Chlorine in PDB 6tck: Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2
Enzymatic activity of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2
All present enzymatic activity of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2:
5.6.2.2;
Protein crystallography data
The structure of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2, PDB code: 6tck
was solved by
M.Welin,
R.Kimbung,
D.Focht,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.59 /
1.60
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
143.594,
55.429,
50.976,
90.00,
101.00,
90.00
|
R / Rfree (%)
|
17.7 /
20
|
Other elements in 6tck:
The structure of Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2 also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2
(pdb code 6tck). 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 the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2, PDB code: 6tck:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 6tck
Go back to
Chlorine Binding Sites List in 6tck
Chlorine binding site 1 out
of 6 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2
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 the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl301
b:29.8
occ:1.00
|
CL1
|
A:N1N301
|
0.0
|
29.8
|
1.0
|
C9
|
A:N1N301
|
1.8
|
25.8
|
1.0
|
C10
|
A:N1N301
|
2.8
|
24.6
|
1.0
|
C8
|
A:N1N301
|
3.0
|
24.9
|
1.0
|
N1
|
A:N1N301
|
3.2
|
25.9
|
1.0
|
CL
|
A:N1N301
|
3.4
|
26.1
|
1.0
|
C7
|
A:N1N301
|
3.5
|
25.1
|
1.0
|
CD1
|
A:ILE86
|
3.5
|
21.6
|
1.0
|
CB
|
A:ASN54
|
3.8
|
25.6
|
1.0
|
CG1
|
A:ILE86
|
3.8
|
21.4
|
1.0
|
CG
|
A:ASN54
|
4.0
|
28.4
|
1.0
|
N2
|
A:N1N301
|
4.0
|
23.3
|
1.0
|
C11
|
A:N1N301
|
4.0
|
23.0
|
1.0
|
CG2
|
A:ILE102
|
4.1
|
24.4
|
1.0
|
O
|
A:HOH428
|
4.3
|
39.6
|
1.0
|
C6
|
A:N1N301
|
4.3
|
25.0
|
1.0
|
OD1
|
A:ASN54
|
4.3
|
33.2
|
1.0
|
ND2
|
A:ASN54
|
4.4
|
29.8
|
1.0
|
N
|
A:N1N301
|
4.6
|
27.4
|
1.0
|
O
|
A:N1N301
|
4.7
|
25.5
|
1.0
|
CG2
|
A:ILE86
|
5.0
|
22.3
|
1.0
|
CB
|
A:ILE86
|
5.0
|
21.5
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 6tck
Go back to
Chlorine Binding Sites List in 6tck
Chlorine binding site 2 out
of 6 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2
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 the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl301
b:26.1
occ:1.00
|
CL
|
A:N1N301
|
0.0
|
26.1
|
1.0
|
C10
|
A:N1N301
|
1.8
|
24.6
|
1.0
|
C9
|
A:N1N301
|
2.9
|
25.8
|
1.0
|
C11
|
A:N1N301
|
2.9
|
23.0
|
1.0
|
C12
|
A:N1N301
|
3.4
|
22.7
|
1.0
|
CL1
|
A:N1N301
|
3.4
|
29.8
|
1.0
|
ND2
|
A:ASN54
|
3.6
|
29.8
|
1.0
|
CG1
|
A:ILE175
|
3.8
|
20.6
|
1.0
|
CB
|
A:ASN54
|
3.9
|
25.6
|
1.0
|
N2
|
A:N1N301
|
4.0
|
23.3
|
1.0
|
C8
|
A:N1N301
|
4.0
|
24.9
|
1.0
|
CD1
|
A:ILE51
|
4.1
|
24.4
|
1.0
|
CG
|
A:ASN54
|
4.1
|
28.4
|
1.0
|
CG2
|
A:ILE51
|
4.1
|
22.0
|
1.0
|
CD1
|
A:ILE175
|
4.1
|
22.1
|
1.0
|
O
|
A:ILE51
|
4.4
|
23.6
|
1.0
|
CD2
|
A:LEU103
|
4.5
|
25.1
|
1.0
|
CD1
|
A:ILE86
|
4.5
|
21.6
|
1.0
|
CA
|
A:ILE51
|
4.7
|
22.4
|
1.0
|
CB
|
A:ILE51
|
4.8
|
22.1
|
1.0
|
CB
|
A:ILE175
|
4.9
|
19.8
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 6tck
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Chlorine Binding Sites List in 6tck
Chlorine binding site 3 out
of 6 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2
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 the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl306
b:40.5
occ:1.00
|
NE
|
A:ARG144
|
3.1
|
26.0
|
1.0
|
N
|
A:VAL88
|
3.3
|
27.7
|
1.0
|
OD2
|
A:ASP89
|
3.3
|
51.2
|
1.0
|
CG2
|
A:VAL88
|
3.5
|
30.8
|
1.0
|
N
|
A:ASP89
|
3.6
|
35.0
|
1.0
|
ND2
|
A:ASN145
|
3.7
|
30.2
|
1.0
|
NH2
|
A:ARG144
|
3.7
|
28.0
|
1.0
|
CZ
|
A:ARG144
|
3.8
|
26.4
|
1.0
|
CD
|
A:ARG144
|
3.9
|
24.5
|
1.0
|
CA
|
A:PRO87
|
3.9
|
24.7
|
1.0
|
C
|
A:PRO87
|
4.1
|
25.5
|
1.0
|
CG
|
A:ASP89
|
4.1
|
47.3
|
1.0
|
CB
|
A:PRO87
|
4.1
|
26.2
|
1.0
|
CA
|
A:VAL88
|
4.1
|
29.0
|
1.0
|
CB
|
A:ASP89
|
4.2
|
43.8
|
1.0
|
C
|
A:VAL88
|
4.2
|
31.9
|
1.0
|
CB
|
A:VAL88
|
4.4
|
29.2
|
1.0
|
CA
|
A:ASP89
|
4.4
|
39.1
|
1.0
|
OD1
|
A:ASN145
|
4.4
|
31.2
|
1.0
|
CG
|
A:ASN145
|
4.5
|
30.2
|
1.0
|
CG
|
A:ARG144
|
4.6
|
24.8
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 6tck
Go back to
Chlorine Binding Sites List in 6tck
Chlorine binding site 4 out
of 6 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2
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 the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl301
b:30.2
occ:1.00
|
CL1
|
B:N1N301
|
0.0
|
30.2
|
1.0
|
C9
|
B:N1N301
|
1.8
|
25.8
|
1.0
|
C10
|
B:N1N301
|
2.8
|
25.6
|
1.0
|
C8
|
B:N1N301
|
3.0
|
25.7
|
1.0
|
N1
|
B:N1N301
|
3.2
|
25.0
|
1.0
|
CL
|
B:N1N301
|
3.4
|
26.8
|
1.0
|
C7
|
B:N1N301
|
3.5
|
26.1
|
1.0
|
CD1
|
B:ILE86
|
3.6
|
22.2
|
1.0
|
CB
|
B:ASN54
|
3.8
|
26.8
|
1.0
|
CG1
|
B:ILE86
|
3.8
|
22.4
|
1.0
|
CG
|
B:ASN54
|
4.0
|
30.5
|
1.0
|
O
|
B:HOH484
|
4.0
|
52.5
|
1.0
|
N2
|
B:N1N301
|
4.1
|
23.8
|
1.0
|
C11
|
B:N1N301
|
4.1
|
24.8
|
1.0
|
ND2
|
B:ASN54
|
4.1
|
33.5
|
1.0
|
C6
|
B:N1N301
|
4.3
|
24.4
|
1.0
|
O
|
B:HOH440
|
4.3
|
34.5
|
1.0
|
CG2
|
B:ILE102
|
4.3
|
28.6
|
1.0
|
OD1
|
B:ASN54
|
4.5
|
36.7
|
1.0
|
N
|
B:N1N301
|
4.6
|
25.8
|
1.0
|
O
|
B:N1N301
|
4.7
|
25.8
|
1.0
|
CG2
|
B:ILE86
|
4.9
|
22.8
|
1.0
|
CB
|
B:ILE86
|
5.0
|
21.9
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 6tck
Go back to
Chlorine Binding Sites List in 6tck
Chlorine binding site 5 out
of 6 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2
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 the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl301
b:26.8
occ:1.00
|
CL
|
B:N1N301
|
0.0
|
26.8
|
1.0
|
C10
|
B:N1N301
|
1.8
|
25.6
|
1.0
|
C9
|
B:N1N301
|
2.8
|
25.8
|
1.0
|
C11
|
B:N1N301
|
2.9
|
24.8
|
1.0
|
CL1
|
B:N1N301
|
3.4
|
30.2
|
1.0
|
ND2
|
B:ASN54
|
3.4
|
33.5
|
1.0
|
C12
|
B:N1N301
|
3.4
|
24.7
|
1.0
|
CG1
|
B:ILE175
|
3.7
|
21.4
|
1.0
|
CB
|
B:ASN54
|
3.8
|
26.8
|
1.0
|
N2
|
B:N1N301
|
4.0
|
23.8
|
1.0
|
C8
|
B:N1N301
|
4.0
|
25.7
|
1.0
|
CG
|
B:ASN54
|
4.0
|
30.5
|
1.0
|
CD1
|
B:ILE175
|
4.1
|
23.3
|
1.0
|
CG2
|
B:ILE51
|
4.1
|
21.1
|
1.0
|
CD1
|
B:ILE51
|
4.1
|
22.6
|
1.0
|
O
|
B:ILE51
|
4.3
|
23.0
|
1.0
|
CD1
|
B:ILE86
|
4.5
|
22.2
|
1.0
|
CA
|
B:ILE51
|
4.7
|
22.3
|
1.0
|
CD2
|
B:LEU103
|
4.7
|
28.2
|
1.0
|
CB
|
B:ILE51
|
4.8
|
21.4
|
1.0
|
CB
|
B:ILE175
|
4.8
|
19.9
|
1.0
|
C
|
B:ILE51
|
5.0
|
22.6
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 6tck
Go back to
Chlorine Binding Sites List in 6tck
Chlorine binding site 6 out
of 6 in the Crystal Structure of the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2
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 the Atp Binding Domain of S. Aureus Gyrb Complexed with Uld-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl305
b:41.8
occ:1.00
|
OD2
|
B:ASP89
|
3.1
|
49.8
|
1.0
|
NE
|
B:ARG144
|
3.2
|
27.7
|
1.0
|
N
|
B:VAL88
|
3.2
|
26.9
|
1.0
|
CG2
|
B:VAL88
|
3.5
|
29.1
|
1.0
|
N
|
B:ASP89
|
3.5
|
33.9
|
1.0
|
ND2
|
B:ASN145
|
3.8
|
32.3
|
1.0
|
NH2
|
B:ARG144
|
3.9
|
30.2
|
1.0
|
CG
|
B:ASP89
|
3.9
|
46.4
|
1.0
|
CA
|
B:PRO87
|
3.9
|
25.0
|
1.0
|
CZ
|
B:ARG144
|
4.0
|
27.4
|
1.0
|
CD
|
B:ARG144
|
4.0
|
25.2
|
1.0
|
CB
|
B:ASP89
|
4.0
|
42.5
|
1.0
|
CA
|
B:VAL88
|
4.1
|
28.7
|
1.0
|
C
|
B:PRO87
|
4.1
|
25.4
|
1.0
|
C
|
B:VAL88
|
4.1
|
31.6
|
1.0
|
CB
|
B:PRO87
|
4.2
|
25.9
|
1.0
|
CA
|
B:ASP89
|
4.3
|
38.4
|
1.0
|
CB
|
B:VAL88
|
4.3
|
28.6
|
1.0
|
OD1
|
B:ASN145
|
4.6
|
33.5
|
1.0
|
CG
|
B:ASN145
|
4.6
|
32.2
|
1.0
|
CG
|
B:ARG144
|
4.7
|
25.4
|
1.0
|
OD1
|
B:ASP89
|
5.0
|
51.3
|
1.0
|
|
Reference:
A.Nyerges,
T.Tomasic,
M.Durcik,
T.Revesz,
P.Szili,
G.Draskovits,
F.Bogar,
Z.Skok,
N.Zidar,
J.Ilas,
A.Zega,
D.Kikelj,
L.Daruka,
B.Kintses,
B.Vasarhelyi,
I.Foldesi,
D.Kata,
M.Welin,
R.Kimbung,
D.Focht,
L.P.Masic,
C.Pal.
Rational Design of Balanced Dual-Targeting Antibiotics with Limited Resistance. Plos Biol. V. 18 00819 2020.
ISSN: ESSN 1545-7885
PubMed: 33017402
DOI: 10.1371/JOURNAL.PBIO.3000819
Page generated: Mon Jul 29 15:21:41 2024
|