Atomistry » Ruthenium » PDB 5iu5-6bo1 » 5top
Atomistry »
  Ruthenium »
    PDB 5iu5-6bo1 »
      5top »

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

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: Wed Dec 16 02:08:40 2020

Last articles

Zn in 7RRP
Zn in 7OKY
Zn in 7OL0
Zn in 7OKX
Zn in 7ONB
Zn in 7RSF
Zn in 7OUF
Zn in 7OUG
Zn in 7OUH
Zn in 7RGN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy