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Potassium 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:

Ruthenium (Ru) 5 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 2 binding sites of Potassium 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 Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6vnu

Go back to Potassium Binding Sites List in 6vnu
Potassium binding site 1 out of 2 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 Potassium with other atoms in the K 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:K304

b:20.4
occ:1.00
O A:HOH566 2.4 32.8 1.0
O A:HOH512 2.7 18.0 1.0
O A:GLY238 2.7 13.0 1.0
O A:HOH402 2.8 35.4 1.0
O A:HOH473 2.9 23.2 1.0
O A:HOH480 2.9 13.0 1.0
C A:GLY238 3.6 12.4 1.0
O A:ALA272 4.1 14.9 1.0
N A:ASP240 4.3 11.7 1.0
CA A:ASP240 4.3 11.7 1.0
CA A:GLY242 4.4 10.5 1.0
N A:GLY238 4.4 11.6 1.0
N A:GLY242 4.4 10.5 1.0
CA A:GLY238 4.4 12.4 1.0
O28 A:TDJ303 4.6 23.0 0.8
OG A:SER274 4.6 17.4 0.7
C A:ASP240 4.8 11.0 1.0
N A:THR243 4.8 10.3 1.0
O A:HOH464 4.9 34.8 1.0
C A:GLY242 4.9 10.6 1.0
OD1 A:ASP240 5.0 23.6 1.0
O A:HOH586 5.0 31.2 1.0

Potassium binding site 2 out of 2 in 6vnu

Go back to Potassium Binding Sites List in 6vnu
Potassium binding site 2 out of 2 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 Potassium with other atoms in the K 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
B:K303

b:26.9
occ:1.00
O B:HOH583 2.5 28.3 1.0
O B:HOH561 2.6 25.8 1.0
O B:HOH463 2.7 27.9 1.0
O B:GLY238 2.7 15.6 1.0
O B:HOH449 2.8 15.9 1.0
O B:HOH549 3.0 21.4 0.5
C B:GLY238 3.6 13.7 1.0
O B:ALA272 4.0 18.4 1.0
N B:ASP240 4.3 17.1 1.0
CA B:ASP240 4.3 18.3 1.0
CA B:GLY242 4.4 12.3 1.0
CA B:GLY238 4.5 14.2 1.0
O28 B:TDJ302 4.5 38.4 0.8
N B:GLY242 4.5 12.2 1.0
N B:GLY238 4.5 13.1 1.0
OG B:SER274 4.5 26.0 1.0
O B:HOH420 4.7 41.4 1.0
C B:ASP240 4.8 15.6 1.0
N B:THR243 5.0 12.5 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: Mon Dec 14 02:07:50 2020

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