Chlorine in PDB 1hhy: Deglucobalhimycin in Complex with D-Ala-D-Ala
Protein crystallography data
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
|
Other elements in 1hhy:
The structure of Deglucobalhimycin in Complex with D-Ala-D-Ala also contains other interesting chemical elements:
Chlorine Binding Sites:
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 1hhy
Go back to
Chlorine Binding Sites List in 1hhy
Chlorine binding site 1 out
of 4 in the Deglucobalhimycin in Complex with D-Ala-D-Ala
![](/pictures/CL/pdb/hh/1hhy-CL-sphere_01.jpg) Mono view
![](/pictures/CL/pdb/hh/1hhy-CL-sphere_01_stereo.jpg) 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 1hhy
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Chlorine Binding Sites List in 1hhy
Chlorine binding site 2 out
of 4 in the Deglucobalhimycin in Complex with D-Ala-D-Ala
![](/pictures/CL/pdb/hh/1hhy-CL-sphere_02.jpg) Mono view
![](/pictures/CL/pdb/hh/1hhy-CL-sphere_02_stereo.jpg) 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 1hhy
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Chlorine Binding Sites List in 1hhy
Chlorine binding site 3 out
of 4 in the Deglucobalhimycin in Complex with D-Ala-D-Ala
![](/pictures/CL/pdb/hh/1hhy-CL-sphere_03.jpg) Mono view
![](/pictures/CL/pdb/hh/1hhy-CL-sphere_03_stereo.jpg) 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 1hhy
Go back to
Chlorine Binding Sites List in 1hhy
Chlorine binding site 4 out
of 4 in the Deglucobalhimycin in Complex with D-Ala-D-Ala
![](/pictures/CL/pdb/hh/1hhy-CL-sphere_04.jpg) Mono view
![](/pictures/CL/pdb/hh/1hhy-CL-sphere_04_stereo.jpg) 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
|
|
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 22:30:30 2024
|