Atomistry » Chlorine » PDB 2xzk-2y57 » 2y2o
Atomistry »
  Chlorine »
    PDB 2xzk-2y57 »
      2y2o »

Chlorine in PDB 2y2o: Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9)

Enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9)

All present enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9):
2.4.1.129;

Protein crystallography data

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9), PDB code: 2y2o 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) 41.92 / 1.88
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 97.575, 149.109, 97.702, 90.00, 90.00, 90.00
R / Rfree (%) 22.158 / 26.403

Other elements in 2y2o:

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9) also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Chlorine atom in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9) (pdb code 2y2o). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 14 binding sites of Chlorine where determined in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9), PDB code: 2y2o:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 14 in 2y2o

Go back to Chlorine Binding Sites List in 2y2o
Chlorine binding site 1 out of 14 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9)


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 (EO9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1200

b:43.3
occ:1.00
 O A:HOH2101 2.8 39.6 1.0
NH1 A:ARG529 3.1 42.6 1.0
NH2 A:ARG529 3.4 40.5 1.0
CZ A:ARG529 3.7 45.0 1.0
N A:GLY550 4.1 40.7 1.0
OE2 A:GLU548 4.2 43.6 1.0
CB A:TYR549 4.2 39.6 1.0
C A:TYR549 4.4 42.8 1.0
CA A:GLY550 4.5 48.6 1.0
CA A:TYR549 4.7 43.3 1.0
N A:TYR549 4.7 41.0 1.0
NE A:ARG529 5.0 48.4 1.0
O A:TYR549 5.0 42.1 1.0

Chlorine binding site 2 out of 14 in 2y2o

Go back to Chlorine Binding Sites List in 2y2o
Chlorine binding site 2 out of 14 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9)


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 (EO9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1201

b:42.0
occ:1.00
 N A:LYS536 3.2 38.3 1.0
O A:HOH2091 3.2 37.3 1.0
N A:VAL535 3.4 38.7 1.0
CB A:LYS536 3.6 39.0 1.0
CB A:VAL535 3.9 37.0 1.0
CA A:VAL535 4.0 43.0 1.0
CA A:LYS536 4.0 38.3 1.0
O A:VAL533 4.0 43.8 1.0
C A:VAL535 4.0 39.6 1.0
CG A:TYR549 4.2 43.0 1.0
C A:ASP534 4.2 44.0 1.0
CB A:TYR549 4.3 39.6 1.0
CD2 A:TYR549 4.3 42.4 1.0
OD1 A:ASP534 4.3 44.7 1.0
CA A:ASP534 4.5 45.9 1.0
CG2 A:VAL535 4.7 41.8 1.0
CD1 A:TYR549 4.8 44.1 1.0
CG A:LYS536 4.9 37.4 1.0
NH1 A:ARG529 4.9 42.6 1.0
CE2 A:TYR549 5.0 37.2 1.0
CG1 A:VAL535 5.0 34.3 1.0

Chlorine binding site 3 out of 14 in 2y2o

Go back to Chlorine Binding Sites List in 2y2o
Chlorine binding site 3 out of 14 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9)


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 (EO9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1202

b:49.7
occ:1.00
 NH1 A:ARG627 3.1 49.0 1.0
NZ A:LYS633 3.2 47.3 1.0
NH2 A:ARG627 3.8 45.1 1.0
OG A:SER625 3.9 43.4 1.0
CE A:LYS633 3.9 46.1 1.0
CZ A:ARG627 3.9 42.4 1.0
CB A:LYS633 4.0 30.1 1.0
CG A:LYS633 4.1 51.9 1.0
CA A:SER625 4.2 33.6 1.0
CB A:SER625 4.5 32.9 1.0
O A:SER625 4.6 37.6 1.0
CD A:LYS633 4.7 52.7 1.0
C A:SER625 4.9 39.3 1.0

Chlorine binding site 4 out of 14 in 2y2o

Go back to Chlorine Binding Sites List in 2y2o
Chlorine binding site 4 out of 14 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9)


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 (EO9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1206

b:49.1
occ:1.00
 NH2 A:ARG595 3.1 51.3 1.0
O A:HOH2114 3.4 48.2 1.0
N A:ASP593 3.4 52.2 1.0
CG A:ASP593 3.4 48.6 1.0
OD2 A:ASP593 3.5 49.2 1.0
N A:ALA592 3.7 50.2 1.0
CB A:ALA591 3.7 45.0 1.0
CB A:ASP593 3.7 49.2 1.0
OD1 A:ASP593 3.7 43.9 1.0
CB A:ALA592 3.9 50.8 1.0
CA A:ALA592 4.1 49.4 1.0
CA A:ASP593 4.2 52.3 1.0
C A:ALA592 4.2 57.5 1.0
CZ A:ARG595 4.3 58.0 1.0
C A:ALA591 4.3 50.5 1.0
CA A:ALA591 4.6 45.0 1.0
NE A:ARG595 4.7 57.8 1.0

Chlorine binding site 5 out of 14 in 2y2o

Go back to Chlorine Binding Sites List in 2y2o
Chlorine binding site 5 out of 14 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9)


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 (EO9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1211

b:38.6
occ:1.00
 O A:HOH2199 3.1 36.7 1.0
O A:HOH2200 3.1 43.6 1.0
N A:GLU545 3.2 39.7 1.0
CA A:TYR544 3.7 36.0 1.0
CG A:GLN566 3.8 33.5 1.0
CG1 A:VAL562 3.9 32.8 1.0
C A:TYR544 3.9 42.8 1.0
O A:GLU545 4.0 44.9 1.0
O A:GLU561 4.1 34.7 1.0
O A:GLY543 4.1 38.2 1.0
CD1 A:TYR544 4.1 30.4 1.0
CA A:GLU545 4.2 41.5 1.0
CB A:TYR544 4.4 31.8 1.0
CB A:GLU545 4.4 43.5 1.0
C A:GLU545 4.5 42.5 1.0
O1 A:SO41100 4.5 34.6 1.0
CB A:VAL562 4.6 29.6 1.0
CG A:GLU545 4.6 56.7 1.0
CA A:VAL562 4.6 31.1 1.0
CD A:GLN566 4.7 33.7 1.0
CG A:TYR544 4.7 33.8 1.0
CB A:GLN566 4.7 33.7 1.0
N A:TYR544 4.7 40.5 1.0
OE1 A:GLU545 4.8 77.5 1.0
C A:GLY543 4.8 37.7 1.0
CE A:LYS455 4.9 52.6 1.0
CD A:GLU545 5.0 68.5 1.0

Chlorine binding site 6 out of 14 in 2y2o

Go back to Chlorine Binding Sites List in 2y2o
Chlorine binding site 6 out of 14 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9)


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 (EO9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1212

b:40.2
occ:1.00
 N A:VAL585 3.1 33.3 1.0
CG A:GLU346 3.2 54.1 1.0
N A:ILE586 3.4 37.0 1.0
CA A:HIS584 3.5 29.3 1.0
CD A:GLU346 3.5 72.8 1.0
OE2 A:GLU346 3.6 55.5 1.0
CB A:HIS584 3.7 29.9 1.0
C A:HIS584 3.8 34.6 1.0
CG1 A:VAL585 3.9 39.9 1.0
CA A:VAL585 4.1 38.3 1.0
C A:VAL585 4.2 40.0 1.0
CB A:ILE586 4.3 35.3 1.0
NH2 A:ARG350 4.3 45.1 1.0
OE1 A:GLU346 4.3 59.6 1.0
CA A:ILE586 4.3 33.1 1.0
O A:ILE586 4.4 40.2 1.0
CG1 A:ILE586 4.4 37.1 1.0
CB A:VAL585 4.6 42.7 1.0
CB A:GLU346 4.6 37.1 1.0
NE A:ARG350 4.6 43.8 1.0
N A:HIS584 4.8 31.2 1.0
O A:LYS583 4.8 33.3 1.0
C A:ILE586 4.9 34.4 1.0
CZ A:ARG350 4.9 50.4 1.0

Chlorine binding site 7 out of 14 in 2y2o

Go back to Chlorine Binding Sites List in 2y2o
Chlorine binding site 7 out of 14 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9)


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 (EO9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1213

b:47.0
occ:1.00
 N A:LEU339 3.2 43.8 1.0
NE2 A:HIS399 3.2 37.5 1.0
OE1 A:GLN403 3.4 41.1 1.0
OD1 A:ASP337 3.5 56.1 1.0
O A:HOH2053 3.5 46.2 1.0
CG A:ASP337 3.6 71.4 1.0
O A:HOH2030 3.6 49.8 1.0
CB A:TYR338 3.6 38.6 1.0
CD A:GLN403 3.6 41.0 1.0
CB A:ASP337 3.7 56.0 1.0
N A:TYR338 3.7 39.8 1.0
CB A:LEU339 3.8 42.7 1.0
CA A:TYR338 4.0 42.1 1.0
C A:TYR338 4.0 42.4 1.0
CE1 A:HIS399 4.1 32.3 1.0
CA A:LEU339 4.1 42.6 1.0
CG A:GLN403 4.1 37.4 1.0
OD2 A:ASP337 4.1 79.7 1.0
NE2 A:GLN403 4.2 36.6 1.0
CD2 A:HIS399 4.2 36.8 1.0
CD2 A:TYR338 4.4 34.4 1.0
C A:ASP337 4.4 48.2 1.0
O A:HOH2006 4.5 41.6 1.0
CG A:TYR338 4.5 38.7 1.0
CA A:ASP337 4.7 53.8 1.0
CE1 A:PHE437 4.9 36.4 1.0
CZ A:PHE437 4.9 35.2 1.0

Chlorine binding site 8 out of 14 in 2y2o

Go back to Chlorine Binding Sites List in 2y2o
Chlorine binding site 8 out of 14 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9)


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 (EO9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1214

b:50.6
occ:1.00
 N A:LYS610 3.2 43.6 1.0
O A:HOH2185 3.3 41.7 1.0
CA A:SER609 3.7 40.5 1.0
CG A:LYS610 3.9 46.6 1.0
CB A:LYS610 3.9 42.9 1.0
C A:SER609 4.0 45.5 1.0
CB A:SER609 4.0 45.5 1.0
CA A:LYS610 4.2 42.6 1.0
CD A:GLN606 4.2 51.2 1.0
CD A:LYS610 4.4 51.9 1.0
NE2 A:GLN606 4.4 51.2 1.0
OE1 A:GLN606 4.4 48.7 1.0
CG A:GLN606 4.5 43.4 1.0
CE A:LYS610 4.6 55.8 1.0
NZ A:LYS610 4.8 55.4 1.0

Chlorine binding site 9 out of 14 in 2y2o

Go back to Chlorine Binding Sites List in 2y2o
Chlorine binding site 9 out of 14 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9)


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 (EO9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1216

b:49.1
occ:1.00
 O A:HOH2026 2.8 43.2 1.0
N A:GLN396 3.1 32.9 1.0
OD1 A:ASP112 3.3 54.3 1.0
CG A:ASP112 3.4 60.0 1.0
OD2 A:ASP112 3.5 74.2 1.0
CB A:TYR110 3.5 47.3 1.0
CB A:GLN396 3.7 40.1 1.0
CA A:ASP395 3.9 37.0 1.0
C A:ASP395 4.0 34.2 1.0
O A:ILE394 4.0 34.6 1.0
OG A:SER111 4.0 51.1 1.0
CA A:GLN396 4.0 36.1 1.0
N A:ASP112 4.0 46.5 1.0
CB A:ASP112 4.2 52.7 1.0
N A:SER111 4.2 43.1 1.0
CG A:TYR110 4.2 51.6 1.0
OD1 A:ASP395 4.4 36.6 1.0
CG A:ASP395 4.6 46.5 1.0
CD1 A:TYR110 4.6 39.9 1.0
C A:TYR110 4.7 46.0 1.0
CA A:TYR110 4.7 48.6 1.0
CA A:ASP112 4.7 50.8 1.0
CB A:ASP395 4.8 35.2 1.0
C A:ILE394 4.9 37.8 1.0
CA A:SER111 4.9 44.7 1.0
N A:ASP395 4.9 34.5 1.0
C A:SER111 4.9 46.2 1.0
OD2 A:ASP395 5.0 41.8 1.0
CB A:SER111 5.0 46.4 1.0

Chlorine binding site 10 out of 14 in 2y2o

Go back to Chlorine Binding Sites List in 2y2o
Chlorine binding site 10 out of 14 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (EO9)


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 (EO9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1217

b:60.4
occ:1.00
 N A:SER761 2.9 93.5 1.0
N A:LYS760 3.1 82.0 1.0
O A:HOH2191 3.1 60.9 1.0
OG A:SER761 3.2 0.9 1.0
O A:HOH2192 3.3 48.3 1.0
CG A:LYS760 3.5 98.9 1.0
CA A:LYS760 3.5 87.1 1.0
CB A:LYS760 3.6 90.4 1.0
C A:LYS760 3.6 90.5 1.0
CB A:SER761 3.7 0.5 1.0
CB A:ASN759 3.7 75.8 1.0
ND2 A:ASN759 3.7 76.8 1.0
CG A:ASN759 3.8 76.0 1.0
CA A:SER761 3.9 96.2 1.0
C A:ASN759 4.2 76.5 1.0
CA A:ASN759 4.5 73.5 1.0
OD1 A:ASN759 4.6 76.4 1.0
O A:LYS760 4.8 91.7 1.0
CD A:LYS760 4.9 0.1 1.0
N A:GLY762 5.0 84.9 1.0
C A:SER761 5.0 92.0 1.0

Reference:

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
Page generated: Sat Jul 20 14:31:31 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy