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

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy