Zinc in PDB 4n4r: Structure Basis of Lipopolysaccharide Biogenesis

The structure of Structure Basis of Lipopolysaccharide Biogenesis, PDB code: 4n4r was solved by H.Dong, Q.Xiang, Z.Wang, N.G.Paterson, C.He, Y.Zhang, W.Wang, C.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	107.49 / 2.80
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	173.430, 76.082, 213.596, 90.00, 111.52, 90.00
R / Rfree (%)	28.5 / 30.5

The structure of Structure Basis of Lipopolysaccharide Biogenesis also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Structure Basis of Lipopolysaccharide Biogenesis (pdb code 4n4r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure Basis of Lipopolysaccharide Biogenesis, PDB code: 4n4r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure Basis of Lipopolysaccharide Biogenesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure Basis of Lipopolysaccharide Biogenesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:0.4 occ:1.00 NE2 B:HIS22 2.4 0.7 1.0 OD1 A:ASP498 2.4 0.7 1.0 OE1 A:GLU496 2.8 0.7 1.0 CE1 B:HIS22 2.9 0.9 1.0 CD A:GLU496 3.2 1.0 1.0 CG A:ASP498 3.3 0.3 1.0 OD2 A:ASP498 3.6 0.5 1.0 CD2 B:HIS22 3.6 0.6 1.0 OE2 A:GLU496 3.6 0.8 1.0 CG A:GLU496 4.1 0.6 1.0 OG B:SER25 4.2 0.8 1.0 ND1 B:HIS22 4.2 0.8 1.0 N A:ASP498 4.5 0.1 1.0 CG B:HIS22 4.5 0.2 1.0 CB A:ASP498 4.6 0.9 1.0 CB A:GLU496 4.6 99.1 1.0 O A:GLU496 4.7 0.7 1.0 CA A:ASP498 4.8 0.6 1.0 C A:ARG497 4.9 0.6 1.0 C A:GLU496 4.9 98.8 1.0

Zinc binding site 2 out of 2 in the Structure Basis of Lipopolysaccharide Biogenesis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure Basis of Lipopolysaccharide Biogenesis within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn802 b:0.4 occ:1.00 OD1 C:ASP498 2.5 0.9 1.0 NE2 D:HIS22 2.6 0.9 1.0 OE1 C:GLU496 3.0 0.3 1.0 CE1 D:HIS22 3.2 0.0 1.0 CG C:ASP498 3.3 0.6 1.0 CD C:GLU496 3.4 0.8 1.0 OD2 C:ASP498 3.6 0.8 1.0 OE2 C:GLU496 3.7 0.8 1.0 CD2 D:HIS22 3.7 0.0 1.0 OG D:SER25 4.0 0.2 1.0 CG C:GLU496 4.3 0.9 1.0 ND1 D:HIS22 4.5 0.2 1.0 CB C:ASP498 4.6 0.1 1.0 N C:ASP498 4.7 0.6 1.0 CG D:HIS22 4.8 0.6 1.0 CB C:GLU496 4.9 0.7 1.0 O C:GLU496 4.9 99.3 1.0

H.Dong, Q.Xiang, Y.Gu, Z.Wang, N.G.Paterson, P.J.Stansfeld, C.He, Y.Zhang, W.Wang, C.Dong. Structural Basis For Outer Membrane Lipopolysaccharide Insertion. Nature V. 511 52 2014.
ISSN: ISSN 0028-0836
PubMed: 24990744
DOI: 10.1038/NATURE13464