Zinc in PDB 5gne: Crystal Structure of Lapb From Legionella Pneumophila

The structure of Crystal Structure of Lapb From Legionella Pneumophila, PDB code: 5gne was solved by N.Zhang, H.Ge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.50
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	152.970, 152.970, 108.410, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.7

The binding sites of Zinc atom in the Crystal Structure of Lapb From Legionella Pneumophila (pdb code 5gne). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Lapb From Legionella Pneumophila, PDB code: 5gne:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Lapb From Legionella Pneumophila


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 Lapb From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:0.5 occ:1.00 O A:HOH529 2.1 37.5 1.0 OE2 A:GLU261 2.3 40.8 1.0 OD2 A:ASP226 2.6 62.6 1.0 NE2 A:HIS366 2.6 68.3 1.0 CD A:GLU261 3.1 54.6 1.0 ZN A:ZN402 3.2 86.2 1.0 CE1 A:HIS366 3.2 58.0 1.0 OE1 A:GLU261 3.3 66.0 1.0 CG A:ASP226 3.5 58.4 1.0 OD1 A:ASP226 3.5 77.2 1.0 OE1 A:GLU260 3.7 43.5 1.0 CD2 A:HIS366 3.8 58.2 1.0 NH2 A:ARG74 3.8 71.1 1.0 NH1 A:ARG74 4.0 49.1 1.0 OE2 A:GLU260 4.1 36.7 1.0 CZ A:ARG74 4.2 66.8 1.0 NE2 A:HIS213 4.3 41.9 1.0 CD A:GLU260 4.4 42.4 1.0 ND1 A:HIS366 4.4 65.2 1.0 CG A:GLU261 4.5 51.2 1.0 O A:HOH528 4.6 50.6 1.0 CE1 A:HIS213 4.7 36.3 1.0 CG A:HIS366 4.7 56.2 1.0 NE2 A:GLN289 4.8 64.5 1.0 CB A:ASP226 4.9 60.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Lapb From Legionella Pneumophila


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 Lapb From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:86.2 occ:1.00 OD1 A:ASP288 2.0 50.3 1.0 OD1 A:ASP226 2.3 77.2 1.0 NE2 A:HIS213 2.3 41.9 1.0 OD2 A:ASP288 2.5 58.0 1.0 CG A:ASP288 2.5 50.9 1.0 O A:HOH529 3.0 37.5 1.0 CD2 A:HIS213 3.1 30.9 1.0 ZN A:ZN401 3.2 0.5 1.0 CG A:ASP226 3.3 58.4 1.0 CE1 A:HIS213 3.4 36.3 1.0 OD2 A:ASP226 3.6 62.6 1.0 OE1 A:GLU260 3.9 43.5 1.0 OE2 A:GLU260 3.9 36.7 1.0 NE2 A:GLN289 3.9 64.5 1.0 CB A:ASP288 4.0 41.4 1.0 CD A:GLU260 4.0 42.4 1.0 CG A:HIS213 4.3 38.3 1.0 OE2 A:GLU261 4.3 40.8 1.0 ND1 A:HIS213 4.4 46.5 1.0 CB A:ASP226 4.6 60.7 1.0 CG A:ASP227 4.6 53.3 1.0 CB A:ASP227 4.7 56.4 1.0 CA A:ASP288 4.7 42.2 1.0 CA A:ASP226 4.7 53.7 1.0 OD2 A:ASP227 4.7 59.7 1.0 C A:ASP226 4.9 65.8 1.0 CG A:GLN289 4.9 56.1 1.0 OG A:SER338 4.9 46.2 1.0 CD A:GLN289 4.9 62.9 1.0 C A:ASP288 5.0 50.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Lapb From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Lapb From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:77.4 occ:1.00 OE2 B:GLU261 2.1 48.3 1.0 O B:HOH509 2.1 29.2 1.0 NE2 B:HIS366 2.2 62.1 1.0 OD2 B:ASP226 2.6 85.2 1.0 CD B:GLU261 2.9 66.0 1.0 CE1 B:HIS366 3.0 54.6 1.0 OE1 B:GLU261 3.0 77.2 1.0 OD1 B:ASP226 3.2 74.0 1.0 CG B:ASP226 3.2 73.7 1.0 ZN B:ZN402 3.3 76.0 1.0 CD2 B:HIS366 3.3 62.8 1.0 OE1 B:GLU260 3.7 49.2 1.0 NH1 B:ARG74 4.0 82.6 1.0 NH2 B:ARG74 4.1 99.2 1.0 ND1 B:HIS366 4.2 57.6 1.0 CG B:GLU261 4.3 48.4 1.0 NE2 B:HIS213 4.3 49.6 1.0 CZ B:ARG74 4.4 94.6 1.0 CG B:HIS366 4.4 56.7 1.0 CE1 B:HIS213 4.4 49.3 1.0 OE2 B:GLU260 4.5 62.7 1.0 CD B:GLU260 4.5 53.2 1.0 CB B:ASP226 4.7 64.5 1.0 NE2 B:GLN289 4.8 60.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Lapb From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Lapb From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:76.0 occ:1.00 NE2 B:HIS213 2.2 49.6 1.0 OD2 B:ASP288 2.3 64.0 1.0 OD1 B:ASP288 2.3 71.2 1.0 OD1 B:ASP226 2.4 74.0 1.0 CG B:ASP288 2.6 61.1 1.0 O B:HOH509 2.9 29.2 1.0 CD2 B:HIS213 3.1 50.2 1.0 CE1 B:HIS213 3.2 49.3 1.0 ZN B:ZN401 3.3 77.4 1.0 CG B:ASP226 3.6 73.7 1.0 OE1 B:GLU260 3.9 49.2 1.0 NE2 B:GLN289 3.9 60.0 1.0 OE2 B:GLU260 3.9 62.7 1.0 CD B:GLU260 4.0 53.2 1.0 OD2 B:ASP226 4.1 85.2 1.0 CB B:ASP288 4.1 61.0 1.0 ND1 B:HIS213 4.3 50.8 1.0 CG B:HIS213 4.3 50.2 1.0 OE2 B:GLU261 4.4 48.3 1.0 CB B:ASP227 4.6 65.3 1.0 CG B:ASP227 4.7 69.5 1.0 CA B:ASP226 4.7 55.7 1.0 CB B:ASP226 4.7 64.5 1.0 C B:ASP226 4.8 70.4 1.0 OD2 B:ASP227 4.8 68.7 1.0 CG B:GLN289 4.8 58.8 1.0 OG B:SER338 4.8 63.3 1.0 CA B:ASP288 4.8 64.0 1.0 CD B:GLN289 4.9 68.9 1.0

N.Zhang, S.Yin, W.Zhang, X.Gong, N.Zhang, K.Fang, H.Ge. Crystal Structure and Biochemical Characterization of An Aminopeptidase Lapb From Legionella Pneumophila. J. Agric. Food Chem. V. 65 7569 2017.
ISSN: ESSN 1520-5118
PubMed: 28776986
DOI: 10.1021/ACS.JAFC.7B02849