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Ruthenium in PDB 4xxr: Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 E166A Beta-Lactamase

Enzymatic activity of Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 E166A 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 E166A 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 E166A Beta-Lactamase, PDB code: 4xxr 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) 46.92 / 1.18
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.899, 106.775, 47.903, 90.00, 101.87, 90.00
R / Rfree (%) 12.5 / 15.3

Other elements in 4xxr:

The structure of Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 E166A Beta-Lactamase also contains other interesting chemical elements:

Potassium (K) 2 atoms

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 E166A Beta-Lactamase (pdb code 4xxr). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 6 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 E166A Beta-Lactamase, PDB code: 4xxr:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5; 6;

Ruthenium binding site 1 out of 6 in 4xxr

Go back to Ruthenium Binding Sites List in 4xxr
Ruthenium binding site 1 out of 6 in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 E166A 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 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru302

b:11.4
occ:1.00
RU A:JSD302 0.0 11.4 1.0
C18 A:JSD302 2.2 12.0 1.0
C17 A:JSD302 2.2 11.8 1.0
C14 A:JSD302 2.2 18.1 1.0
C19 A:JSD302 2.2 13.8 1.0
C13 A:JSD302 2.2 25.9 1.0
C12 A:JSD302 2.2 23.0 1.0
C20 A:JSD302 2.2 13.7 1.0
C15 A:JSD302 2.2 15.6 1.0
C16 A:JSD302 2.2 11.1 1.0
C11 A:JSD302 2.2 20.1 1.0
C24 A:JSD302 3.1 14.3 1.0
C25 A:JSD302 3.8 11.6 1.0
O28 A:JSD302 3.9 13.9 1.0
O A:HOH438 4.5 39.0 1.0
O A:HOH526 4.7 24.0 1.0
CB A:PRO167 4.9 8.2 1.0
O A:PRO167 4.9 5.9 1.0

Ruthenium binding site 2 out of 6 in 4xxr

Go back to Ruthenium Binding Sites List in 4xxr
Ruthenium binding site 2 out of 6 in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 E166A 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 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru303

b:15.2
occ:1.00
RU A:JSC303 0.0 15.2 1.0
C18 A:JSC303 2.2 16.0 1.0
C20 A:JSC303 2.2 16.3 1.0
C15 A:JSC303 2.2 18.1 1.0
C12 A:JSC303 2.2 22.0 1.0
C19 A:JSC303 2.2 14.1 1.0
C11 A:JSC303 2.2 17.4 1.0
C14 A:JSC303 2.2 20.8 1.0
C13 A:JSC303 2.2 22.8 1.0
C17 A:JSC303 2.2 15.7 1.0
C16 A:JSC303 2.2 21.5 1.0
C24 A:JSC303 3.2 15.8 1.0
O28 A:JSC303 3.8 17.5 1.0
C25 A:JSC303 4.0 15.1 1.0
O A:HOH432 4.7 12.9 1.0
O29 A:JSC303 4.8 18.5 1.0
CD A:LYS82 4.8 9.0 1.0
O38 A:JSC303 4.9 15.2 1.0

Ruthenium binding site 3 out of 6 in 4xxr

Go back to Ruthenium Binding Sites List in 4xxr
Ruthenium binding site 3 out of 6 in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 E166A 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 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru304

b:11.6
occ:0.70
RU A:JSE304 0.0 11.6 0.7
C18 A:JSE304 2.2 10.0 0.7
C14 A:JSE304 2.2 16.6 0.7
C20 A:JSE304 2.2 15.2 0.7
C15 A:JSE304 2.2 14.3 0.7
C19 A:JSE304 2.2 12.8 0.7
C13 A:JSE304 2.2 14.3 0.7
C12 A:JSE304 2.2 13.9 0.7
C17 A:JSE304 2.2 11.0 0.7
C11 A:JSE304 2.2 15.3 0.7
C16 A:JSE304 2.2 13.5 0.7
C24 A:JSE304 3.2 10.7 0.7
C25 A:JSE304 3.9 10.1 0.7
O28 A:JSE304 3.9 12.5 0.7
C20 A:JSC305 4.3 11.2 0.3
NH1 A:ARG191 4.8 7.8 0.3
O A:HOH577 4.8 19.4 1.0
CZ A:ARG191 5.0 10.9 0.3

Ruthenium binding site 4 out of 6 in 4xxr

Go back to Ruthenium Binding Sites List in 4xxr
Ruthenium binding site 4 out of 6 in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 E166A 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 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru305

b:6.0
occ:0.30
RU A:JSC305 0.0 6.0 0.3
C17 A:JSC305 2.2 6.6 0.3
C19 A:JSC305 2.2 8.1 0.3
C20 A:JSC305 2.2 11.2 0.3
C12 A:JSC305 2.2 11.2 0.3
C15 A:JSC305 2.2 67.4 0.3
C14 A:JSC305 2.2 21.1 0.3
C18 A:JSC305 2.2 7.8 0.3
C11 A:JSC305 2.2 12.3 0.3
C13 A:JSC305 2.2 12.6 0.3
C16 A:JSC305 2.2 9.8 0.3
C13 A:JSE304 4.4 14.3 0.7
ND2 A:ASN54 4.4 27.4 0.3

Ruthenium binding site 5 out of 6 in 4xxr

Go back to Ruthenium Binding Sites List in 4xxr
Ruthenium binding site 5 out of 6 in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 E166A 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 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru302

b:12.3
occ:1.00
RU B:JSD302 0.0 12.3 1.0
C18 B:JSD302 2.2 13.6 1.0
C12 B:JSD302 2.2 23.4 1.0
C13 B:JSD302 2.2 19.1 1.0
C15 B:JSD302 2.2 17.9 1.0
C19 B:JSD302 2.2 14.2 1.0
C20 B:JSD302 2.2 14.0 1.0
C17 B:JSD302 2.2 12.5 1.0
C14 B:JSD302 2.2 16.5 1.0
C11 B:JSD302 2.2 19.7 1.0
C16 B:JSD302 2.2 13.2 1.0
C24 B:JSD302 3.2 14.7 1.0
C25 B:JSD302 3.8 12.6 1.0
O28 B:JSD302 3.9 16.6 1.0
O B:HOH549 4.4 28.2 1.0
O B:HOH459 4.4 37.1 1.0
CB B:PRO167 4.8 9.2 1.0
O B:PRO167 4.9 7.6 1.0

Ruthenium binding site 6 out of 6 in 4xxr

Go back to Ruthenium Binding Sites List in 4xxr
Ruthenium binding site 6 out of 6 in the Atomic Resolution X-Ray Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with Ctx-M-14 E166A 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 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru303

b:16.8
occ:1.00
RU B:JSC303 0.0 16.8 1.0
C12 B:JSC303 2.2 25.2 1.0
C11 B:JSC303 2.2 18.0 1.0
C20 B:JSC303 2.2 44.0 1.0
C13 B:JSC303 2.2 19.0 1.0
C15 B:JSC303 2.2 16.4 1.0
C19 B:JSC303 2.2 34.8 1.0
C17 B:JSC303 2.2 23.8 1.0
C14 B:JSC303 2.2 14.4 1.0
C18 B:JSC303 2.2 21.4 1.0
C16 B:JSC303 2.2 36.7 1.0
CE1 B:TYR129 4.8 6.5 1.0
CB B:ALA124 4.9 7.2 1.0

Reference:

E.M.Lewandowski, J.Skiba, N.J.Torelli, A.Rajnisz, J.Solecka, K.Kowalski, Y.Chen. Antibacterial Properties and Atomic Resolution X-Ray Complex Crystal Structure of A Ruthenocene Conjugated Beta-Lactam Antibiotic. Chem.Commun.(Camb.) 2015.
ISSN: ESSN 1364-548X
PubMed: 25753149
DOI: 10.1039/C5CC00904A
Page generated: Wed Dec 16 02:08:26 2020

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