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Chlorine in PDB 2y68: Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase

Enzymatic activity of Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase

All present enzymatic activity of Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase:
6.3.2.9;

Protein crystallography data

The structure of Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase, PDB code: 2y68 was solved by T.Tomasic, N.Zidar, R.Sink, A.Kovac, D.Patin, D.Blanot, C.Contreras-Martel, A.Dessen, M.Muller-Premru, A.Zega, S.Gobec, L.Peterlin-Masic, D.Kikelj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.35 / 1.49
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 65.544, 65.544, 134.959, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.4

Other elements in 2y68:

The structure of Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase also contains other interesting chemical elements:

Fluorine (F) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase (pdb code 2y68). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase, PDB code: 2y68:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 2y68

Go back to Chlorine Binding Sites List in 2y68
Chlorine binding site 1 out of 3 in the Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1444

b:53.0
occ:1.00
 O A:HOH2401 3.2 28.7 1.0
O A:ARG395 3.6 23.4 1.0
C A:ARG395 3.9 22.0 1.0
CA A:LEU396 4.0 21.4 1.0
N A:LEU396 4.0 21.1 1.0
CD1 A:LEU396 4.3 27.5 1.0
CB A:ARG395 4.5 21.4 1.0
O A:HOH2181 4.6 34.1 1.0
CB A:LEU396 4.6 24.1 1.0
O A:HOH2182 4.8 39.5 1.0
CA A:ARG395 4.8 20.8 1.0
O A:HOH2409 4.9 45.5 1.0
O A:HOH2404 5.0 25.0 1.0

Chlorine binding site 2 out of 3 in 2y68

Go back to Chlorine Binding Sites List in 2y68
Chlorine binding site 2 out of 3 in the Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1445

b:45.5
occ:1.00
 O A:HOH2103 2.5 49.5 1.0
N A:LEU57 3.0 19.4 1.0
CB A:SER56 3.7 20.7 1.0
CA A:SER56 3.7 20.5 1.0
C A:SER56 3.9 19.1 1.0
CB A:LEU57 4.0 18.7 1.0
NE2 A:HIS78 4.0 29.8 1.0
CA A:LEU57 4.0 20.1 1.0
CG A:LEU57 4.2 19.4 1.0
O A:LEU57 4.2 23.0 1.0
CE1 A:HIS78 4.2 27.6 1.0
C A:LEU57 4.6 19.1 1.0
CG2 A:THR36 4.7 20.9 1.0
OG A:SER56 4.9 21.3 1.0
CD1 A:LEU57 4.9 24.5 1.0

Chlorine binding site 3 out of 3 in 2y68

Go back to Chlorine Binding Sites List in 2y68
Chlorine binding site 3 out of 3 in the Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure-Based Design of A New Series of D-Glutamic Acid-Based Inhibitors of Bacterial Murd Ligase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1505

b:64.7
occ:1.00
 O A:HOH2376 3.3 33.8 1.0
O A:HOH2375 3.8 41.2 1.0
ND2 A:ASN363 3.9 40.3 1.0
CA A:GLY361 4.5 35.7 1.0
O A:HOH2373 4.7 42.5 1.0
CB A:ASN363 4.7 30.7 1.0
O A:ASN360 4.8 36.1 1.0
CG A:ASN363 4.8 33.8 1.0

Reference:

T.Tomasic, N.Zidar, R.Sink, A.Kovac, D.Blanot, C.Contreras-Martel, A.Dessen, M.Muller-Premru, A.Zega, S.Gobec, D.Kikelj, L.P.Masic. Structure-Based Design of A New Series of D-Glutamic Acid Based Inhibitors of Bacterial Udp-N-Acetylmuramoyl-L-Alanine:D-Glutamate Ligase (Murd). J. Med. Chem. V. 54 4600 2011.
ISSN: ISSN 1520-4804
PubMed: 21591605
DOI: 10.1021/JM2002525
Page generated: Sat Jul 20 14:49:05 2024

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