Chlorine in PDB 7lkc: Crystal Structure of Keratinimicin A
Protein crystallography data
The structure of Crystal Structure of Keratinimicin A, PDB code: 7lkc
was solved by
K.M.Davis,
P.D.Jeffrey,
M.R.Seyedsayamdost,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
18.97 /
0.95
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
20.72,
32.251,
37.941,
90,
90,
90
|
R / Rfree (%)
|
15.4 /
16.8
|
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of Keratinimicin A
(pdb code 7lkc). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
Crystal Structure of Keratinimicin A, PDB code: 7lkc:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 7lkc
Go back to
Chlorine Binding Sites List in 7lkc
Chlorine binding site 1 out
of 6 in the Crystal Structure of Keratinimicin A
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 Keratinimicin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1
b:10.9
occ:0.64
|
CL3
|
A:0UZ1
|
0.0
|
10.9
|
0.6
|
O4
|
A:0UZ1
|
0.7
|
12.1
|
0.4
|
C4
|
A:0UZ1
|
1.5
|
11.8
|
0.4
|
H7
|
A:0UZ1
|
1.5
|
14.5
|
0.4
|
C3
|
A:0UZ1
|
1.7
|
9.8
|
0.6
|
H8
|
A:0UZ1
|
1.9
|
14.4
|
0.4
|
C5
|
A:0UZ1
|
2.0
|
12.0
|
0.4
|
H7
|
A:0UZ1
|
2.6
|
12.5
|
0.6
|
C2
|
A:0UZ1
|
2.7
|
9.3
|
0.6
|
C4
|
A:0UZ1
|
2.7
|
9.8
|
0.6
|
C3
|
A:0UZ1
|
2.8
|
11.4
|
0.4
|
H6
|
A:0UZ1
|
2.8
|
11.2
|
0.6
|
O4
|
A:0UZ1
|
3.1
|
10.4
|
0.6
|
O
|
A:HOH202
|
3.3
|
18.2
|
1.0
|
C6
|
A:0UZ1
|
3.4
|
11.9
|
0.4
|
CL3
|
A:0UZ1
|
3.6
|
11.2
|
0.4
|
O
|
A:HOH209
|
3.7
|
15.2
|
1.0
|
C2
|
A:0UZ1
|
3.9
|
11.3
|
0.4
|
H9
|
A:0UZ1
|
4.0
|
14.3
|
0.4
|
C1
|
A:0UZ1
|
4.0
|
9.6
|
0.6
|
C5
|
A:0UZ1
|
4.0
|
9.8
|
0.6
|
C1
|
A:0UZ1
|
4.1
|
11.6
|
0.4
|
HO2
|
A:MAN101
|
4.2
|
22.4
|
1.0
|
H2
|
A:MAN101
|
4.3
|
20.9
|
1.0
|
H1
|
A:MAN101
|
4.4
|
18.5
|
1.0
|
O2
|
A:MAN101
|
4.5
|
18.7
|
1.0
|
C6
|
A:0UZ1
|
4.5
|
9.5
|
0.6
|
H6
|
A:0UZ1
|
4.7
|
13.6
|
0.4
|
H8
|
A:0UZ1
|
4.7
|
11.8
|
0.6
|
C2
|
A:MAN101
|
4.8
|
17.4
|
1.0
|
O2
|
A:FMT103
|
4.8
|
11.1
|
1.0
|
H
|
A:FMT103
|
5.0
|
13.2
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 7lkc
Go back to
Chlorine Binding Sites List in 7lkc
Chlorine binding site 2 out
of 6 in the Crystal Structure of Keratinimicin A
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 Keratinimicin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1
b:11.2
occ:0.36
|
CL3
|
A:0UZ1
|
0.0
|
11.2
|
0.4
|
C4
|
A:0UZ1
|
1.1
|
9.8
|
0.6
|
C5
|
A:0UZ1
|
1.1
|
9.8
|
0.6
|
H8
|
A:0UZ1
|
1.3
|
11.8
|
0.6
|
O4
|
A:0UZ1
|
1.6
|
10.4
|
0.6
|
C3
|
A:0UZ1
|
1.7
|
11.4
|
0.4
|
H7
|
A:0UZ1
|
2.3
|
12.5
|
0.6
|
C6
|
A:0UZ1
|
2.3
|
9.5
|
0.6
|
C3
|
A:0UZ1
|
2.3
|
9.8
|
0.6
|
H7
|
A:0UZ1
|
2.6
|
14.5
|
0.4
|
C2
|
A:0UZ1
|
2.7
|
11.3
|
0.4
|
C4
|
A:0UZ1
|
2.7
|
11.8
|
0.4
|
H6
|
A:0UZ1
|
2.8
|
13.6
|
0.4
|
H9
|
A:0UZ1
|
3.0
|
11.4
|
0.6
|
O4
|
A:0UZ1
|
3.1
|
12.1
|
0.4
|
C2
|
A:0UZ1
|
3.1
|
9.3
|
0.6
|
C1
|
A:0UZ1
|
3.1
|
9.6
|
0.6
|
HE2
|
A:PHE3
|
3.1
|
13.3
|
1.0
|
HD2
|
A:PHE3
|
3.1
|
12.5
|
1.0
|
CL3
|
A:0UZ1
|
3.6
|
10.9
|
0.6
|
CE2
|
A:PHE3
|
3.7
|
11.1
|
1.0
|
CD2
|
A:PHE3
|
3.7
|
10.4
|
1.0
|
C1
|
A:0UZ1
|
4.0
|
11.6
|
0.4
|
H6
|
A:0UZ1
|
4.0
|
11.2
|
0.6
|
C5
|
A:0UZ1
|
4.0
|
12.0
|
0.4
|
O
|
A:HOH202
|
4.0
|
18.2
|
1.0
|
O2
|
A:MAN101
|
4.1
|
18.7
|
1.0
|
O
|
A:HOH209
|
4.3
|
15.2
|
1.0
|
HO2
|
A:MAN101
|
4.3
|
22.4
|
1.0
|
HO3
|
A:MAN101
|
4.5
|
23.4
|
1.0
|
C6
|
A:0UZ1
|
4.5
|
11.9
|
0.4
|
CA
|
A:0UZ1
|
4.6
|
10.6
|
0.6
|
H8
|
A:0UZ1
|
4.7
|
14.4
|
0.4
|
H2
|
A:MAN101
|
4.8
|
20.9
|
1.0
|
CZ
|
A:PHE3
|
5.0
|
10.8
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 7lkc
Go back to
Chlorine Binding Sites List in 7lkc
Chlorine binding site 3 out
of 6 in the Crystal Structure of Keratinimicin A
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Crystal Structure of Keratinimicin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl6
b:10.2
occ:1.00
|
CL
|
A:OMY6
|
0.0
|
10.2
|
1.0
|
CE1
|
A:OMY6
|
1.7
|
8.2
|
1.0
|
HO4
|
G:RAM2
|
2.4
|
15.9
|
1.0
|
CD1
|
A:OMY6
|
2.7
|
7.8
|
1.0
|
CZ
|
A:OMY6
|
2.7
|
7.8
|
1.0
|
HD1
|
A:OMY6
|
2.8
|
9.4
|
1.0
|
H62
|
G:RAM2
|
3.0
|
15.4
|
1.0
|
OCZ
|
A:OMY6
|
3.0
|
7.9
|
1.0
|
C5
|
A:GHP4
|
3.2
|
7.8
|
1.0
|
H5
|
G:RAM2
|
3.2
|
14.9
|
1.0
|
O4
|
G:RAM2
|
3.4
|
13.3
|
1.0
|
C6
|
A:GHP4
|
3.5
|
7.3
|
1.0
|
H6
|
A:GHP4
|
3.6
|
8.8
|
1.0
|
O
|
A:HOH207
|
3.7
|
17.1
|
1.0
|
C6
|
G:RAM2
|
3.7
|
12.9
|
1.0
|
C5
|
G:RAM2
|
3.9
|
12.4
|
1.0
|
C4
|
A:GHP4
|
4.0
|
8.3
|
1.0
|
H61
|
G:RAM2
|
4.0
|
15.4
|
1.0
|
CG
|
A:OMY6
|
4.0
|
7.7
|
1.0
|
CE2
|
A:OMY6
|
4.0
|
7.8
|
1.0
|
C4
|
G:RAM2
|
4.2
|
13.0
|
1.0
|
O
|
A:GHP4
|
4.2
|
7.9
|
1.0
|
H
|
A:FMT103
|
4.2
|
13.2
|
1.0
|
H62
|
K:RAM2
|
4.3
|
12.7
|
1.0
|
H3
|
G:RAM2
|
4.3
|
16.3
|
1.0
|
C1
|
A:GHP4
|
4.3
|
7.5
|
1.0
|
HA
|
A:GHP5
|
4.4
|
8.6
|
1.0
|
O4
|
A:GHP4
|
4.4
|
8.8
|
1.0
|
CD2
|
A:OMY6
|
4.5
|
7.8
|
1.0
|
H63
|
G:RAM2
|
4.7
|
15.4
|
1.0
|
C
|
A:GHP4
|
4.7
|
7.4
|
1.0
|
C3
|
A:GHP4
|
4.7
|
8.4
|
1.0
|
HE2
|
A:OMY6
|
4.8
|
9.4
|
1.0
|
C3
|
G:RAM2
|
4.9
|
13.6
|
1.0
|
C2
|
A:GHP4
|
4.9
|
8.1
|
1.0
|
H61
|
K:RAM2
|
4.9
|
12.7
|
1.0
|
HA
|
A:OMY6
|
5.0
|
9.1
|
1.0
|
CL
|
A:CL104
|
5.0
|
15.0
|
0.7
|
|
Chlorine binding site 4 out
of 6 in 7lkc
Go back to
Chlorine Binding Sites List in 7lkc
Chlorine binding site 4 out
of 6 in the Crystal Structure of Keratinimicin A
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Crystal Structure of Keratinimicin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl1
b:18.1
occ:1.00
|
CL3
|
B:0UZ1
|
0.0
|
18.1
|
1.0
|
C3
|
B:0UZ1
|
1.7
|
15.7
|
1.0
|
C2
|
B:0UZ1
|
2.6
|
14.7
|
1.0
|
H7
|
B:0UZ1
|
2.6
|
19.6
|
1.0
|
C4
|
B:0UZ1
|
2.7
|
15.5
|
1.0
|
H6
|
B:0UZ1
|
2.7
|
17.6
|
1.0
|
O
|
B:HOH211
|
2.8
|
15.9
|
0.7
|
O4
|
B:0UZ1
|
3.1
|
16.3
|
1.0
|
HB2
|
B:PHE3
|
3.2
|
15.2
|
1.0
|
C1
|
B:0UZ1
|
3.9
|
13.6
|
1.0
|
HB3
|
B:PHE3
|
3.9
|
15.2
|
1.0
|
C5
|
B:0UZ1
|
4.0
|
14.8
|
1.0
|
CB
|
B:PHE3
|
4.0
|
12.7
|
1.0
|
C6
|
B:0UZ1
|
4.5
|
13.8
|
1.0
|
H8
|
B:0UZ1
|
4.7
|
17.7
|
1.0
|
H
|
B:PHE3
|
4.9
|
12.6
|
1.0
|
N
|
B:PHE3
|
4.9
|
10.5
|
1.0
|
CG
|
B:PHE3
|
4.9
|
14.3
|
1.0
|
HD2
|
B:PHE3
|
4.9
|
19.0
|
1.0
|
CA
|
B:PHE3
|
5.0
|
10.5
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 7lkc
Go back to
Chlorine Binding Sites List in 7lkc
Chlorine binding site 5 out
of 6 in the Crystal Structure of Keratinimicin A
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Crystal Structure of Keratinimicin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl6
b:11.4
occ:1.00
|
CL
|
B:OMY6
|
0.0
|
11.4
|
1.0
|
CE1
|
B:OMY6
|
1.7
|
9.2
|
1.0
|
CD1
|
B:OMY6
|
2.7
|
8.9
|
1.0
|
CZ
|
B:OMY6
|
2.7
|
8.5
|
1.0
|
HD1
|
B:OMY6
|
2.8
|
10.7
|
1.0
|
H62
|
K:BGC1
|
2.9
|
14.6
|
1.0
|
OCZ
|
B:OMY6
|
3.0
|
8.6
|
1.0
|
C5
|
B:GHP4
|
3.2
|
8.0
|
1.0
|
C6
|
B:GHP4
|
3.5
|
8.2
|
1.0
|
H6
|
B:GHP4
|
3.5
|
9.9
|
1.0
|
O5
|
K:BGC1
|
3.6
|
9.9
|
1.0
|
H62
|
G:BGC1
|
3.7
|
15.0
|
1.0
|
C6
|
K:BGC1
|
3.8
|
12.1
|
1.0
|
C4
|
B:GHP4
|
3.9
|
8.2
|
1.0
|
CE2
|
B:OMY6
|
4.0
|
8.4
|
1.0
|
CG
|
B:OMY6
|
4.0
|
8.5
|
1.0
|
H61
|
G:BGC1
|
4.0
|
15.0
|
1.0
|
HO6
|
K:BGC1
|
4.1
|
15.7
|
1.0
|
O6
|
K:BGC1
|
4.1
|
13.1
|
1.0
|
C5
|
K:BGC1
|
4.2
|
10.8
|
1.0
|
HA
|
B:GHP5
|
4.3
|
9.4
|
1.0
|
C1
|
B:GHP4
|
4.3
|
8.0
|
1.0
|
O4
|
B:GHP4
|
4.4
|
8.7
|
1.0
|
O
|
B:GHP4
|
4.4
|
8.7
|
1.0
|
C6
|
G:BGC1
|
4.4
|
12.5
|
1.0
|
H5
|
K:BGC1
|
4.4
|
13.0
|
1.0
|
C1
|
K:BGC1
|
4.4
|
9.3
|
1.0
|
CD2
|
B:OMY6
|
4.5
|
8.2
|
1.0
|
H5
|
G:BGC1
|
4.5
|
12.9
|
1.0
|
H61
|
K:BGC1
|
4.6
|
14.6
|
1.0
|
C3
|
B:GHP4
|
4.7
|
8.3
|
1.0
|
HE2
|
B:OMY6
|
4.7
|
10.1
|
1.0
|
C
|
B:GHP4
|
4.8
|
7.9
|
1.0
|
HA
|
B:OMY6
|
4.8
|
10.1
|
1.0
|
C2
|
B:GHP4
|
4.9
|
8.2
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 7lkc
Go back to
Chlorine Binding Sites List in 7lkc
Chlorine binding site 6 out
of 6 in the Crystal Structure of Keratinimicin A
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Crystal Structure of Keratinimicin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl104
b:15.0
occ:0.66
|
HN1
|
A:3FG7
|
2.2
|
10.2
|
1.0
|
HC2
|
A:GHP5
|
2.5
|
8.9
|
1.0
|
HA
|
A:OMY6
|
2.6
|
9.1
|
1.0
|
O
|
A:HOH207
|
2.7
|
17.1
|
1.0
|
HD1
|
A:OMY6
|
2.8
|
9.4
|
1.0
|
N
|
A:3FG7
|
3.0
|
8.5
|
1.0
|
O
|
A:HOH211
|
3.2
|
23.4
|
0.9
|
HB
|
A:OMY6
|
3.3
|
9.1
|
1.0
|
CA
|
A:OMY6
|
3.4
|
7.6
|
1.0
|
HA
|
A:GHP5
|
3.5
|
8.6
|
1.0
|
C2
|
A:GHP5
|
3.6
|
7.4
|
1.0
|
CD1
|
A:OMY6
|
3.7
|
7.8
|
1.0
|
C
|
A:OMY6
|
3.7
|
8.5
|
1.0
|
CB
|
A:OMY6
|
3.7
|
7.6
|
1.0
|
CB
|
A:3FG7
|
3.9
|
9.1
|
1.0
|
CA
|
A:3FG7
|
4.0
|
9.2
|
1.0
|
CG1
|
A:3FG7
|
4.1
|
8.9
|
1.0
|
CG
|
A:OMY6
|
4.2
|
7.7
|
1.0
|
C3
|
A:GHP5
|
4.3
|
8.3
|
1.0
|
CG2
|
A:3FG7
|
4.3
|
9.9
|
1.0
|
CA
|
A:GHP5
|
4.5
|
7.2
|
1.0
|
C1
|
A:GHP5
|
4.5
|
7.4
|
1.0
|
HG2
|
A:3FG7
|
4.7
|
11.9
|
1.0
|
N
|
A:OMY6
|
4.7
|
7.2
|
1.0
|
H6
|
A:YBJ102
|
4.7
|
12.9
|
1.0
|
CE1
|
A:OMY6
|
4.7
|
8.2
|
1.0
|
HA
|
A:3FG7
|
4.7
|
11.1
|
1.0
|
O
|
A:3FG7
|
4.8
|
11.7
|
1.0
|
CD1
|
A:3FG7
|
4.8
|
10.0
|
1.0
|
H
|
A:YBJ102
|
4.8
|
11.5
|
1.0
|
O
|
A:OMY6
|
4.9
|
9.6
|
1.0
|
C
|
A:3FG7
|
4.9
|
10.7
|
1.0
|
ODE
|
A:OMY6
|
4.9
|
7.7
|
1.0
|
CD2
|
A:3FG7
|
5.0
|
10.6
|
1.0
|
CL
|
A:OMY6
|
5.0
|
10.2
|
1.0
|
O
|
A:GHP4
|
5.0
|
7.9
|
1.0
|
|
Reference:
K.L.Mcwhorter,
V.T.Chioti,
F.Xu,
P.D.Jeffrey,
K.M.Davis,
M.R.Seyedsayamdost.
Structural and Functional Analysis of Keratinicyclin Reveals Synergistic Antibiosis with Vancomycin Against Clostridium Difficile To Be Published.
Page generated: Tue Apr 4 20:43:58 2023
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