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Chlorine in PDB 2y2n: Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07)

Enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07)

All present enzymatic activity of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07):
2.4.1.129;

Protein crystallography data

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07), PDB code: 2y2n 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) 43.94 / 2.07
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 96.744, 147.956, 98.778, 90.00, 90.00, 90.00
R / Rfree (%) 19.141 / 24.31

Other elements in 2y2n:

The structure of Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Chlorine atom in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07) (pdb code 2y2n). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 22 binding sites of Chlorine where determined in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07), PDB code: 2y2n:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 22 in 2y2n

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Chlorine binding site 1 out of 22 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07)


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 (E07) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1200

b:34.5
occ:1.00
NH1 A:ARG529 3.1 29.7 1.0
O A:HOH2128 3.2 28.1 1.0
NH2 A:ARG529 3.4 25.0 1.0
CZ A:ARG529 3.7 28.5 1.0
OE2 A:GLU548 4.1 30.3 1.0
CB A:TYR549 4.1 32.7 1.0
N A:GLY550 4.5 30.5 1.0
C A:TYR549 4.6 33.3 1.0
N A:TYR549 4.6 31.6 1.0
CA A:TYR549 4.7 32.3 1.0
CA A:GLY550 4.9 35.6 1.0

Chlorine binding site 2 out of 22 in 2y2n

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Chlorine binding site 2 out of 22 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07)


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 (E07) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1201

b:25.4
occ:1.00
N A:LYS536 3.3 28.3 1.0
O A:HOH2106 3.3 32.9 1.0
N A:VAL535 3.6 27.0 1.0
CB A:LYS536 3.8 26.4 1.0
CB A:VAL535 3.9 23.8 1.0
CG A:TYR549 4.0 30.7 1.0
O A:VAL533 4.0 29.4 1.0
CB A:TYR549 4.0 32.7 1.0
CD2 A:TYR549 4.0 37.1 1.0
CA A:VAL535 4.1 24.2 1.0
C A:VAL535 4.2 29.0 1.0
CA A:LYS536 4.2 26.9 1.0
C A:ASP534 4.3 30.2 1.0
OD1 A:ASP534 4.3 31.1 1.0
CA A:ASP534 4.4 28.5 1.0
NH1 A:ARG529 4.5 29.7 1.0
O A:HOH2108 4.5 40.6 1.0
CG2 A:VAL535 4.7 25.4 1.0
CE2 A:TYR549 4.7 31.6 1.0
CD1 A:TYR549 4.7 30.9 1.0
CG1 A:VAL535 4.9 18.5 1.0
CE A:LYS536 5.0 38.7 1.0

Chlorine binding site 3 out of 22 in 2y2n

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Chlorine binding site 3 out of 22 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07)


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 (E07) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1202

b:54.9
occ:1.00
O A:HOH2170 2.6 37.4 1.0
NZ A:LYS633 2.9 29.5 1.0
O A:HOH2174 3.1 32.6 1.0
NH1 A:ARG627 3.2 26.4 1.0
CB A:SER625 3.6 24.9 0.5
CE A:LYS633 3.6 31.8 1.0
OG A:SER625 3.7 18.6 0.5
CB A:SER625 3.7 22.0 0.5
CA A:SER625 3.8 24.4 0.5
CA A:SER625 3.8 23.0 0.5
NH2 A:ARG627 4.0 33.5 1.0
CZ A:ARG627 4.0 39.3 1.0
CB A:LYS633 4.2 20.1 1.0
CG A:LYS633 4.3 28.9 1.0
O A:SER625 4.5 28.9 1.0
CD A:LYS633 4.5 34.0 1.0
C A:SER625 4.7 25.3 1.0
N A:SER625 4.8 28.0 1.0
OG A:SER625 4.9 27.7 0.5

Chlorine binding site 4 out of 22 in 2y2n

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Chlorine binding site 4 out of 22 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07)


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 (E07) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1206

b:44.0
occ:1.00
N A:ASP593 3.3 45.2 1.0
CG A:ASP593 3.4 37.4 1.0
NH1 A:ARG595 3.6 37.3 1.0
CB A:ASP593 3.6 45.5 1.0
OD2 A:ASP593 3.7 37.2 1.0
N A:ALA592 3.8 40.1 1.0
OD1 A:ASP593 3.8 36.9 1.0
CB A:ALA592 3.8 39.6 1.0
O A:HOH2152 3.9 34.2 1.0
CB A:ALA591 4.0 32.8 1.0
CA A:ASP593 4.0 43.4 1.0
CA A:ALA592 4.1 43.3 1.0
C A:ALA592 4.1 47.3 1.0
C A:ALA591 4.5 37.0 1.0
CZ A:ARG595 4.6 41.5 1.0
CA A:ALA591 4.8 33.5 1.0
NH2 A:ARG595 5.0 43.7 1.0

Chlorine binding site 5 out of 22 in 2y2n

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Chlorine binding site 5 out of 22 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07)


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 (E07) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1208

b:53.5
occ:1.00
N A:GLU727 3.1 44.7 1.0
O A:HOH2221 3.4 38.0 1.0
CE A:LYS735 3.5 51.2 1.0
CA A:SER726 3.6 43.9 1.0
C A:SER726 3.9 43.8 1.0
CD A:LYS735 4.1 53.3 1.0
CB A:GLU727 4.1 47.4 0.5
CA A:GLU727 4.1 45.7 0.5
CA A:GLU727 4.1 45.6 0.5
CB A:GLU727 4.2 47.4 0.5
O A:LYS725 4.2 43.3 1.0
CB A:SER726 4.2 46.3 1.0
O A:GLU727 4.3 45.0 1.0
CG A:GLU727 4.3 46.9 0.5
NZ A:LYS735 4.6 52.2 1.0
OG A:SER726 4.7 48.2 1.0
C A:GLU727 4.7 45.8 1.0
N A:SER726 4.8 40.1 1.0
C A:LYS725 4.9 41.0 1.0

Chlorine binding site 6 out of 22 in 2y2n

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Chlorine binding site 6 out of 22 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07)


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 (E07) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1211

b:32.0
occ:1.00
O A:HOH2138 3.0 18.1 1.0
O A:HOH2119 3.2 28.2 1.0
N A:GLU545 3.2 23.8 1.0
O A:HOH2137 3.3 34.5 1.0
CA A:TYR544 3.6 23.0 1.0
CG A:GLN566 3.9 20.5 1.0
CG1 A:VAL562 3.9 18.8 1.0
C A:TYR544 3.9 25.1 1.0
O A:GLU561 3.9 24.0 1.0
O A:GLU545 4.0 31.5 1.0
O A:GLY543 4.1 22.7 1.0
CD1 A:TYR544 4.2 21.6 1.0
CA A:GLU545 4.3 25.1 1.0
CB A:TYR544 4.3 22.1 1.0
CG A:GLU545 4.5 33.9 1.0
CB A:GLU545 4.5 27.7 1.0
CB A:VAL562 4.5 20.8 1.0
NZ A:LYS455 4.5 44.6 1.0
C A:GLU545 4.6 28.2 1.0
CA A:VAL562 4.6 21.6 1.0
CD A:GLN566 4.6 21.3 1.0
CG A:TYR544 4.7 22.9 1.0
N A:TYR544 4.7 23.2 1.0
CB A:GLN566 4.7 18.8 1.0
O A:HOH2117 4.8 29.4 1.0
C A:GLY543 4.8 23.4 1.0
C A:GLU561 4.9 27.3 1.0

Chlorine binding site 7 out of 22 in 2y2n

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Chlorine binding site 7 out of 22 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07)


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 (E07) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1212

b:31.8
occ:1.00
N A:ILE586 3.3 24.0 1.0
CG A:GLU346 3.3 42.0 1.0
N A:VAL585 3.4 24.4 1.0
CD A:GLU346 3.5 48.0 1.0
OE2 A:GLU346 3.5 37.0 1.0
NH2 A:ARG350 3.6 44.3 1.0
CB A:HIS584 3.6 18.9 1.0
CA A:HIS584 3.8 22.7 1.0
CG1 A:ILE586 3.8 27.5 1.0
CB A:ILE586 3.9 25.2 1.0
CG2 A:VAL585 3.9 23.4 1.0
C A:HIS584 4.1 22.9 1.0
CA A:ILE586 4.1 25.0 1.0
OE1 A:GLU346 4.1 43.1 1.0
C A:VAL585 4.2 25.9 1.0
CA A:VAL585 4.2 23.5 1.0
NE A:ARG350 4.3 38.4 1.0
O A:ILE586 4.3 27.5 1.0
CZ A:ARG350 4.4 45.6 1.0
CL A:CL1223 4.6 32.1 1.0
CB A:GLU346 4.7 28.8 1.0
C A:ILE586 4.7 29.0 1.0
CB A:VAL585 4.7 22.5 1.0

Chlorine binding site 8 out of 22 in 2y2n

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Chlorine binding site 8 out of 22 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07)


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 (E07) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1213

b:37.8
occ:1.00
NE2 A:HIS399 3.2 23.0 1.0
N A:LEU339 3.3 25.8 1.0
CB A:LEU339 3.6 27.8 1.0
O A:HOH2036 3.6 30.1 1.0
NE2 A:GLN403 3.7 25.5 1.0
CB A:TYR338 3.7 25.4 1.0
N A:ASP337 3.8 37.7 1.0
N A:TYR338 3.9 31.8 1.0
CD A:GLN403 3.9 35.9 1.0
CE1 A:HIS399 3.9 27.4 1.0
CA A:LEU339 4.0 30.5 1.0
CA A:TYR338 4.2 30.9 1.0
C A:TYR338 4.2 30.3 1.0
CG A:GLN403 4.3 28.2 1.0
CD2 A:HIS399 4.4 26.2 1.0
OE1 A:GLN403 4.4 35.8 1.0
CD2 A:TYR338 4.4 26.6 1.0
C A:ASP337 4.6 34.4 1.0
CG A:TYR338 4.6 27.0 1.0
CA A:ASP337 4.8 41.2 1.0
CG A:LEU339 5.0 28.7 1.0
CZ A:PHE437 5.0 23.2 1.0

Chlorine binding site 9 out of 22 in 2y2n

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Chlorine binding site 9 out of 22 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07)


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 (E07) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1214

b:41.2
occ:1.00
N A:LYS610 3.3 23.7 1.0
O A:HOH2219 3.4 34.1 1.0
NZ A:LYS610 3.5 57.2 1.0
CG A:LYS610 3.7 42.6 1.0
CA A:SER609 3.9 25.5 1.0
CE A:LYS610 3.9 50.1 1.0
CB A:LYS610 4.0 33.5 1.0
C A:SER609 4.1 27.0 1.0
CB A:SER609 4.1 26.6 1.0
CA A:LYS610 4.2 30.6 1.0
CD A:GLN606 4.3 43.4 1.0
OE1 A:GLN606 4.4 39.4 1.0
CD A:LYS610 4.5 40.7 1.0
CG A:GLN606 4.5 37.7 1.0
NE2 A:GLN606 4.6 37.9 1.0

Chlorine binding site 10 out of 22 in 2y2n

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Chlorine binding site 10 out of 22 in the Penicillin-Binding Protein 1B (Pbp-1B) in Complex with An Alkyl Boronate (E07)


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 (E07) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1215

b:52.7
occ:1.00
ND2 A:ASN702 2.8 22.2 1.0
O A:HOH2204 3.2 38.1 1.0
CD2 A:HIS699 3.4 24.3 1.0
CG A:ASN702 3.9 23.9 1.0
CG A:HIS699 4.0 27.9 1.0
CE2 A:TYR409 4.0 27.0 1.0
CD1 A:LEU639 4.0 19.8 1.0
CB A:ASN702 4.0 18.6 1.0
OH A:TYR409 4.0 44.8 1.0
O A:HIS699 4.1 22.1 1.0
CZ A:TYR409 4.1 35.4 1.0
CD2 A:LEU639 4.2 21.9 1.0
CA A:HIS699 4.2 19.5 1.0
CB A:HIS699 4.2 18.5 1.0
NE2 A:HIS699 4.3 22.4 1.0
C A:HIS699 4.7 20.5 1.0
NE2 A:GLN706 4.7 21.0 0.5
CG A:LEU639 4.7 23.9 1.0
CD2 A:TYR409 4.8 29.6 1.0
CE1 A:TYR409 5.0 32.4 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 Dec 12 09:27:40 2020

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