Chlorine in PDB 1hhy: Deglucobalhimycin in Complex with D-Ala-D-Ala

The structure of Deglucobalhimycin in Complex with D-Ala-D-Ala, PDB code: 1hhy was solved by C.Lehmann, G.Bunkoczi, G.M.Sheldrick, L.Vertesy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.06 / 0.89
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	48.444, 48.444, 43.086, 90.00, 90.00, 120.00
R / Rfree (%)	12.1 / 13.9

The structure of Deglucobalhimycin in Complex with D-Ala-D-Ala also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Deglucobalhimycin in Complex with D-Ala-D-Ala (pdb code 1hhy). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Deglucobalhimycin in Complex with D-Ala-D-Ala, PDB code: 1hhy:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Deglucobalhimycin in Complex with D-Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Deglucobalhimycin in Complex with D-Ala-D-Ala within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2 b:8.1 occ:1.00 CL A:OMZ2 0.0 8.1 1.0 CE1 A:OMZ2 1.8 7.6 1.0 CD1 A:OMZ2 2.7 8.3 1.0 CZ A:OMZ2 2.7 7.9 1.0 OH A:OMZ2 3.0 7.9 1.0 C3 A:GHP4 3.4 7.2 1.0 C2 A:GHP4 3.5 6.6 1.0 CD2 B:OMY6 3.6 5.6 1.0 CE2 B:OMY6 3.7 5.6 1.0 CG A:OMZ2 4.0 8.7 1.0 CE2 A:OMZ2 4.0 9.1 1.0 C2 B:DVC9 4.2 7.5 1.0 C4 A:GHP4 4.4 7.5 1.0 C1 B:DVC9 4.4 6.3 1.0 C1 A:GHP4 4.5 6.4 1.0 CD2 A:OMZ2 4.5 8.8 1.0 O A:ASN3 4.7 6.3 1.0 CG B:OMY6 4.7 5.3 1.0 CZ B:OMY6 4.8 5.6 1.0 C A:ASN3 4.9 5.6 1.0 O4 A:GHP4 4.9 9.4 1.0 ODE B:OMY6 5.0 5.7 1.0

Chlorine binding site 2 out of 4 in the Deglucobalhimycin in Complex with D-Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Deglucobalhimycin in Complex with D-Ala-D-Ala within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl6 b:9.1 occ:1.00 CL A:OMY6 0.0 9.1 1.0 CE1 A:OMY6 1.7 7.3 1.0 CD1 A:OMY6 2.7 6.8 1.0 CZ A:OMY6 2.7 7.5 1.0 OCZ A:OMY6 3.0 8.6 1.0 C5 A:GHP4 3.2 7.3 1.0 C4 A:GHP4 3.6 7.5 1.0 C6 A:GHP4 3.6 6.8 1.0 CB A:DAL12 3.9 11.6 1.0 O4 A:GHP4 4.0 9.4 1.0 CE2 A:OMY6 4.0 7.6 1.0 CG A:OMY6 4.0 6.7 1.0 O B:HOH2030 4.1 32.7 1.0 O A:GHP4 4.3 7.3 1.0 C1 A:GHP4 4.4 6.4 1.0 C3 A:GHP4 4.4 7.2 1.0 CD2 A:OMY6 4.5 7.5 1.0 C3 B:PGO1001 4.6 8.4 1.0 C2 A:GHP4 4.7 6.6 1.0 C A:GHP4 4.9 6.2 1.0 N A:DAL12 5.0 9.8 1.0

Chlorine binding site 3 out of 4 in the Deglucobalhimycin in Complex with D-Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Deglucobalhimycin in Complex with D-Ala-D-Ala within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2 b:7.1 occ:1.00 CL B:OMZ2 0.0 7.1 1.0 CE1 B:OMZ2 1.7 6.2 1.0 CD1 B:OMZ2 2.7 6.3 1.0 CZ B:OMZ2 2.7 6.2 1.0 OH B:OMZ2 3.0 6.6 1.0 C3 B:GHP4 3.5 6.0 1.0 C2 B:GHP4 3.7 5.8 1.0 CD2 A:OMY6 3.7 7.5 1.0 CE2 A:OMY6 3.8 7.6 1.0 C2 A:DVC9 4.0 9.3 1.0 CE2 B:OMZ2 4.0 6.3 1.0 CG B:OMZ2 4.0 5.9 1.0 C1 B:PGO1001 4.0 7.6 1.0 C3 B:PGO1001 4.2 8.4 1.0 C1 A:DVC9 4.2 8.3 1.0 C2 B:PGO1001 4.3 7.1 1.0 C4 B:GHP4 4.5 5.7 1.0 CD2 B:OMZ2 4.5 6.4 1.0 CG A:OMY6 4.7 6.7 1.0 C1 B:GHP4 4.8 5.6 1.0 O1 B:PGO1001 4.8 7.0 1.0 ODE A:OMY6 4.8 7.2 1.0 O B:ASN3 4.9 6.4 1.0 CZ A:OMY6 4.9 7.5 1.0 O4 B:GHP4 5.0 6.5 1.0

Chlorine binding site 4 out of 4 in the Deglucobalhimycin in Complex with D-Ala-D-Ala


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Deglucobalhimycin in Complex with D-Ala-D-Ala within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl6 b:6.2 occ:1.00 CL B:OMY6 0.0 6.2 1.0 CE1 B:OMY6 1.7 5.3 1.0 CD1 B:OMY6 2.7 5.3 1.0 CZ B:OMY6 2.7 5.6 1.0 C5 B:GHP4 3.0 5.9 1.0 OCZ B:OMY6 3.0 6.0 1.0 C6 B:GHP4 3.4 5.5 1.0 C4 B:GHP4 3.6 5.7 1.0 CB B:DAL12 3.8 8.7 1.0 O4 B:GHP4 4.0 6.5 1.0 CG B:OMY6 4.0 5.3 1.0 CE2 B:OMY6 4.0 5.6 1.0 O B:GHP4 4.1 6.0 1.0 C1 B:GHP4 4.1 5.6 1.0 C3 B:GHP4 4.2 6.0 1.0 C2 B:GHP4 4.5 5.8 1.0 CD2 B:OMY6 4.5 5.6 1.0 C B:GHP4 4.5 5.4 1.0 N B:DAL12 4.8 6.6 1.0 CA B:DAL12 5.0 6.9 1.0 CA B:GHP4 5.0 5.3 1.0

C.Lehmann, G.Bunkoczi, L.Vertesy, G.M.Sheldrick. Structures of Glycopeptide Antibiotics with Peptides That Model Bacterial Cell-Wall Precursors J.Mol.Biol. V. 318 723 2002.
ISSN: ISSN 0022-2836
PubMed: 12054818
DOI: 10.1016/S0022-2836(02)00146-8