Zinc in PDB 6ica: The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase

The structure of The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase, PDB code: 6ica was solved by G.Honghua, Z.Nannan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.52 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.424, 121.913, 130.812, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 18.3

The binding sites of Zinc atom in the The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase (pdb code 6ica). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase, PDB code: 6ica:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:19.4 occ:1.00 O A:HOH653 1.9 16.5 1.0 OD1 A:ASP251 2.1 19.6 1.0 NE2 A:HIS238 2.1 18.1 1.0 OD1 A:ASP313 2.2 14.8 1.0 OD2 A:ASP313 2.4 18.4 1.0 O A:HOH784 2.4 25.7 1.0 CG A:ASP313 2.6 19.6 1.0 CG A:ASP251 3.0 20.8 1.0 CE1 A:HIS238 3.1 14.4 1.0 CD2 A:HIS238 3.2 13.4 1.0 ZN A:ZN505 3.3 55.1 1.0 OD2 A:ASP251 3.3 29.9 1.0 OE1 A:GLU285 3.9 26.3 1.0 OE2 A:GLU286 3.9 27.4 1.0 CB A:ASP252 4.0 13.7 1.0 CB A:ASP313 4.1 19.5 1.0 ND1 A:HIS238 4.2 13.1 1.0 CD A:GLU285 4.3 29.6 1.0 CB A:ASP251 4.3 15.4 1.0 CG A:HIS238 4.3 13.7 1.0 OE2 A:GLU285 4.4 38.6 1.0 CG A:MET314 4.6 11.0 1.0 CA A:ASP251 4.7 12.6 1.0 CG A:ASP252 4.7 17.9 1.0 C A:ASP251 4.8 14.1 1.0 CD A:GLU286 4.8 24.7 1.0 CA A:ASP313 4.8 14.3 1.0 N A:ASP252 4.9 12.1 1.0 OG A:SER363 4.9 12.2 1.0 CA A:ASP252 4.9 15.3 1.0

Zinc binding site 2 out of 6 in the The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:55.1 occ:1.00 OD2 A:ASP251 2.2 29.9 1.0 O A:HOH653 2.2 16.5 1.0 NE2 A:HIS391 2.2 20.0 1.0 OE2 A:GLU286 2.2 27.4 1.0 OE1 A:GLU286 2.9 23.8 1.0 CD A:GLU286 2.9 24.7 1.0 CG A:ASP251 3.1 20.8 1.0 CE1 A:HIS391 3.1 20.0 1.0 CD2 A:HIS391 3.2 20.6 1.0 O A:HOH669 3.3 39.1 1.0 ZN A:ZN504 3.3 19.4 1.0 OD1 A:ASP251 3.4 19.6 1.0 O A:HOH784 3.4 25.7 1.0 OE1 A:GLU285 4.1 26.3 1.0 O A:HOH624 4.1 23.5 1.0 ND1 A:HIS391 4.3 19.6 1.0 CG A:HIS391 4.3 21.3 1.0 CG A:GLU286 4.4 19.8 1.0 CB A:ASP251 4.4 15.4 1.0 NE2 A:HIS238 4.5 18.1 1.0 CE1 A:HIS238 4.6 14.4 1.0 CD A:GLU285 4.9 29.6 1.0

Zinc binding site 3 out of 6 in the The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:20.0 occ:1.00 OD1 B:ASP251 2.0 16.2 1.0 NE2 B:HIS238 2.2 17.7 1.0 OD1 B:ASP313 2.2 16.6 1.0 O B:HOH745 2.3 34.2 1.0 OD2 B:ASP313 2.3 18.4 1.0 CG B:ASP313 2.6 18.1 1.0 CG B:ASP251 3.0 22.1 1.0 CE1 B:HIS238 3.1 10.5 1.0 CD2 B:HIS238 3.1 10.9 1.0 ZN B:ZN505 3.2 54.8 1.0 OD2 B:ASP251 3.5 32.3 1.0 OE1 B:GLU285 3.8 23.1 1.0 CB B:ASP252 4.1 17.4 1.0 OE2 B:GLU286 4.1 31.4 1.0 CB B:ASP313 4.1 15.1 1.0 CD B:GLU285 4.2 24.1 1.0 ND1 B:HIS238 4.2 14.4 1.0 CG B:HIS238 4.3 13.4 1.0 OE2 B:GLU285 4.3 30.9 1.0 CB B:ASP251 4.3 16.4 1.0 CG B:MET314 4.6 14.4 1.0 CA B:ASP251 4.7 13.9 1.0 CG B:ASP252 4.7 21.7 1.0 C B:ASP251 4.8 14.7 1.0 CD B:GLU286 4.9 28.3 1.0 N B:ASP252 4.9 13.1 1.0 CA B:ASP313 4.9 15.3 1.0 OG B:SER363 4.9 16.7 1.0 CA B:ASP252 4.9 12.5 1.0 SD B:MET314 5.0 24.1 1.0

Zinc binding site 4 out of 6 in the The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:54.8 occ:1.00 OD2 B:ASP251 2.3 32.3 1.0 OE2 B:GLU286 2.4 31.4 1.0 NE2 B:HIS391 2.5 28.9 1.0 OE1 B:GLU286 2.8 29.9 1.0 CD B:GLU286 3.0 28.3 1.0 CG B:ASP251 3.1 22.1 1.0 ZN B:ZN504 3.2 20.0 1.0 OD1 B:ASP251 3.2 16.2 1.0 O B:HOH745 3.3 34.2 1.0 CE1 B:HIS391 3.4 28.4 1.0 CD2 B:HIS391 3.5 25.7 1.0 OE1 B:GLU285 3.9 23.1 1.0 O B:HOH640 4.4 19.5 1.0 NE2 B:HIS238 4.4 17.7 1.0 CG B:GLU286 4.4 21.4 1.0 ND1 B:HIS391 4.5 31.5 1.0 CE1 B:HIS238 4.5 10.5 1.0 CB B:ASP251 4.5 16.4 1.0 CG B:HIS391 4.6 26.8 1.0 CD B:GLU285 4.7 24.1 1.0 OE2 B:GLU285 4.8 30.9 1.0 CG2 B:ILE390 4.9 34.5 1.0

Zinc binding site 5 out of 6 in the The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn504 b:19.8 occ:1.00 OD1 C:ASP251 2.0 15.0 1.0 O C:HOH688 2.2 32.0 1.0 NE2 C:HIS238 2.2 15.8 1.0 OD1 C:ASP313 2.2 16.5 1.0 OD2 C:ASP313 2.4 17.7 1.0 O C:HOH783 2.6 28.1 1.0 CG C:ASP313 2.6 19.1 1.0 CG C:ASP251 3.0 16.8 1.0 CE1 C:HIS238 3.1 9.5 1.0 CD2 C:HIS238 3.2 10.1 1.0 ZN C:ZN505 3.3 53.4 1.0 OD2 C:ASP251 3.4 24.1 1.0 OE2 C:GLU285 3.9 21.9 1.0 OE2 C:GLU286 4.0 36.2 1.0 CB C:ASP252 4.0 13.7 1.0 CB C:ASP313 4.2 12.7 1.0 ND1 C:HIS238 4.2 16.3 1.0 CD C:GLU285 4.3 28.6 1.0 CB C:ASP251 4.3 18.1 1.0 O C:HOH806 4.3 43.5 1.0 CG C:HIS238 4.3 13.1 1.0 OE1 C:GLU285 4.4 33.0 1.0 CG C:MET314 4.6 15.9 1.0 CA C:ASP251 4.7 20.2 1.0 CG C:ASP252 4.7 16.7 1.0 C C:ASP251 4.8 16.4 1.0 CD C:GLU286 4.9 33.6 1.0 N C:ASP252 4.9 13.4 1.0 OG C:SER363 4.9 20.2 1.0 CA C:ASP252 4.9 14.7 1.0 CA C:ASP313 4.9 13.8 1.0 SD C:MET314 5.0 24.2 1.0 OD2 C:ASP252 5.0 13.8 1.0

Zinc binding site 6 out of 6 in the The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn505 b:53.4 occ:1.00 OD2 C:ASP251 2.1 24.1 1.0 O C:HOH688 2.2 32.0 1.0 NE2 C:HIS391 2.3 30.1 1.0 OE2 C:GLU286 2.4 36.2 1.0 OE1 C:GLU286 2.8 32.5 1.0 CD C:GLU286 3.0 33.6 1.0 CG C:ASP251 3.1 16.8 1.0 O C:HOH806 3.1 43.5 1.0 CE1 C:HIS391 3.2 21.1 1.0 O C:HOH783 3.3 28.1 1.0 ZN C:ZN504 3.3 19.8 1.0 CD2 C:HIS391 3.3 27.8 1.0 OD1 C:ASP251 3.3 15.0 1.0 OE2 C:GLU285 4.0 21.9 1.0 O C:HOH628 4.3 21.6 1.0 ND1 C:HIS391 4.3 27.6 1.0 CG C:HIS391 4.4 27.8 1.0 CB C:ASP251 4.4 18.1 1.0 CG C:GLU286 4.5 30.1 1.0 NE2 C:HIS238 4.6 15.8 1.0 CG2 C:ILE390 4.6 41.5 1.0 CE1 C:HIS238 4.6 9.5 1.0 CD C:GLU285 4.9 28.6 1.0 OE1 C:GLU285 5.0 33.0 1.0

G.Honghua, Z.Nannan. The Crystal Structure of Legionella Pneumophila Lapa Aminopeptidase To Be Published.