Chlorine in PDB 2y3p: Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8

All present enzymatic activity of Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8:
5.99.1.3;

The structure of Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8, PDB code: 2y3p was solved by M.J.Edwards, R.H.Flatman, L.A.Mitchenall, C.E.M.Stevenson, T.B.K.Le, T.A.Clarke, A.R.Mckay, H.-P.Fiedler, M.J.Buttner, D.M.Lawson, A.Maxwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.47 / 2.62
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	143.910, 153.090, 177.700, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.1

The structure of Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8 also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Chlorine atom in the Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8 (pdb code 2y3p). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8, PDB code: 2y3p:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl901 b:38.0 occ:1.00 CL4 A:SM8901 0.0 38.0 1.0 C4G A:SM8901 1.8 40.0 1.0 C4H A:SM8901 2.7 43.5 1.0 C4F A:SM8901 2.8 39.4 1.0 O4C A:SM8901 2.8 47.9 1.0 O A:GLY170 2.8 32.9 1.0 O4B A:SM8901 3.0 40.8 1.0 O A:ASN169 3.7 31.4 1.0 O A:HOH2025 3.7 28.3 1.0 CB A:ASN169 3.8 31.4 1.0 C A:GLY170 4.0 32.1 1.0 C A:ASN169 4.0 32.4 1.0 C4C A:SM8901 4.0 39.0 1.0 C4E A:SM8901 4.1 39.1 1.0 C4I A:SM8901 4.1 47.4 1.0 CD1 A:LEU98 4.3 36.9 1.0 O A:GLY40 4.5 33.5 1.0 N A:GLY170 4.5 32.6 1.0 CA A:ASN169 4.5 32.5 1.0 C4D A:SM8901 4.6 36.0 1.0 CG A:ASN169 4.6 33.9 1.0 CG A:LEU98 4.7 35.2 1.0 O4D A:SM8901 4.7 56.7 1.0 CA A:GLY170 4.8 32.4 1.0 CA A:SER171 4.8 32.5 1.0 N A:SER171 4.9 32.4 1.0 CE1 A:HIS45 4.9 33.0 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of N-Terminal Domain of Gyra with the Antibiotic Simocyclinone D8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl901 b:42.2 occ:1.00 CL4 B:SM8901 0.0 42.2 1.0 C4G B:SM8901 1.8 40.0 1.0 C4H B:SM8901 2.7 45.0 1.0 O4C B:SM8901 2.8 52.8 1.0 C4F B:SM8901 2.8 36.2 1.0 O4B B:SM8901 3.0 33.7 1.0 O B:GLY170 3.0 37.0 1.0 O B:ASN169 3.5 35.2 1.0 O B:HOH2029 3.6 50.0 1.0 O B:HOH2049 3.8 32.1 1.0 CB B:ASN169 3.9 31.7 1.0 C B:ASN169 3.9 35.1 1.0 C B:GLY170 3.9 37.6 1.0 C4C B:SM8901 4.0 43.1 1.0 C4E B:SM8901 4.1 37.7 1.0 C4I B:SM8901 4.1 57.3 1.0 CD2 B:LEU98 4.5 30.5 1.0 N B:GLY170 4.5 36.1 1.0 CA B:ASN169 4.5 34.0 1.0 C4D B:SM8901 4.6 38.0 1.0 N B:SER171 4.6 38.5 1.0 CA B:SER171 4.7 38.6 1.0 O4D B:SM8901 4.7 63.6 1.0 O B:GLY40 4.8 32.3 1.0 CA B:GLY170 4.8 36.7 1.0 CG B:ASN169 5.0 34.1 1.0

M.J.Edwards, R.H.Flatman, L.A.Mitchenall, C.E.M.Stevenson, T.B.K.Le, T.A.Clarke, A.R.Mckay, H.-P.Fiedler, M.J.Buttner, D.M.Lawson, A.Maxwell. A Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8, Bound to Dna Gyrase. Science V. 326 1415 2009.
ISSN: ISSN 0036-8075
PubMed: 19965760
DOI: 10.1126/SCIENCE.1179123