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Ruthenium in PDB 5ujo: X-Ray Crystal Structure of Ruthenocenyl-7- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme Complex with Ctx-M-14 E166A Beta-Lactamase

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

All present enzymatic activity of X-Ray Crystal Structure of Ruthenocenyl-7- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme 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- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme Complex with Ctx-M-14 E166A Beta-Lactamase, PDB code: 5ujo 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) 53.68 / 1.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.961, 107.351, 47.956, 90.00, 101.36, 90.00
R / Rfree (%) 12.5 / 15

Other elements in 5ujo:

The structure of X-Ray Crystal Structure of Ruthenocenyl-7- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme 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- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme Complex with Ctx-M-14 E166A Beta-Lactamase (pdb code 5ujo). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 6 binding sites of Ruthenium where determined in the X-Ray Crystal Structure of Ruthenocenyl-7- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme Complex with Ctx-M-14 E166A Beta-Lactamase, PDB code: 5ujo:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5; 6;

Ruthenium binding site 1 out of 6 in 5ujo

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Ruthenium binding site 1 out of 6 in the X-Ray Crystal Structure of Ruthenocenyl-7- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme 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- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru302

b:18.2
occ:0.60
 RU A:8CY302 0.0 18.2 0.6
RU A:8CY302 0.0 18.7 0.4
C11 A:8CY302 2.2 20.1 0.4
C19 A:8CY302 2.2 16.7 0.4
C15 A:8CY302 2.2 18.1 0.4
C12 A:8CY302 2.2 19.9 0.4
C19 A:8CY302 2.2 19.0 0.6
C18 A:8CY302 2.2 17.0 0.6
C18 A:8CY302 2.2 16.6 0.4
C15 A:8CY302 2.2 18.6 0.6
C12 A:8CY302 2.2 19.1 0.6
C14 A:8CY302 2.2 19.2 0.6
C13 A:8CY302 2.2 17.9 0.6
C11 A:8CY302 2.2 20.6 0.6
C16 A:8CY302 2.2 18.3 0.6
C20 A:8CY302 2.2 20.2 0.6
C17 A:8CY302 2.2 16.9 0.6
C14 A:8CY302 2.2 21.1 0.4
C20 A:8CY302 2.2 17.6 0.4
C13 A:8CY302 2.2 19.4 0.4
C16 A:8CY302 2.2 18.2 0.4
C17 A:8CY302 2.2 17.5 0.4
C24 A:8CY302 3.1 15.7 0.4
C24 A:8CY302 3.2 17.3 0.6
O28 A:8CY302 3.9 18.8 0.6
C25 A:8CY302 3.9 15.7 0.6
O28 A:8CY302 3.9 17.0 0.4
C25 A:8CY302 3.9 14.2 0.4
O A:HOH544 4.7 60.3 1.0
OD2 A:ASP240 5.0 15.7 1.0
O A:PRO167 5.0 11.8 1.0

Ruthenium binding site 2 out of 6 in 5ujo

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Ruthenium binding site 2 out of 6 in the X-Ray Crystal Structure of Ruthenocenyl-7- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme 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- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru302

b:18.7
occ:0.40
 RU A:8CY302 0.0 18.7 0.4
RU A:8CY302 0.0 18.2 0.6
C13 A:8CY302 2.2 17.9 0.6
C12 A:8CY302 2.2 19.1 0.6
C14 A:8CY302 2.2 19.2 0.6
C19 A:8CY302 2.2 16.7 0.4
C11 A:8CY302 2.2 20.6 0.6
C18 A:8CY302 2.2 16.6 0.4
C15 A:8CY302 2.2 18.1 0.4
C11 A:8CY302 2.2 20.1 0.4
C14 A:8CY302 2.2 21.1 0.4
C16 A:8CY302 2.2 18.2 0.4
C13 A:8CY302 2.2 19.4 0.4
C12 A:8CY302 2.2 19.9 0.4
C15 A:8CY302 2.2 18.6 0.6
C17 A:8CY302 2.2 17.5 0.4
C20 A:8CY302 2.2 17.6 0.4
C17 A:8CY302 2.2 16.9 0.6
C18 A:8CY302 2.2 17.0 0.6
C16 A:8CY302 2.2 18.3 0.6
C19 A:8CY302 2.2 19.0 0.6
C20 A:8CY302 2.2 20.2 0.6
C24 A:8CY302 3.1 15.7 0.4
C24 A:8CY302 3.2 17.3 0.6
C25 A:8CY302 3.9 15.7 0.6
O28 A:8CY302 3.9 18.8 0.6
C25 A:8CY302 3.9 14.2 0.4
O28 A:8CY302 3.9 17.0 0.4
O A:HOH544 4.7 60.3 1.0
O A:PRO167 4.9 11.8 1.0
OD2 A:ASP240 5.0 15.7 1.0
CB A:PRO167 5.0 15.9 1.0

Ruthenium binding site 3 out of 6 in 5ujo

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Ruthenium binding site 3 out of 6 in the X-Ray Crystal Structure of Ruthenocenyl-7- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme 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- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru303

b:18.4
occ:0.50
 RU A:LSI303 0.0 18.4 0.5
C20 A:LSI303 2.2 17.9 0.5
C16 A:LSI303 2.2 18.6 0.5
C14 A:LSI303 2.2 21.8 0.5
C15 A:LSI303 2.2 22.4 0.5
C19 A:LSI303 2.2 17.1 0.5
C17 A:LSI303 2.2 14.7 0.5
C13 A:LSI303 2.2 19.9 0.5
C18 A:LSI303 2.2 15.2 0.5
C11 A:LSI303 2.2 21.0 0.5
C12 A:LSI303 2.2 20.7 0.5
CB A:ALA124 4.7 11.3 1.0
CE1 A:TYR129 4.7 14.5 1.0

Ruthenium binding site 4 out of 6 in 5ujo

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Ruthenium binding site 4 out of 6 in the X-Ray Crystal Structure of Ruthenocenyl-7- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme 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- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru302

b:22.2
occ:0.50
 RU B:8CY302 0.0 22.2 0.5
RU B:8CY302 0.1 20.3 0.5
C15 B:8CY302 2.1 19.4 0.5
C20 B:8CY302 2.1 17.7 0.5
C14 B:8CY302 2.1 20.0 0.5
C19 B:8CY302 2.2 16.7 0.5
C19 B:8CY302 2.2 19.1 0.5
C18 B:8CY302 2.2 19.1 0.5
C16 B:8CY302 2.2 16.7 0.5
C11 B:8CY302 2.2 22.2 0.5
C15 B:8CY302 2.2 22.9 0.5
C14 B:8CY302 2.2 21.1 0.5
C11 B:8CY302 2.2 22.6 0.5
C16 B:8CY302 2.2 20.0 0.5
C17 B:8CY302 2.2 20.1 0.5
C13 B:8CY302 2.2 20.1 0.5
C20 B:8CY302 2.2 18.6 0.5
C12 B:8CY302 2.2 20.6 0.5
C13 B:8CY302 2.2 20.4 0.5
C18 B:8CY302 2.2 15.5 0.5
C12 B:8CY302 2.2 18.9 0.5
C17 B:8CY302 2.3 17.3 0.5
C24 B:8CY302 3.1 18.0 0.5
C24 B:8CY302 3.2 16.3 0.5
O28 B:8CY302 3.8 21.5 0.5
O28 B:8CY302 3.9 19.4 0.5
C25 B:8CY302 3.9 15.1 0.5
C25 B:8CY302 4.0 16.2 0.5
O B:HOH439 4.4 57.8 1.0
OD2 B:ASP240 5.0 17.3 1.0
CB B:PRO167 5.0 16.2 1.0
O B:PRO167 5.0 12.9 1.0

Ruthenium binding site 5 out of 6 in 5ujo

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Ruthenium binding site 5 out of 6 in the X-Ray Crystal Structure of Ruthenocenyl-7- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme 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- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru302

b:20.3
occ:0.50
 RU B:8CY302 0.0 20.3 0.5
RU B:8CY302 0.1 22.2 0.5
C19 B:8CY302 2.1 19.1 0.5
C18 B:8CY302 2.1 19.1 0.5
C12 B:8CY302 2.2 20.6 0.5
C20 B:8CY302 2.2 18.6 0.5
C11 B:8CY302 2.2 22.6 0.5
C19 B:8CY302 2.2 16.7 0.5
C13 B:8CY302 2.2 20.4 0.5
C18 B:8CY302 2.2 15.5 0.5
C14 B:8CY302 2.2 20.0 0.5
C11 B:8CY302 2.2 22.2 0.5
C16 B:8CY302 2.2 16.7 0.5
C12 B:8CY302 2.2 18.9 0.5
C15 B:8CY302 2.2 19.4 0.5
C13 B:8CY302 2.2 20.1 0.5
C17 B:8CY302 2.2 17.3 0.5
C20 B:8CY302 2.2 17.7 0.5
C17 B:8CY302 2.2 20.1 0.5
C16 B:8CY302 2.2 20.0 0.5
C15 B:8CY302 2.3 22.9 0.5
C14 B:8CY302 2.3 21.1 0.5
C24 B:8CY302 3.0 18.0 0.5
C24 B:8CY302 3.2 16.3 0.5
O28 B:8CY302 3.8 21.5 0.5
O28 B:8CY302 3.8 19.4 0.5
C25 B:8CY302 3.9 15.1 0.5
C25 B:8CY302 3.9 16.2 0.5
O B:HOH439 4.5 57.8 1.0
CB B:PRO167 4.9 16.2 1.0
O B:PRO167 4.9 12.9 1.0

Ruthenium binding site 6 out of 6 in 5ujo

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Ruthenium binding site 6 out of 6 in the X-Ray Crystal Structure of Ruthenocenyl-7- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme 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 6 of X-Ray Crystal Structure of Ruthenocenyl-7- Aminodesacetoxycephalosporanic Acid Covalent Acyl-Enyzme Complex with Ctx-M-14 E166A Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru303

b:21.1
occ:0.50
 RU B:LSI303 0.0 21.1 0.5
C15 B:LSI303 2.2 21.2 0.5
C18 B:LSI303 2.2 22.8 0.5
C17 B:LSI303 2.2 22.7 0.5
C14 B:LSI303 2.2 20.9 0.5
C11 B:LSI303 2.2 21.9 0.5
C13 B:LSI303 2.2 22.2 0.5
C16 B:LSI303 2.2 23.2 0.5
C19 B:LSI303 2.2 22.9 0.5
C20 B:LSI303 2.2 22.6 0.5
C12 B:LSI303 2.2 21.1 0.5
C24 B:LSI303 3.2 22.0 0.5
O28 B:LSI303 3.7 24.4 0.5
C25 B:LSI303 4.0 21.2 0.5
O B:HOH658 4.1 40.9 1.0
O29 B:LSI303 4.5 20.4 0.5
O B:HOH531 4.6 28.5 1.0
NE B:ARG65 4.7 21.1 1.0
C27 B:LSI303 4.9 20.4 0.5
CD B:ARG65 4.9 19.8 1.0
CB B:PRO177 5.0 15.8 1.0

Reference:

E.M.Lewandowski, L.Szczupak, S.Wong, J.Skiba, A.Guspiel, J.Solecka, V.Vrcek, K.Kowalski, Y.Chen. Antibacterial Properties of Metallocenyl-7-Adca Derivatives and Structure in Complex with Ctx-Mbeta-Lactamase. Organometallics V. 36 1673 2017.
ISSN: ISSN 0276-7333
PubMed: 29051683
DOI: 10.1021/ACS.ORGANOMET.6B00888
Page generated: Thu Oct 10 13:02:58 2024

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