Chlorine in PDB 2y2g: Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01)

All present enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01):
2.4.1.129;

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01), PDB code: 2y2g was solved by C.Contreras-Martel, A.Amoroso, E.C.Woon, A.Zervosen, S.Inglis, A.Martins, O.Verlaine, A.Rydzik, V.Job, A.Luxen, B.Joris, C.J.Schofield, A.Dessen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.74 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.526, 97.526, 149.356, 90.00, 90.00, 90.00
R / Rfree (%)	22.221 / 25.97

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Chlorine atom in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) (pdb code 2y2g). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 30 binding sites of Chlorine where determined in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01), PDB code: 2y2g:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 30 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1200 b:51.4 occ:1.00 NH1 A:ARG529 3.2 41.4 1.0 O A:HOH2171 3.2 41.3 1.0 NH2 A:ARG529 3.7 43.6 1.0 CZ A:ARG529 3.9 43.5 1.0 N A:GLY550 3.9 37.2 1.0 CB A:TYR549 4.0 37.6 1.0 OE2 A:GLU548 4.2 43.8 1.0 C A:TYR549 4.3 39.5 1.0 CA A:GLY550 4.4 41.0 1.0 CA A:TYR549 4.6 39.9 1.0 N A:TYR549 4.7 39.7 1.0 O A:HOH2170 4.9 53.3 1.0 O A:HOH2151 4.9 39.8 1.0

Chlorine binding site 2 out of 30 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1201 b:47.8 occ:1.00 O A:HOH2151 2.7 39.8 1.0 N A:LYS536 3.3 37.2 1.0 N A:VAL535 3.4 43.2 1.0 CB A:LYS536 3.7 38.7 1.0 CB A:VAL535 3.8 35.9 1.0 CA A:VAL535 4.0 39.8 1.0 O A:VAL533 4.0 44.4 1.0 CA A:LYS536 4.1 36.7 1.0 C A:VAL535 4.1 40.1 1.0 C A:ASP534 4.2 48.1 1.0 O A:HOH2154 4.2 43.2 1.0 OD1 A:ASP534 4.3 45.2 1.0 CG A:TYR549 4.4 39.6 1.0 CD2 A:TYR549 4.4 36.0 1.0 CA A:ASP534 4.4 40.4 1.0 CG2 A:VAL535 4.5 41.6 1.0 CB A:TYR549 4.5 37.6 1.0 NH1 A:ARG529 4.9 41.4 1.0 CG1 A:VAL535 4.9 32.9 1.0 C A:VAL533 5.0 45.7 1.0

Chlorine binding site 3 out of 30 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1202 b:64.9 occ:1.00 NZ A:LYS633 3.2 48.3 1.0 NH1 A:ARG627 3.3 40.3 1.0 CE A:LYS633 3.6 46.5 1.0 CB A:SER625 3.7 30.1 1.0 CA A:SER625 4.1 33.6 1.0 CZ A:ARG627 4.2 46.7 1.0 CB A:LYS633 4.3 25.6 1.0 NH2 A:ARG627 4.3 49.4 1.0 CG A:LYS633 4.3 46.5 1.0 O A:HOH2229 4.5 48.3 1.0 CD A:LYS633 4.6 56.2 1.0 O A:SER625 4.6 37.1 1.0 O A:HOH2232 4.7 35.6 1.0 C A:SER625 4.9 30.9 1.0 OG A:SER625 5.0 41.2 1.0

Chlorine binding site 4 out of 30 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1203 b:75.3 occ:1.00 N A:LYS760 2.9 60.7 1.0 N A:SER761 3.0 63.9 1.0 CB A:LYS760 3.4 78.2 1.0 OG A:SER761 3.4 71.4 1.0 CA A:LYS760 3.4 67.0 1.0 CB A:ASN759 3.5 53.6 1.0 C A:LYS760 3.7 65.3 1.0 CG A:ASN759 3.7 54.9 1.0 O A:HOH2098 3.7 62.2 1.0 ND2 A:ASN759 3.7 51.6 1.0 CB A:SER761 3.9 67.2 1.0 CA A:SER761 4.0 64.5 1.0 C A:ASN759 4.0 58.8 1.0 CG A:LYS760 4.3 90.7 1.0 CA A:ASN759 4.3 54.1 1.0 OD1 A:ASN759 4.4 62.3 1.0 O A:LYS760 4.9 64.9 1.0 CD A:LYS760 4.9 0.7 1.0 C A:SER761 5.0 62.2 1.0 N A:GLY762 5.0 62.4 1.0

Chlorine binding site 5 out of 30 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1204 b:77.2 occ:1.00 N A:ALA777 3.0 71.6 1.0 N A:ASP776 3.4 69.2 1.0 CB A:SER775 3.5 66.2 1.0 CB A:ASP776 3.5 77.2 1.0 CB A:ALA777 3.6 68.7 1.0 OG A:SER775 3.6 66.6 1.0 CA A:ASP776 3.8 73.2 1.0 C A:ASP776 3.8 72.7 1.0 CA A:ALA777 3.8 69.1 1.0 C A:SER775 4.1 67.5 1.0 CA A:SER775 4.3 65.3 1.0 CG A:ASP776 4.5 78.6 1.0 O A:HOH2304 4.6 42.2 1.0 OD2 A:ASP776 4.9 83.8 1.0 O A:SER775 5.0 64.9 1.0 O A:ASP776 5.0 73.0 1.0

Chlorine binding site 6 out of 30 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1206 b:56.0 occ:1.00 N A:ASP593 3.3 57.3 1.0 NH2 A:ARG595 3.5 65.5 1.0 CG A:ASP593 3.5 54.8 1.0 O A:HOH2198 3.7 62.0 1.0 N A:ALA592 3.7 54.5 1.0 CB A:ASP593 3.7 57.5 1.0 OD2 A:ASP593 3.7 54.6 1.0 CB A:ALA592 3.7 58.9 1.0 OD1 A:ASP593 3.8 47.9 1.0 CA A:ALA592 4.0 55.1 1.0 C A:ALA592 4.1 61.6 1.0 CB A:ALA591 4.1 50.0 1.0 CA A:ASP593 4.1 59.0 1.0 C A:ALA591 4.4 52.9 1.0 CZ A:ARG595 4.7 62.7 1.0 CA A:ALA591 4.8 52.4 1.0

Chlorine binding site 7 out of 30 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1208 b:73.4 occ:1.00 N A:GLU727 3.3 64.2 1.0 CA A:SER726 3.6 64.0 1.0 CE A:LYS735 3.7 95.3 1.0 NZ A:LYS735 3.7 0.0 1.0 CB A:SER726 3.8 64.8 1.0 C A:SER726 4.0 65.2 1.0 O A:LYS725 4.4 70.6 1.0 CA A:GLU727 4.4 67.7 1.0 O A:GLU727 4.4 75.1 1.0 CB A:GLU727 4.4 71.6 1.0 CG A:GLU727 4.6 85.4 1.0 N A:SER726 4.8 63.0 1.0 OG A:SER726 4.8 57.1 1.0 C A:GLU727 4.8 69.6 1.0 CD A:LYS735 5.0 91.3 1.0

Chlorine binding site 8 out of 30 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1211 b:40.2 occ:1.00 N A:GLU545 3.1 39.5 1.0 O A:HOH2310 3.1 33.9 1.0 O A:HOH2309 3.2 50.6 1.0 CA A:TYR544 3.7 30.8 1.0 CG1 A:VAL562 3.9 29.9 1.0 C A:TYR544 3.9 41.8 1.0 CG A:GLN566 3.9 25.9 1.0 O A:GLU545 4.0 48.0 1.0 CA A:GLU545 4.1 36.8 1.0 O A:GLU561 4.1 34.6 1.0 O A:GLY543 4.1 39.5 1.0 CB A:GLU545 4.2 42.2 1.0 CD1 A:TYR544 4.2 28.4 1.0 C A:GLU545 4.4 44.2 1.0 CB A:TYR544 4.4 29.5 1.0 O1 A:SO41100 4.5 45.4 1.0 CB A:VAL562 4.6 30.8 1.0 CD A:GLN566 4.7 39.7 1.0 CG A:GLU545 4.7 65.9 1.0 CA A:VAL562 4.7 31.0 1.0 CG A:TYR544 4.8 32.7 1.0 N A:TYR544 4.8 31.4 1.0 CB A:GLN566 4.9 23.8 1.0 C A:GLY543 4.9 34.7 1.0 NE2 A:GLN566 5.0 29.9 1.0

Chlorine binding site 9 out of 30 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1212 b:48.9 occ:1.00 O A:HOH2196 3.0 45.7 1.0 N A:VAL585 3.4 34.8 1.0 N A:ILE586 3.5 41.2 1.0 O A:HOH2008 3.8 48.8 1.0 CA A:HIS584 3.8 35.4 1.0 CB A:HIS584 3.8 31.6 1.0 CB A:ILE586 4.1 38.5 1.0 CG1 A:ILE586 4.1 37.3 1.0 C A:HIS584 4.1 37.1 1.0 CA A:VAL585 4.3 37.6 1.0 CA A:ILE586 4.3 36.0 1.0 CB A:GLU346 4.4 43.1 1.0 C A:VAL585 4.4 38.0 1.0 NH2 A:ARG350 4.4 56.2 1.0 O A:ILE586 4.4 39.4 1.0 CB A:VAL585 4.5 41.8 1.0 CG A:GLU346 4.6 75.2 1.0 OE1 A:GLU346 4.6 81.2 1.0 NE A:ARG350 4.7 59.3 1.0 CD A:GLU346 4.8 88.0 1.0 C A:ILE586 4.9 36.2 1.0

Chlorine binding site 10 out of 30 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (A01) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1213 b:60.0 occ:1.00 NE2 A:HIS399 3.1 41.0 1.0 N A:LEU339 3.2 45.2 1.0 O A:HOH2037 3.5 40.6 1.0 CB A:TYR338 3.6 36.1 1.0 CB A:LEU339 3.6 44.4 1.0 N A:TYR338 3.7 43.8 1.0 NE2 A:GLN403 3.7 35.5 1.0 N A:ASP337 3.8 53.6 1.0 CD A:GLN403 3.8 41.7 1.0 CE1 A:HIS399 4.0 37.8 1.0 CA A:LEU339 4.0 40.2 1.0 CA A:TYR338 4.0 43.9 1.0 C A:TYR338 4.1 42.9 1.0 CG A:GLN403 4.1 32.9 1.0 CD2 A:HIS399 4.1 36.4 1.0 OE1 A:GLN403 4.2 41.1 1.0 CD2 A:TYR338 4.4 37.8 1.0 C A:ASP337 4.5 61.5 1.0 CG A:TYR338 4.5 38.1 1.0 CA A:ASP337 4.7 55.5 1.0 CZ A:PHE437 4.8 35.9 1.0 CE1 A:PHE437 4.9 38.5 1.0 CG A:LEU339 5.0 50.2 1.0

C.Contreras-Martel, A.Amoroso, E.C.Woon, A.Zervosen, S.Inglis, A.Martins, O.Verlaine, A.Rydzik, V.Job, A.Luxen, B.Joris, C.J.Schofield, A.Dessen. Structure-Guided Design of Cell Wall Biosynthesis Inhibitors That Overcome Beta-Lactam Resistance in Staphylococcus Aureus (Mrsa). Acs Chem.Biol. V. 6 943 2011.
ISSN: ISSN 1554-8929
PubMed: 21732689
DOI: 10.1021/CB2001846