR147 3.8 30.5 1.0
CD2 D:TYR147 3.9 33.3 1.0
C8 D:BH6500 4.1 54.1 1.0
C12 D:BH6500 4.1 53.9 1.0
N4 D:BH6500 4.3 52.7 1.0
CE1 D:TYR147 4.3 34.3 1.0
CE2 D:TYR147 4.4 34.2 1.0
C11 D:BH6500 4.6 53.3 1.0
CZ D:TYR147 4.6 35.8 1.0
ND2 D:ASN300 4.9 31.0 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: Fri Jul 11 02:27:55 2025

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