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Ruthenium in PDB 5toy: X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase

Enzymatic activity of X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase

All present enzymatic activity of X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase:
3.5.2.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase, PDB code: 5toy 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) 53.39 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.012, 106.787, 47.759, 90.00, 101.76, 90.00
R / Rfree (%) 14.3 / 16.3

Other elements in 5toy:

The structure of X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products 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 X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase (pdb code 5toy). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 5 binding sites of Ruthenium where determined in the X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase, PDB code: 5toy:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5;

Ruthenium binding site 1 out of 5 in 5toy

Go back to Ruthenium Binding Sites List in 5toy
Ruthenium binding site 1 out of 5 in the X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products 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 X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru304

b:31.7
occ:0.25
 RU A:JSC304 0.0 31.7 0.2
RU A:JSD305 0.0 16.8 0.8
C17 A:JSC304 2.1 28.1 0.2
C17 A:JSD305 2.1 16.9 0.8
C13 A:JSC304 2.1 33.6 0.2
C13 A:JSD305 2.1 17.5 0.8
C14 A:JSC304 2.2 33.6 0.2
C14 A:JSD305 2.2 17.3 0.8
C18 A:JSC304 2.2 27.9 0.2
C18 A:JSD305 2.2 17.0 0.8
C16 A:JSC304 2.2 28.9 0.2
C16 A:JSD305 2.2 16.9 0.8
C20 A:JSC304 2.2 29.1 0.2
C20 A:JSD305 2.2 16.8 0.8
C12 A:JSD305 2.2 17.4 0.8
C12 A:JSC304 2.2 33.5 0.2
C15 A:JSD305 2.2 17.4 0.8
C15 A:JSC304 2.2 33.5 0.2
C19 A:JSC304 2.2 28.4 0.2
C19 A:JSD305 2.2 16.9 0.8
C11 A:JSC304 2.2 33.6 0.2
C11 A:JSD305 2.2 17.5 0.8
C24 A:JSC304 3.2 26.2 0.2
C24 A:JSD305 3.2 17.4 0.8
C25 A:JSC304 3.9 24.8 0.2
C25 A:JSD305 3.9 17.3 0.8
O28 A:JSC304 4.0 26.2 0.2
O28 A:JSD305 4.0 17.6 0.8
O A:HOH455 4.7 27.6 1.0
O A:PRO167 4.9 13.1 1.0
OD2 A:ASP240 4.9 14.7 1.0
CB A:PRO167 4.9 13.6 1.0
O A:HOH674 5.0 29.0 1.0

Ruthenium binding site 2 out of 5 in 5toy

Go back to Ruthenium Binding Sites List in 5toy
Ruthenium binding site 2 out of 5 in the X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products 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 X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru305

b:16.8
occ:0.75
 RU A:JSC304 0.0 31.7 0.2
RU A:JSD305 0.0 16.8 0.8
C17 A:JSC304 2.1 28.1 0.2
C17 A:JSD305 2.1 16.9 0.8
C13 A:JSC304 2.1 33.6 0.2
C13 A:JSD305 2.1 17.5 0.8
C14 A:JSC304 2.2 33.6 0.2
C14 A:JSD305 2.2 17.3 0.8
C18 A:JSC304 2.2 27.9 0.2
C18 A:JSD305 2.2 17.0 0.8
C16 A:JSC304 2.2 28.9 0.2
C16 A:JSD305 2.2 16.9 0.8
C20 A:JSC304 2.2 29.1 0.2
C20 A:JSD305 2.2 16.8 0.8
C12 A:JSD305 2.2 17.4 0.8
C12 A:JSC304 2.2 33.5 0.2
C15 A:JSD305 2.2 17.4 0.8
C15 A:JSC304 2.2 33.5 0.2
C19 A:JSC304 2.2 28.4 0.2
C19 A:JSD305 2.2 16.9 0.8
C11 A:JSC304 2.2 33.6 0.2
C11 A:JSD305 2.2 17.5 0.8
C24 A:JSC304 3.2 26.2 0.2
C24 A:JSD305 3.2 17.4 0.8
C25 A:JSC304 3.9 24.8 0.2
C25 A:JSD305 3.9 17.3 0.8
O28 A:JSC304 4.0 26.2 0.2
O28 A:JSD305 4.0 17.6 0.8
O A:HOH455 4.7 27.6 1.0
O A:PRO167 4.9 13.1 1.0
OD2 A:ASP240 4.9 14.7 1.0
CB A:PRO167 4.9 13.6 1.0
O A:HOH674 5.0 29.0 1.0

Ruthenium binding site 3 out of 5 in 5toy

Go back to Ruthenium Binding Sites List in 5toy
Ruthenium binding site 3 out of 5 in the X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products 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 X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru304

b:27.0
occ:0.25
 RU B:JSC304 0.0 27.0 0.2
RU B:JSD306 0.0 18.1 0.8
C13 B:JSD306 2.2 18.3 0.8
C11 B:JSC304 2.2 27.9 0.2
C18 B:JSD306 2.2 18.3 0.8
C18 B:JSC304 2.2 24.5 0.2
C19 B:JSC304 2.2 24.7 0.2
C19 B:JSD306 2.2 18.1 0.8
C12 B:JSD306 2.2 18.5 0.8
C15 B:JSC304 2.2 28.0 0.2
C17 B:JSC304 2.2 25.1 0.2
C17 B:JSD306 2.2 18.4 0.8
C14 B:JSC304 2.2 28.0 0.2
C11 B:JSD306 2.2 18.5 0.8
C14 B:JSD306 2.2 18.5 0.8
C12 B:JSC304 2.2 28.0 0.2
C20 B:JSC304 2.2 25.2 0.2
C20 B:JSD306 2.2 18.1 0.8
C13 B:JSC304 2.2 28.1 0.2
C15 B:JSD306 2.2 18.7 0.8
C16 B:JSC304 2.2 25.3 0.2
C16 B:JSD306 2.2 18.2 0.8
C24 B:JSC304 3.2 22.9 0.2
C24 B:JSD306 3.2 18.4 0.8
C25 B:JSC304 3.9 21.7 0.2
C25 B:JSD306 3.9 18.3 0.8
O28 B:JSC304 3.9 22.6 0.2
O28 B:JSD306 3.9 18.6 0.8
O B:PRO167 4.9 14.4 1.0
CB B:PRO167 4.9 15.1 1.0
OD2 B:ASP240 5.0 17.3 1.0

Ruthenium binding site 4 out of 5 in 5toy

Go back to Ruthenium Binding Sites List in 5toy
Ruthenium binding site 4 out of 5 in the X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products 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 X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru305

b:23.1
occ:0.50
 O B:HOH693 2.0 41.6 1.0
O B:HOH666 2.4 30.9 1.0
O B:HOH643 2.4 23.1 1.0
O B:HOH671 2.4 34.2 1.0
O B:HOH548 2.7 23.8 1.0
O B:HOH681 2.8 32.2 1.0
O B:HOH430 4.7 32.3 1.0
CE1 B:TYR129 4.7 12.9 1.0
CB B:ALA124 5.0 11.8 1.0

Ruthenium binding site 5 out of 5 in 5toy

Go back to Ruthenium Binding Sites List in 5toy
Ruthenium binding site 5 out of 5 in the X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products 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 X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru306

b:18.1
occ:0.75
 RU B:JSC304 0.0 27.0 0.2
RU B:JSD306 0.0 18.1 0.8
C13 B:JSD306 2.2 18.3 0.8
C11 B:JSC304 2.2 27.9 0.2
C18 B:JSD306 2.2 18.3 0.8
C18 B:JSC304 2.2 24.5 0.2
C19 B:JSC304 2.2 24.7 0.2
C19 B:JSD306 2.2 18.1 0.8
C12 B:JSD306 2.2 18.5 0.8
C15 B:JSC304 2.2 28.0 0.2
C17 B:JSC304 2.2 25.1 0.2
C17 B:JSD306 2.2 18.4 0.8
C14 B:JSC304 2.2 28.0 0.2
C11 B:JSD306 2.2 18.5 0.8
C14 B:JSD306 2.2 18.5 0.8
C12 B:JSC304 2.2 28.0 0.2
C20 B:JSC304 2.2 25.2 0.2
C20 B:JSD306 2.2 18.1 0.8
C13 B:JSC304 2.2 28.1 0.2
C15 B:JSD306 2.2 18.7 0.8
C16 B:JSC304 2.2 25.3 0.2
C16 B:JSD306 2.2 18.2 0.8
C24 B:JSC304 3.2 22.9 0.2
C24 B:JSD306 3.2 18.4 0.8
C25 B:JSC304 3.9 21.7 0.2
C25 B:JSD306 3.9 18.3 0.8
O28 B:JSC304 3.9 22.6 0.2
O28 B:JSD306 3.9 18.6 0.8
O B:PRO167 4.9 14.4 1.0
CB B:PRO167 4.9 15.1 1.0
OD2 B:ASP240 5.0 17.3 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 13:02:55 2024

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