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Chlorine in PDB 1hhz: Deglucobalhimycin in Complex with Cell Wall Pentapeptide

Protein crystallography data

The structure of Deglucobalhimycin in Complex with Cell Wall Pentapeptide, PDB code: 1hhz 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) 41.85 / 0.99
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 48.290, 48.290, 39.300, 90.00, 90.00, 120.00
R / Rfree (%) 10.8 / 14

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Deglucobalhimycin in Complex with Cell Wall Pentapeptide (pdb code 1hhz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Deglucobalhimycin in Complex with Cell Wall Pentapeptide, PDB code: 1hhz:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 1hhz

Go back to Chlorine Binding Sites List in 1hhz
Chlorine binding site 1 out of 6 in the Deglucobalhimycin in Complex with Cell Wall Pentapeptide


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 Cell Wall Pentapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl2

b:15.1
occ:1.00
 CL A:OMZ2 0.0 15.1 1.0
CE1 A:OMZ2 1.7 11.4 1.0
CZ A:OMZ2 2.6 12.0 1.0
CD1 A:OMZ2 2.7 11.8 1.0
OH A:OMZ2 2.9 12.8 1.0
C3 A:GHP4 3.4 10.6 1.0
C2 A:GHP4 3.5 9.4 1.0
CE2 A:OMZ2 3.9 12.6 1.0
CG A:OMZ2 4.0 11.9 1.0
O2 A:PGR1002 4.1 27.3 0.3
CD2 A:OMZ2 4.4 12.5 1.0
C4 A:GHP4 4.5 10.8 1.0
C1 A:GHP4 4.7 8.2 1.0
O A:ASN3 4.7 8.6 1.0
C A:ASN3 4.9 7.9 1.0

Chlorine binding site 2 out of 6 in 1hhz

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Chlorine binding site 2 out of 6 in the Deglucobalhimycin in Complex with Cell Wall Pentapeptide


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 Cell Wall Pentapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl6

b:15.1
occ:1.00
 CL A:OMY6 0.0 15.1 1.0
CE1 A:OMY6 1.7 10.3 1.0
CD1 A:OMY6 2.7 9.6 1.0
CZ A:OMY6 2.7 10.0 1.0
OCZ A:OMY6 3.0 11.2 1.0
C5 A:GHP4 3.3 10.3 1.0
O D:HOH2001 3.4 53.0 1.0
CB D:DAL5 3.5 13.0 1.0
C6 A:GHP4 3.6 9.3 1.0
OE1 D:FGA2 3.8 21.3 1.0
C D:DAL4 3.8 11.0 1.0
O D:HOH2002 3.9 44.7 1.0
C4 A:GHP4 3.9 10.8 1.0
CG A:OMY6 4.0 8.9 1.0
N D:DAL5 4.0 10.6 1.0
CE2 A:OMY6 4.0 9.8 1.0
C3 A:PGR1001 4.1 23.6 0.4
O D:DAL4 4.2 13.4 1.0
CA D:DAL4 4.3 10.7 1.0
O4 A:GHP4 4.3 13.5 1.0
C1 A:PGR1001 4.3 41.2 0.4
CA D:DAL5 4.4 11.3 1.0
N D:DAL4 4.4 11.5 1.0
C1 A:GHP4 4.5 8.2 1.0
CD2 A:OMY6 4.5 9.4 1.0
C D:LYS3 4.6 9.8 1.0
O D:LYS3 4.6 9.6 1.0
CD D:FGA2 4.7 20.7 1.0
C2 A:PGR1001 4.8 29.5 0.4
C3 A:GHP4 4.8 10.6 1.0
O A:GHP4 4.8 7.9 1.0
C2 A:GHP4 5.0 9.4 1.0

Chlorine binding site 3 out of 6 in 1hhz

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Chlorine binding site 3 out of 6 in the Deglucobalhimycin in Complex with Cell Wall Pentapeptide


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 Cell Wall Pentapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl2

b:11.5
occ:1.00
 CL B:OMZ2 0.0 11.5 1.0
CE1 B:OMZ2 1.7 8.8 1.0
CZ B:OMZ2 2.6 8.9 1.0
CD1 B:OMZ2 2.7 9.1 1.0
OH B:OMZ2 2.9 8.9 1.0
O B:HOH2008 3.4 44.3 1.0
C3 B:GHP4 3.4 7.4 1.0
C2 B:GHP4 3.5 7.0 1.0
CD2 C:OMY6 3.5 6.5 1.0
O B:HOH2015 3.6 41.7 1.0
C2 C:DVC9 3.7 9.8 1.0
C1 C:DVC9 3.7 9.2 1.0
CE2 C:OMY6 3.9 6.5 1.0
O C:HOH2008 3.9 58.6 1.0
CE2 B:OMZ2 3.9 9.1 1.0
CG B:OMZ2 4.0 9.2 1.0
O C:HOH2014 4.4 64.3 1.0
ODE C:OMY6 4.4 7.2 1.0
CG C:OMY6 4.4 6.3 1.0
CD2 B:OMZ2 4.4 9.4 1.0
O B:HOH2007 4.5 62.5 1.0
C4 B:GHP4 4.5 7.3 1.0
C1 B:GHP4 4.6 6.2 1.0
O B:ASN3 4.7 9.3 1.0
O5 C:DVC9 4.8 10.8 1.0
C B:ASN3 4.9 7.5 1.0
CZ C:OMY6 5.0 6.3 1.0

Chlorine binding site 4 out of 6 in 1hhz

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Chlorine binding site 4 out of 6 in the Deglucobalhimycin in Complex with Cell Wall Pentapeptide


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 Cell Wall Pentapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl6

b:8.5
occ:1.00
 CL B:OMY6 0.0 8.5 1.0
CE1 B:OMY6 1.7 6.4 1.0
CD1 B:OMY6 2.7 6.1 1.0
CZ B:OMY6 2.7 6.3 1.0
OCZ B:OMY6 3.0 7.3 1.0
C5 B:GHP4 3.3 6.9 1.0
C6 B:GHP4 3.6 6.2 1.0
C E:DAL4 3.6 6.0 1.0
CB E:DAL5 3.7 8.3 1.0
N E:DAL5 3.8 6.6 1.0
OE1 E:FGA2 3.8 6.8 1.0
CA E:DAL4 3.9 5.8 1.0
O E:DAL4 4.0 6.8 1.0
C4 B:GHP4 4.0 7.3 1.0
CE2 B:OMY6 4.0 6.4 1.0
CG B:OMY6 4.0 5.9 1.0
CB E:DAL1 4.1 22.6 0.4
N E:DAL4 4.3 6.0 1.0
O4 B:GHP4 4.4 9.9 1.0
CA E:DAL5 4.4 7.0 1.0
O B:GHP4 4.5 6.4 1.0
C1 B:GHP4 4.5 6.2 1.0
CD2 B:OMY6 4.5 6.2 1.0
CD E:FGA2 4.6 6.3 1.0
CB E:FGA2 4.6 8.9 1.0
C E:LYS3 4.7 5.4 1.0
O E:LYS3 4.8 5.9 1.0
C3 B:GHP4 4.8 7.4 1.0
C B:GHP4 4.9 5.7 1.0
C2 B:GHP4 5.0 7.0 1.0

Chlorine binding site 5 out of 6 in 1hhz

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Chlorine binding site 5 out of 6 in the Deglucobalhimycin in Complex with Cell Wall Pentapeptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Deglucobalhimycin in Complex with Cell Wall Pentapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl2

b:10.6
occ:1.00
 CL C:OMZ2 0.0 10.6 1.0
CE1 C:OMZ2 1.7 6.3 1.0
CZ C:OMZ2 2.7 6.2 1.0
CD1 C:OMZ2 2.7 5.9 1.0
OH C:OMZ2 2.9 7.0 1.0
C3 C:GHP4 3.5 6.2 1.0
CD2 B:OMY6 3.6 6.2 1.0
C2 C:GHP4 3.7 5.9 1.0
C2 B:DVC9 3.7 6.2 1.0
C1 B:DVC9 3.8 6.7 1.0
CE2 C:OMZ2 3.9 6.2 1.0
CE2 B:OMY6 4.0 6.4 1.0
CG C:OMZ2 4.0 5.8 1.0
CD2 C:OMZ2 4.5 5.7 1.0
O B:HOH2025 4.5 11.8 1.0
ODE B:OMY6 4.5 6.1 1.0
C4 C:GHP4 4.5 6.3 1.0
CG B:OMY6 4.6 5.9 1.0
C1 C:GHP4 4.8 5.2 1.0
O5 B:DVC9 4.9 6.7 1.0

Chlorine binding site 6 out of 6 in 1hhz

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Chlorine binding site 6 out of 6 in the Deglucobalhimycin in Complex with Cell Wall Pentapeptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Deglucobalhimycin in Complex with Cell Wall Pentapeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl6

b:9.6
occ:1.00
 CL C:OMY6 0.0 9.6 1.0
CE1 C:OMY6 1.7 6.4 1.0
CD1 C:OMY6 2.7 6.6 1.0
CZ C:OMY6 2.7 6.3 1.0
OCZ C:OMY6 3.0 7.0 1.0
C5 C:GHP4 3.2 6.1 1.0
C6 C:GHP4 3.6 6.0 1.0
O F:HOH2003 3.6 43.9 1.0
OE1 F:FGA2 3.7 15.0 1.0
CB F:DAL5 3.8 6.8 1.0
O F:HOH2002 3.8 32.3 1.0
C4 C:GHP4 3.9 6.3 1.0
O B:HOH2009 4.0 46.1 1.0
C F:DAL4 4.0 5.7 1.0
CG C:OMY6 4.0 6.3 1.0
CE2 C:OMY6 4.0 6.5 1.0
O C:HOH2009 4.0 29.8 1.0
N F:DAL5 4.2 5.7 1.0
CA F:DAL4 4.2 6.6 1.0
O F:DAL4 4.3 6.2 1.0
O4 C:GHP4 4.3 8.2 1.0
N F:DAL4 4.3 7.3 1.0
C F:LYS3 4.4 6.8 1.0
O C:GHP4 4.4 5.8 1.0
C1 C:GHP4 4.4 5.2 1.0
O F:LYS3 4.5 7.2 1.0
CD2 C:OMY6 4.5 6.5 1.0
CD F:FGA2 4.6 11.4 1.0
CA F:DAL5 4.6 5.7 1.0
C3 C:GHP4 4.7 6.2 1.0
C C:GHP4 4.9 5.2 1.0
C2 C:GHP4 4.9 5.9 1.0

Reference:

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
Page generated: Fri Jul 19 22:30:40 2024

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