Ruthenium in PDB 5top: Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase
Enzymatic activity of Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase
All present enzymatic activity of Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase:
3.5.2.6;
Protein crystallography data
The structure of Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase, PDB code: 5top
was solved by
E.M.Lewandowski,
Y.Chen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
1.18
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.093,
106.821,
47.933,
90.00,
101.66,
90.00
|
R / Rfree (%)
|
12.8 /
14.6
|
Other elements in 5top:
The structure of Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase also contains other interesting chemical elements:
Ruthenium Binding Sites:
The binding sites of Ruthenium atom in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase
(pdb code 5top). This binding sites where shown within
5.0 Angstroms radius around Ruthenium atom.
In total 8 binding sites of Ruthenium where determined in the
Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase, PDB code: 5top:
Jump to Ruthenium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Ruthenium binding site 1 out
of 8 in 5top
Go back to
Ruthenium Binding Sites List in 5top
Ruthenium binding site 1 out
of 8 in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 1 of Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ru302
b:18.6
occ:1.00
|
RU
|
A:JSE302
|
0.0
|
18.6
|
1.0
|
C18
|
A:JSE302
|
2.2
|
20.1
|
1.0
|
C19
|
A:JSE302
|
2.2
|
20.9
|
1.0
|
C17
|
A:JSE302
|
2.2
|
20.4
|
1.0
|
C13
|
A:JSE302
|
2.2
|
22.5
|
1.0
|
C12
|
A:JSE302
|
2.2
|
22.6
|
1.0
|
C20
|
A:JSE302
|
2.2
|
20.4
|
1.0
|
C14
|
A:JSE302
|
2.2
|
21.3
|
1.0
|
C16
|
A:JSE302
|
2.2
|
20.2
|
1.0
|
C11
|
A:JSE302
|
2.2
|
22.8
|
1.0
|
C15
|
A:JSE302
|
2.2
|
22.4
|
1.0
|
C24
|
A:JSE302
|
3.1
|
18.6
|
1.0
|
C25
|
A:JSE302
|
3.9
|
17.2
|
1.0
|
O28
|
A:JSE302
|
3.9
|
20.5
|
1.0
|
O
|
A:HOH513
|
4.5
|
35.5
|
1.0
|
O
|
A:HOH659
|
4.8
|
30.0
|
1.0
|
O
|
A:PRO167
|
4.8
|
12.2
|
1.0
|
CB
|
A:PRO167
|
4.9
|
13.2
|
1.0
|
O
|
A:HOH668
|
5.0
|
33.4
|
1.0
|
|
Ruthenium binding site 2 out
of 8 in 5top
Go back to
Ruthenium Binding Sites List in 5top
Ruthenium binding site 2 out
of 8 in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 2 of Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ru303
b:20.9
occ:0.25
|
O
|
A:HOH597
|
2.0
|
16.4
|
0.5
|
O
|
A:GLY143
|
4.7
|
16.8
|
1.0
|
N
|
A:GLY147
|
4.7
|
13.2
|
1.0
|
CA
|
A:GLY147
|
4.9
|
13.4
|
1.0
|
|
Ruthenium binding site 3 out
of 8 in 5top
Go back to
Ruthenium Binding Sites List in 5top
Ruthenium binding site 3 out
of 8 in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 3 of Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ru304
b:21.9
occ:0.25
|
RU
|
A:JSC304
|
0.0
|
21.9
|
0.2
|
RU
|
A:JSC304
|
0.1
|
21.3
|
0.2
|
C18
|
A:JSC304
|
2.1
|
20.9
|
0.2
|
C17
|
A:JSC304
|
2.1
|
21.2
|
0.2
|
C19
|
A:JSC304
|
2.1
|
21.2
|
0.2
|
C16
|
A:JSC304
|
2.2
|
21.2
|
0.2
|
C20
|
A:JSC304
|
2.2
|
21.5
|
0.2
|
C14
|
A:JSC304
|
2.2
|
22.2
|
0.2
|
C20
|
A:JSC304
|
2.2
|
22.2
|
0.2
|
C16
|
A:JSC304
|
2.2
|
21.7
|
0.2
|
C13
|
A:JSC304
|
2.2
|
22.2
|
0.2
|
C19
|
A:JSC304
|
2.2
|
22.0
|
0.2
|
C15
|
A:JSC304
|
2.2
|
22.2
|
0.2
|
C17
|
A:JSC304
|
2.2
|
22.0
|
0.2
|
C11
|
A:JSC304
|
2.2
|
22.1
|
0.2
|
C18
|
A:JSC304
|
2.2
|
22.0
|
0.2
|
C12
|
A:JSC304
|
2.2
|
22.2
|
0.2
|
C13
|
A:JSC304
|
2.2
|
21.9
|
0.2
|
C14
|
A:JSC304
|
2.2
|
22.0
|
0.2
|
C12
|
A:JSC304
|
2.3
|
22.0
|
0.2
|
C15
|
A:JSC304
|
2.3
|
21.9
|
0.2
|
C11
|
A:JSC304
|
2.3
|
21.8
|
0.2
|
C26
|
A:JSC304
|
2.9
|
21.0
|
0.2
|
C24
|
A:JSC304
|
3.1
|
20.3
|
0.2
|
C24
|
A:JSC304
|
3.3
|
21.7
|
0.2
|
C25
|
A:JSC304
|
3.6
|
21.1
|
0.2
|
O28
|
A:JSC304
|
3.8
|
20.4
|
0.2
|
C25
|
A:JSC304
|
3.9
|
19.5
|
0.2
|
C27
|
A:JSC304
|
4.0
|
21.3
|
0.2
|
O29
|
A:JSC304
|
4.0
|
22.6
|
0.2
|
O28
|
A:JSC304
|
4.3
|
21.9
|
0.2
|
O29
|
A:JSC304
|
4.8
|
17.8
|
0.2
|
O
|
A:HOH465
|
4.8
|
18.1
|
1.0
|
CD
|
A:LYS82
|
4.8
|
15.3
|
1.0
|
O67
|
A:JSC304
|
4.9
|
16.3
|
0.2
|
C27
|
A:JSC304
|
5.0
|
18.0
|
0.2
|
|
Ruthenium binding site 4 out
of 8 in 5top
Go back to
Ruthenium Binding Sites List in 5top
Ruthenium binding site 4 out
of 8 in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 4 of Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ru304
b:21.3
occ:0.25
|
RU
|
A:JSC304
|
0.0
|
21.3
|
0.2
|
RU
|
A:JSC304
|
0.1
|
21.9
|
0.2
|
C15
|
A:JSC304
|
2.1
|
22.2
|
0.2
|
C11
|
A:JSC304
|
2.1
|
22.1
|
0.2
|
C14
|
A:JSC304
|
2.1
|
22.2
|
0.2
|
C12
|
A:JSC304
|
2.2
|
22.2
|
0.2
|
C13
|
A:JSC304
|
2.2
|
22.2
|
0.2
|
C20
|
A:JSC304
|
2.2
|
21.5
|
0.2
|
C14
|
A:JSC304
|
2.2
|
22.0
|
0.2
|
C15
|
A:JSC304
|
2.2
|
21.9
|
0.2
|
C16
|
A:JSC304
|
2.2
|
21.2
|
0.2
|
C18
|
A:JSC304
|
2.2
|
20.9
|
0.2
|
C17
|
A:JSC304
|
2.2
|
21.2
|
0.2
|
C20
|
A:JSC304
|
2.2
|
22.2
|
0.2
|
C11
|
A:JSC304
|
2.2
|
21.8
|
0.2
|
C13
|
A:JSC304
|
2.2
|
21.9
|
0.2
|
C12
|
A:JSC304
|
2.2
|
22.0
|
0.2
|
C19
|
A:JSC304
|
2.2
|
21.2
|
0.2
|
C16
|
A:JSC304
|
2.2
|
21.7
|
0.2
|
C19
|
A:JSC304
|
2.3
|
22.0
|
0.2
|
C17
|
A:JSC304
|
2.3
|
22.0
|
0.2
|
C18
|
A:JSC304
|
2.3
|
22.0
|
0.2
|
C26
|
A:JSC304
|
3.0
|
21.0
|
0.2
|
C24
|
A:JSC304
|
3.3
|
20.3
|
0.2
|
C24
|
A:JSC304
|
3.4
|
21.7
|
0.2
|
C25
|
A:JSC304
|
3.7
|
21.1
|
0.2
|
O28
|
A:JSC304
|
3.9
|
20.4
|
0.2
|
C25
|
A:JSC304
|
4.1
|
19.5
|
0.2
|
C27
|
A:JSC304
|
4.1
|
21.3
|
0.2
|
O29
|
A:JSC304
|
4.1
|
22.6
|
0.2
|
O28
|
A:JSC304
|
4.5
|
21.9
|
0.2
|
O
|
A:HOH465
|
4.8
|
18.1
|
1.0
|
CD
|
A:LYS82
|
4.8
|
15.3
|
1.0
|
O29
|
A:JSC304
|
4.9
|
17.8
|
0.2
|
O67
|
A:JSC304
|
5.0
|
16.3
|
0.2
|
|
Ruthenium binding site 5 out
of 8 in 5top
Go back to
Ruthenium Binding Sites List in 5top
Ruthenium binding site 5 out
of 8 in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 5 of Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ru302
b:22.4
occ:1.00
|
RU
|
B:JSE302
|
0.0
|
22.4
|
1.0
|
C18
|
B:JSE302
|
2.2
|
22.6
|
1.0
|
C19
|
B:JSE302
|
2.2
|
23.4
|
1.0
|
C17
|
B:JSE302
|
2.2
|
23.8
|
1.0
|
C20
|
B:JSE302
|
2.2
|
24.0
|
1.0
|
C13
|
B:JSE302
|
2.2
|
25.2
|
1.0
|
C12
|
B:JSE302
|
2.2
|
26.7
|
1.0
|
C16
|
B:JSE302
|
2.2
|
23.4
|
1.0
|
C11
|
B:JSE302
|
2.2
|
26.0
|
1.0
|
C15
|
B:JSE302
|
2.2
|
25.6
|
1.0
|
C14
|
B:JSE302
|
2.2
|
25.4
|
1.0
|
C24
|
B:JSE302
|
3.2
|
21.0
|
1.0
|
C25
|
B:JSE302
|
4.0
|
19.0
|
1.0
|
O28
|
B:JSE302
|
4.0
|
23.9
|
1.0
|
O
|
B:PRO167
|
4.8
|
13.8
|
1.0
|
CB
|
B:PRO167
|
4.8
|
14.6
|
1.0
|
|
Ruthenium binding site 6 out
of 8 in 5top
Go back to
Ruthenium Binding Sites List in 5top
Ruthenium binding site 6 out
of 8 in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 6 of Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ru303
b:17.3
occ:0.50
|
RU
|
B:7G4303
|
0.0
|
17.3
|
0.5
|
C12
|
B:7G4303
|
2.2
|
17.8
|
0.5
|
C13
|
B:7G4303
|
2.2
|
17.1
|
0.5
|
C11
|
B:7G4303
|
2.2
|
17.8
|
0.5
|
C14
|
B:7G4303
|
2.2
|
16.7
|
0.5
|
C19
|
B:7G4303
|
2.2
|
19.3
|
0.5
|
C20
|
B:7G4303
|
2.2
|
18.7
|
0.5
|
C16
|
B:7G4303
|
2.2
|
19.1
|
0.5
|
C18
|
B:7G4303
|
2.2
|
19.1
|
0.5
|
C17
|
B:7G4303
|
2.2
|
19.2
|
0.5
|
C15
|
B:7G4303
|
2.2
|
17.0
|
0.5
|
CE1
|
B:TYR129
|
4.7
|
14.0
|
1.0
|
CB
|
B:ALA124
|
4.8
|
13.6
|
1.0
|
|
Ruthenium binding site 7 out
of 8 in 5top
Go back to
Ruthenium Binding Sites List in 5top
Ruthenium binding site 7 out
of 8 in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 7 of Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ru304
b:17.7
occ:0.25
|
O
|
B:HOH630
|
2.7
|
31.9
|
1.0
|
O
|
B:HOH552
|
3.5
|
22.8
|
1.0
|
CG
|
B:LYS82
|
4.5
|
14.2
|
1.0
|
|
Ruthenium binding site 8 out
of 8 in 5top
Go back to
Ruthenium Binding Sites List in 5top
Ruthenium binding site 8 out
of 8 in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase
Mono view
Stereo pair view
|
A full contact list of Ruthenium with other atoms in the Ru binding
site number 8 of Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 S70G Beta-Lactamase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ru305
b:16.2
occ:0.25
|
O
|
B:HOH690
|
2.0
|
38.9
|
1.0
|
O
|
B:HOH633
|
4.1
|
31.9
|
1.0
|
|
Reference:
E.M.Lewandowski,
K.G.Lethbridge,
R.Sanishvili,
J.Skiba,
K.Kowalski,
Y.Chen.
Mechanisms of Proton Relay and Product Release By Class A Beta-Lactamase at Ultrahigh Resolution. Febs J. V. 285 87 2018.
ISSN: ISSN 1742-4658
PubMed: 29095570
DOI: 10.1111/FEBS.14315
Page generated: Thu Oct 10 13:02:39 2024
|