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Zinc in PDB 6mae: Chain A. Udp-3-O-[3-Hydroxymyristoyl] N-Acetylglucosamine Deacetylase Pa-Lpxc Complexed with (R)-3-((S)-3-(4-(Cyclopropylethynyl)Phenyl)-2- Oxooxazolidin-5-Yl)-N-Hydroxy-2-Methyl-2-(Methylsulfonyl)Propenamide

Enzymatic activity of Chain A. Udp-3-O-[3-Hydroxymyristoyl] N-Acetylglucosamine Deacetylase Pa-Lpxc Complexed with (R)-3-((S)-3-(4-(Cyclopropylethynyl)Phenyl)-2- Oxooxazolidin-5-Yl)-N-Hydroxy-2-Methyl-2-(Methylsulfonyl)Propenamide

All present enzymatic activity of Chain A. Udp-3-O-[3-Hydroxymyristoyl] N-Acetylglucosamine Deacetylase Pa-Lpxc Complexed with (R)-3-((S)-3-(4-(Cyclopropylethynyl)Phenyl)-2- Oxooxazolidin-5-Yl)-N-Hydroxy-2-Methyl-2-(Methylsulfonyl)Propenamide:
3.5.1.108;

Protein crystallography data

The structure of Chain A. Udp-3-O-[3-Hydroxymyristoyl] N-Acetylglucosamine Deacetylase Pa-Lpxc Complexed with (R)-3-((S)-3-(4-(Cyclopropylethynyl)Phenyl)-2- Oxooxazolidin-5-Yl)-N-Hydroxy-2-Methyl-2-(Methylsulfonyl)Propenamide, PDB code: 6mae was solved by W.Shu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.86 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.002, 67.346, 62.864, 90.00, 90.47, 90.00
R / Rfree (%) 15.9 / 19.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Chain A. Udp-3-O-[3-Hydroxymyristoyl] N-Acetylglucosamine Deacetylase Pa-Lpxc Complexed with (R)-3-((S)-3-(4-(Cyclopropylethynyl)Phenyl)-2- Oxooxazolidin-5-Yl)-N-Hydroxy-2-Methyl-2-(Methylsulfonyl)Propenamide (pdb code 6mae). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Chain A. Udp-3-O-[3-Hydroxymyristoyl] N-Acetylglucosamine Deacetylase Pa-Lpxc Complexed with (R)-3-((S)-3-(4-(Cyclopropylethynyl)Phenyl)-2- Oxooxazolidin-5-Yl)-N-Hydroxy-2-Methyl-2-(Methylsulfonyl)Propenamide, PDB code: 6mae:

Zinc binding site 1 out of 1 in 6mae

Go back to Zinc Binding Sites List in 6mae
Zinc binding site 1 out of 1 in the Chain A. Udp-3-O-[3-Hydroxymyristoyl] N-Acetylglucosamine Deacetylase Pa-Lpxc Complexed with (R)-3-((S)-3-(4-(Cyclopropylethynyl)Phenyl)-2- Oxooxazolidin-5-Yl)-N-Hydroxy-2-Methyl-2-(Methylsulfonyl)Propenamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Chain A. Udp-3-O-[3-Hydroxymyristoyl] N-Acetylglucosamine Deacetylase Pa-Lpxc Complexed with (R)-3-((S)-3-(4-(Cyclopropylethynyl)Phenyl)-2- Oxooxazolidin-5-Yl)-N-Hydroxy-2-Methyl-2-(Methylsulfonyl)Propenamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:12.0
occ:1.00
 OD1 A:ASP241 2.0 11.5 1.0
NE2 A:HIS78 2.1 14.5 1.0
NE2 A:HIS237 2.1 11.1 1.0
O2 A:JBA301 2.1 15.8 0.9
O3 A:JBA301 2.2 17.0 0.9
H18 A:JBA301 2.6 17.4 0.9
CG A:ASP241 2.7 11.6 1.0
OD2 A:ASP241 2.8 11.9 1.0
C17 A:JBA301 2.9 15.6 0.9
N1 A:JBA301 2.9 16.6 0.9
CE1 A:HIS237 3.1 11.0 1.0
CD2 A:HIS78 3.1 14.3 1.0
CD2 A:HIS237 3.1 11.4 1.0
CE1 A:HIS78 3.1 15.0 1.0
H17 A:JBA301 3.7 17.2 0.9
H19 A:JBA301 3.8 20.3 0.9
OG1 A:THR190 4.0 12.7 1.0
CB A:ASP241 4.2 10.9 1.0
CG A:HIS237 4.2 11.4 1.0
ND1 A:HIS237 4.2 12.1 1.0
CG A:HIS78 4.2 13.5 1.0
ND1 A:HIS78 4.2 16.6 1.0
CB A:THR190 4.3 11.5 1.0
CG A:GLU77 4.3 16.2 1.0
C1 A:JBA301 4.4 13.3 0.9
OE2 A:GLU77 4.4 14.2 1.0
C18 A:JBA301 4.6 20.7 0.9
O A:HOH558 4.7 43.5 1.0
H A:JBA301 4.7 9.6 0.9
CE1 A:HIS264 4.8 13.9 1.0
CA A:ASP241 4.8 9.0 1.0
H4 A:JBA301 4.8 10.2 0.9
CA A:THR190 4.9 9.5 1.0
NE2 A:HIS264 4.9 13.7 1.0
CD A:GLU77 4.9 21.1 1.0
O A:HIS237 4.9 12.9 1.0
H21 A:JBA301 4.9 20.7 0.9

Reference:

P.S.Lee, G.Lapointe, A.M.Madera, R.L.Simmons, W.Xu, A.Yifru, M.Tjandra, S.Karur, A.Rico, K.Thompson, J.Bojkovic, L.Xie, K.Uehara, A.Liu, W.Shu, C.Bellamacina, D.Mckenney, L.Morris, G.R.Tonn, C.Osborne, B.M.Benton, L.Mcdowell, J.Fu, Z.K.Sweeney. Application of Virtual Screening to the Identification of New Lpxc Inhibitor Chemotypes, Oxazolidinone and Isoxazoline. J. Med. Chem. V. 61 9360 2018.
ISSN: ISSN 1520-4804
PubMed: 30226381
DOI: 10.1021/ACS.JMEDCHEM.8B01287
Page generated: Thu Aug 21 17:22:06 2025

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