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Ruthenium in PDB 6vnu: X-Ray Crystal Structure of Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme Complex with Ctx-M-14 E166A Beta-Lactamase

Enzymatic activity of X-Ray Crystal Structure of Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme Complex with Ctx-M-14 E166A Beta-Lactamase

All present enzymatic activity of X-Ray Crystal Structure of Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme Complex with Ctx-M-14 E166A Beta-Lactamase:
3.5.2.6;

Protein crystallography data

The structure of X-Ray Crystal Structure of Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme Complex with Ctx-M-14 E166A Beta-Lactamase, PDB code: 6vnu was solved by E.M.Lewandowski, L.M.C.Jacobs, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.16 / 1.47
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.152, 106.894, 47.908, 90.00, 101.68, 90.00
R / Rfree (%) 17.3 / 21.8

Other elements in 6vnu:

The structure of X-Ray Crystal Structure of Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme 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 Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme Complex with Ctx-M-14 E166A Beta-Lactamase (pdb code 6vnu). 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 Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme Complex with Ctx-M-14 E166A Beta-Lactamase, PDB code: 6vnu:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5;

Ruthenium binding site 1 out of 5 in 6vnu

Go back to Ruthenium Binding Sites List in 6vnu
Ruthenium binding site 1 out of 5 in the X-Ray Crystal Structure of Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme 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 Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru301

b:26.8
occ:0.50
 RU A:7G4301 0.0 26.8 0.5
C16 A:7G4301 2.2 24.9 0.5
C17 A:7G4301 2.2 24.9 0.5
C14 A:7G4301 2.2 26.2 0.5
C20 A:7G4301 2.2 26.9 0.5
C12 A:7G4301 2.2 26.8 0.5
C15 A:7G4301 2.2 26.7 0.5
C13 A:7G4301 2.2 24.6 0.5
C18 A:7G4301 2.2 22.2 0.5
C11 A:7G4301 2.2 26.1 0.5
C19 A:7G4301 2.2 24.9 0.5
CB A:ALA124 4.7 11.2 1.0
O A:HOH537 4.7 35.7 1.0
CE1 A:TYR129 4.8 13.3 1.0

Ruthenium binding site 2 out of 5 in 6vnu

Go back to Ruthenium Binding Sites List in 6vnu
Ruthenium binding site 2 out of 5 in the X-Ray Crystal Structure of Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme 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 Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru302

b:23.6
occ:0.50
 RU A:7G4302 0.0 23.6 0.5
C11 A:7G4302 2.2 21.7 0.5
C12 A:7G4302 2.2 21.1 0.5
C18 A:7G4302 2.2 20.5 0.5
C19 A:7G4302 2.2 20.2 0.5
C20 A:7G4302 2.2 20.7 0.5
C17 A:7G4302 2.2 20.9 0.5
C15 A:7G4302 2.2 21.0 0.5
C16 A:7G4302 2.2 21.2 0.5
C13 A:7G4302 2.2 22.3 0.5
C14 A:7G4302 2.2 22.2 0.5
O A:HOH620 4.0 28.0 1.0
NE2 A:GLN83 4.5 15.3 1.0
CG A:GLN83 4.6 12.6 1.0

Ruthenium binding site 3 out of 5 in 6vnu

Go back to Ruthenium Binding Sites List in 6vnu
Ruthenium binding site 3 out of 5 in the X-Ray Crystal Structure of Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme 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 Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru303

b:23.0
occ:0.75
 RU A:TDJ303 0.0 23.0 0.8
C18 A:TDJ303 2.2 22.7 0.8
C19 A:TDJ303 2.2 23.8 0.8
C17 A:TDJ303 2.2 22.7 0.8
C12 A:TDJ303 2.2 27.2 0.8
C13 A:TDJ303 2.2 24.7 0.8
C14 A:TDJ303 2.2 25.4 0.8
C20 A:TDJ303 2.2 22.8 0.8
C16 A:TDJ303 2.2 22.8 0.8
C11 A:TDJ303 2.2 25.3 0.8
C15 A:TDJ303 2.2 26.7 0.8
C24 A:TDJ303 3.2 24.1 0.8
C25 A:TDJ303 3.9 20.7 0.8
O28 A:TDJ303 4.0 23.0 0.8
OD2 A:ASP240 4.6 23.3 1.0
O A:PRO167 4.8 13.0 1.0
O A:HOH428 4.8 40.6 1.0
CB A:PRO167 4.9 14.9 1.0
CG A:ASP240 5.0 19.7 1.0

Ruthenium binding site 4 out of 5 in 6vnu

Go back to Ruthenium Binding Sites List in 6vnu
Ruthenium binding site 4 out of 5 in the X-Ray Crystal Structure of Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme 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 Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru301

b:21.5
occ:0.50
 RU B:7G4301 0.0 21.5 0.5
C17 B:7G4301 2.2 22.4 0.5
C20 B:7G4301 2.2 22.7 0.5
C12 B:7G4301 2.2 22.4 0.5
C13 B:7G4301 2.2 22.0 0.5
C18 B:7G4301 2.2 22.8 0.5
C14 B:7G4301 2.2 21.5 0.5
C11 B:7G4301 2.2 21.9 0.5
C19 B:7G4301 2.2 23.0 0.5
C15 B:7G4301 2.2 22.1 0.5
C16 B:7G4301 2.2 22.0 0.5
CE1 B:TYR129 4.8 14.6 1.0
CB B:ALA124 4.8 11.2 1.0
O B:HOH416 4.9 28.7 1.0

Ruthenium binding site 5 out of 5 in 6vnu

Go back to Ruthenium Binding Sites List in 6vnu
Ruthenium binding site 5 out of 5 in the X-Ray Crystal Structure of Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme 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 Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru302

b:42.3
occ:0.75
 RU B:TDJ302 0.0 42.3 0.8
C19 B:TDJ302 2.2 40.6 0.8
C18 B:TDJ302 2.2 41.8 0.8
C17 B:TDJ302 2.2 42.4 0.8
C15 B:TDJ302 2.2 44.1 0.8
C14 B:TDJ302 2.2 41.4 0.8
C13 B:TDJ302 2.2 40.8 0.8
C11 B:TDJ302 2.2 44.7 0.8
C12 B:TDJ302 2.2 41.2 0.8
C20 B:TDJ302 2.2 39.4 0.8
C16 B:TDJ302 2.2 39.5 0.8
C24 B:TDJ302 3.2 37.9 0.8
O28 B:TDJ302 4.0 38.4 0.8
C25 B:TDJ302 4.0 34.6 0.8
OD2 B:ASP240 4.1 29.0 1.0
O B:PRO167 4.7 14.6 1.0
CG B:ASP240 4.8 27.0 1.0
CB B:PRO167 4.8 16.2 1.0
OD1 B:ASP240 4.9 35.0 1.0

Reference:

E.M.Lewandowski, L.Szczupak, A.Kowalczyk, G.Mendoza, M.Arruebo, L.M.C.Jacobs, P.Staczek, Y.Chen, K.Kowalski. Metallocenyl 7-Aca Conjugates: Antibacterial Activity Studies and Atomic-Resolution X-Ray Crystal Structure with Ctx-M Beta-Lactamase. Chembiochem 2020.
ISSN: ESSN 1439-7633
PubMed: 32182393
DOI: 10.1002/CBIC.202000054
Page generated: Thu Oct 10 13:08:45 2024

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