Zinc in PDB 7k99: Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor 19

Enzymatic activity of Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor 19

All present enzymatic activity of Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor 19:
3.5.1.108;

Protein crystallography data

The structure of Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor 19, PDB code: 7k99 was solved by M.Sacco, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.51 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.763, 158.047, 49.072, 90.00, 101.90, 90.00
R / Rfree (%) 16.6 / 22.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor 19 (pdb code 7k99). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor 19, PDB code: 7k99:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7k99

Go back to Zinc Binding Sites List in 7k99
Zinc binding site 1 out of 2 in the Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor 19


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:14.8
occ:1.00
OD1 A:ASP241 2.0 12.1 1.0
NE2 A:HIS78 2.1 12.5 1.0
O30 A:W4M402 2.1 21.9 1.0
NE2 A:HIS237 2.1 14.0 1.0
O32 A:W4M402 2.3 20.7 1.0
CG A:ASP241 2.7 12.3 1.0
OD2 A:ASP241 2.8 12.8 1.0
N29 A:W4M402 3.0 20.5 1.0
CE1 A:HIS78 3.0 12.7 1.0
C31 A:W4M402 3.0 19.4 1.0
CD2 A:HIS78 3.0 13.5 1.0
CE1 A:HIS237 3.1 14.1 1.0
CD2 A:HIS237 3.1 13.8 1.0
O A:HOH532 4.0 27.8 1.0
ND1 A:HIS78 4.1 13.2 1.0
ND1 A:HIS237 4.1 12.4 1.0
CB A:ASP241 4.2 11.3 1.0
CG A:HIS78 4.2 12.2 1.0
CG A:HIS237 4.2 13.0 1.0
OG1 A:THR190 4.2 13.6 1.0
CG A:GLU77 4.3 16.6 1.0
C03 A:W4M402 4.4 21.4 1.0
CB A:THR190 4.4 12.8 1.0
NE2 A:HIS264 4.5 22.4 1.0
OE2 A:GLU77 4.5 22.8 1.0
O A:HIS237 4.7 10.5 1.0
CA A:ASP241 4.8 11.0 1.0
S02 A:W4M402 4.9 23.2 1.0
CD A:GLU77 5.0 18.6 1.0
C01 A:W4M402 5.0 22.4 1.0

Zinc binding site 2 out of 2 in 7k99

Go back to Zinc Binding Sites List in 7k99
Zinc binding site 2 out of 2 in the Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor 19


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of P. Aeruginosa Lpxc with N-Hydroxyformamide Inhibitor 19 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn408

b:20.6
occ:1.00
OD1 C:ASP241 2.0 17.5 1.0
NE2 C:HIS237 2.1 17.3 1.0
O30 C:W4M402 2.1 27.4 1.0
NE2 C:HIS78 2.1 17.4 1.0
O32 C:W4M402 2.2 30.2 1.0
CG C:ASP241 2.7 17.9 1.0
OD2 C:ASP241 2.8 17.3 1.0
N29 C:W4M402 3.0 26.5 1.0
C31 C:W4M402 3.0 27.9 1.0
CE1 C:HIS237 3.0 18.2 1.0
CD2 C:HIS237 3.1 16.0 1.0
CD2 C:HIS78 3.1 18.6 1.0
CE1 C:HIS78 3.2 18.6 1.0
OG1 C:THR190 4.1 23.8 1.0
ND1 C:HIS237 4.1 17.0 1.0
CG C:HIS237 4.2 15.7 1.0
CB C:ASP241 4.2 17.8 1.0
CG C:HIS78 4.2 16.6 1.0
ND1 C:HIS78 4.3 17.5 1.0
C03 C:W4M402 4.3 30.9 1.0
CG C:GLU77 4.4 20.4 1.0
CB C:THR190 4.5 21.8 1.0
OE2 C:GLU77 4.6 25.1 1.0
NE2 C:HIS264 4.7 26.2 1.0
O C:HIS237 4.8 15.2 1.0
CA C:ASP241 4.8 16.8 1.0
S02 C:W4M402 4.9 32.2 1.0
CA C:THR190 5.0 20.7 1.0

Reference:

T.Furuya, A.B.Shapiro, J.Comita-Prevoir, E.J.Kuenstner, J.Zhang, S.D.Ribe, A.Chen, D.Hines, S.H.Moussa, N.M.Carter, M.A.Sylvester, J.A.C.Romero, C.V.Vega, M.D.Sacco, Y.Chen, J.P.O'donnell, T.F.Durand-Reville, A.A.Miller, R.A.Tommasi. N-Hydroxyformamide Lpxc Inhibitors, Their in Vivo Efficacy in A Mouse Escherichia Coli Infection Model, and Their Safety in A Rat Hemodynamic Assay. Bioorg.Med.Chem. V. 28 15826 2020.
ISSN: ESSN 1464-3391
PubMed: 33160146
DOI: 10.1016/J.BMC.2020.115826
Page generated: Wed Dec 16 14:03:41 2020

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