Zinc in PDB 4mdt: Structure of Lpxc Bound to the Reaction Product Udp-(3-O-(R-3- Hydroxymyristoyl))-Glucosamine

The structure of Structure of Lpxc Bound to the Reaction Product Udp-(3-O-(R-3- Hydroxymyristoyl))-Glucosamine, PDB code: 4mdt was solved by G.M.Clayton, D.J.Klein, K.W.Rickert, S.B.Patel, M.Kornienko, J.Zugay-Murphy, J.C.Reid, S.Tummala, S.Sharma, S.B.Singh, L.Miesel, K.J.Lumb, S.M.Soisson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.45 / 2.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	168.973, 103.520, 103.968, 90.00, 103.96, 90.00
R / Rfree (%)	19.7 / 24

The binding sites of Zinc atom in the Structure of Lpxc Bound to the Reaction Product Udp-(3-O-(R-3- Hydroxymyristoyl))-Glucosamine (pdb code 4mdt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Lpxc Bound to the Reaction Product Udp-(3-O-(R-3- Hydroxymyristoyl))-Glucosamine, PDB code: 4mdt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Lpxc Bound to the Reaction Product Udp-(3-O-(R-3- Hydroxymyristoyl))-Glucosamine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Lpxc Bound to the Reaction Product Udp-(3-O-(R-3- Hydroxymyristoyl))-Glucosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:39.5 occ:1.00 O2 A:PO4403 1.9 50.1 1.0 NE2 A:HIS238 1.9 36.6 1.0 NE2 A:HIS79 2.0 39.7 1.0 OD1 A:ASP242 2.0 43.7 1.0 CG A:ASP242 2.7 40.9 1.0 OD2 A:ASP242 2.8 41.5 1.0 CE1 A:HIS238 2.8 36.7 1.0 CD2 A:HIS238 2.9 37.2 1.0 CD2 A:HIS79 3.0 39.7 1.0 CE1 A:HIS79 3.0 39.6 1.0 P A:PO4403 3.2 43.7 1.0 O4 A:PO4403 3.7 48.8 1.0 OG1 A:THR191 3.7 46.3 1.0 O3 A:PO4403 3.8 47.5 1.0 ND1 A:HIS238 4.0 38.2 1.0 CG A:HIS238 4.0 37.1 1.0 CB A:THR191 4.0 44.2 1.0 CG A:HIS79 4.1 37.6 1.0 ND1 A:HIS79 4.1 40.1 1.0 CB A:ASP242 4.2 34.3 1.0 CG A:GLU78 4.3 40.9 1.0 O1 A:PO4403 4.4 53.8 1.0 OE2 A:GLU78 4.6 42.1 1.0 CE1 A:HIS265 4.7 35.1 1.0 NE2 A:HIS265 4.7 35.4 1.0 CA A:THR191 4.8 38.4 1.0 CA A:ASP242 4.8 34.1 1.0 O A:HIS238 4.9 37.8 1.0

Zinc binding site 2 out of 4 in the Structure of Lpxc Bound to the Reaction Product Udp-(3-O-(R-3- Hydroxymyristoyl))-Glucosamine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Lpxc Bound to the Reaction Product Udp-(3-O-(R-3- Hydroxymyristoyl))-Glucosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:40.6 occ:1.00 O2 B:PO4403 1.9 50.1 1.0 NE2 B:HIS238 1.9 38.3 1.0 OD1 B:ASP242 2.0 40.7 1.0 NE2 B:HIS79 2.1 45.8 1.0 CG B:ASP242 2.7 39.1 1.0 CE1 B:HIS238 2.7 38.1 1.0 OD2 B:ASP242 2.8 40.3 1.0 CE1 B:HIS79 3.1 45.8 1.0 CD2 B:HIS238 3.1 38.0 1.0 CD2 B:HIS79 3.1 46.0 1.0 P B:PO4403 3.2 43.4 1.0 O1 B:PO4403 3.6 46.3 1.0 ND1 B:HIS238 3.9 38.4 1.0 O3 B:PO4403 4.0 51.0 1.0 OG1 B:THR191 4.0 48.2 1.0 CG B:HIS238 4.1 35.5 1.0 CB B:THR191 4.1 42.5 1.0 CB B:ASP242 4.1 33.3 1.0 CG B:GLU78 4.2 46.4 1.0 ND1 B:HIS79 4.2 46.6 1.0 CG B:HIS79 4.2 44.8 1.0 O4 B:PO4403 4.2 46.7 1.0 O B:HOH553 4.4 51.1 1.0 CE1 B:HIS265 4.5 35.2 1.0 OE2 B:GLU78 4.6 48.0 1.0 NE2 B:HIS265 4.7 34.9 1.0 CA B:ASP242 4.8 32.6 1.0 CA B:THR191 4.8 36.0 1.0 O B:HIS238 4.9 36.0 1.0 CD B:GLU78 4.9 53.5 1.0 O B:GLY106 5.0 43.7 1.0

Zinc binding site 3 out of 4 in the Structure of Lpxc Bound to the Reaction Product Udp-(3-O-(R-3- Hydroxymyristoyl))-Glucosamine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Lpxc Bound to the Reaction Product Udp-(3-O-(R-3- Hydroxymyristoyl))-Glucosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:63.1 occ:1.00 O2 C:PO4403 1.9 67.7 1.0 OD1 C:ASP242 1.9 53.9 1.0 NE2 C:HIS238 2.2 73.0 1.0 NE2 C:HIS79 2.4 62.2 1.0 OD2 C:ASP242 2.4 70.8 1.0 CG C:ASP242 2.5 57.8 1.0 CE1 C:HIS238 2.9 72.5 1.0 P C:PO4403 3.0 63.0 1.0 O3 C:PO4403 3.1 67.7 1.0 CD2 C:HIS79 3.2 62.1 1.0 CD2 C:HIS238 3.2 73.3 1.0 CE1 C:HIS79 3.5 61.9 1.0 O1 C:PO4403 3.8 68.4 1.0 CB C:ASP242 3.9 55.3 1.0 ND1 C:HIS238 4.0 73.0 1.0 CG C:HIS238 4.2 71.3 1.0 CG C:GLU78 4.3 56.2 1.0 OG1 C:THR191 4.3 85.9 1.0 O4 C:PO4403 4.3 70.4 1.0 CE1 C:HIS265 4.4 63.1 1.0 CG C:HIS79 4.4 59.8 1.0 CB C:THR191 4.4 79.5 1.0 NE2 C:HIS265 4.5 63.6 1.0 ND1 C:HIS79 4.6 62.2 1.0 CA C:ASP242 4.6 55.4 1.0 OE2 C:GLU78 4.6 55.0 1.0 O C:HIS238 4.7 76.3 1.0 N C:ASP242 4.9 57.9 1.0 CA C:THR191 4.9 70.3 1.0 CD C:GLU78 5.0 68.5 1.0

Zinc binding site 4 out of 4 in the Structure of Lpxc Bound to the Reaction Product Udp-(3-O-(R-3- Hydroxymyristoyl))-Glucosamine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Lpxc Bound to the Reaction Product Udp-(3-O-(R-3- Hydroxymyristoyl))-Glucosamine within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:55.8 occ:1.00 NE2 D:HIS79 2.0 57.7 1.0 O1 D:PO4403 2.0 42.2 1.0 OD1 D:ASP242 2.1 52.3 1.0 NE2 D:HIS238 2.3 65.9 1.0 CE1 D:HIS238 2.8 65.2 1.0 CG D:ASP242 2.8 53.3 1.0 CD2 D:HIS79 2.8 57.6 1.0 OD2 D:ASP242 2.9 52.0 1.0 P D:PO4403 3.0 48.1 1.0 CE1 D:HIS79 3.1 57.0 1.0 O2 D:PO4403 3.3 52.4 1.0 CD2 D:HIS238 3.5 65.9 1.0 O3 D:PO4403 3.6 57.4 1.0 ND1 D:HIS238 3.9 65.6 1.0 CG D:GLU78 4.0 67.4 1.0 CG D:HIS79 4.0 55.4 1.0 OE2 D:GLU78 4.0 59.1 1.0 ND1 D:HIS79 4.1 57.5 1.0 CB D:THR191 4.2 65.7 1.0 CB D:ASP242 4.3 53.2 1.0 CG D:HIS238 4.3 63.5 1.0 OG1 D:THR191 4.4 62.0 1.0 O4 D:PO4403 4.4 52.7 1.0 CD D:GLU78 4.5 70.5 1.0 CE1 D:HIS265 4.6 47.7 1.0 CA D:ASP242 4.8 53.1 1.0 NE2 D:HIS265 4.8 47.3 1.0 CA D:THR191 4.9 55.6 1.0 O D:HIS238 5.0 59.0 1.0 CD2 D:LEU241 5.0 64.5 1.0

G.M.Clayton, D.J.Klein, K.W.Rickert, S.B.Patel, M.Kornienko, J.Zugay-Murphy, J.C.Reid, S.Tummala, S.Sharma, S.B.Singh, L.Miesel, K.J.Lumb, S.M.Soisson. Structure of the Bacterial Deacetylase Lpxc Bound to the Nucleotide Reaction Product Reveals Mechanisms of Oxyanion Stabilization and Proton Transfer. J.Biol.Chem. V. 288 34073 2013.
ISSN: ISSN 0021-9258
PubMed: 24108127
DOI: 10.1074/JBC.M113.513028