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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:

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 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

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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

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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

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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

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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

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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

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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

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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

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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

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