Zinc in PDB 1xfo: Crystal Structure of An Archaeal Aminopeptidase

The structure of Crystal Structure of An Archaeal Aminopeptidase, PDB code: 1xfo was solved by S.Russo, U.Baumann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.92 / 1.96
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	158.340, 158.340, 114.460, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 20.9

The binding sites of Zinc atom in the Crystal Structure of An Archaeal Aminopeptidase (pdb code 1xfo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of An Archaeal Aminopeptidase, PDB code: 1xfo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of An Archaeal Aminopeptidase


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 An Archaeal Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn354 b:39.9 occ:1.00 OD1 A:ASP182 2.0 40.4 1.0 OD1 A:ASP235 2.2 38.7 1.0 NE2 A:HIS68 2.2 36.6 1.0 O A:HOH465 2.3 41.1 1.0 OD2 A:ASP235 2.6 38.9 1.0 CG A:ASP235 2.7 38.3 1.0 CG A:ASP182 3.0 39.1 1.0 CD2 A:HIS68 3.1 36.6 1.0 CE1 A:HIS68 3.3 36.9 1.0 OD2 A:ASP182 3.3 40.6 1.0 ZN A:ZN382 3.6 61.0 1.0 CB A:ASP183 3.8 38.1 1.0 OE1 A:GLU212 3.9 38.4 1.0 CG A:ASP183 4.1 38.9 1.0 OE2 A:GLU213 4.1 39.6 1.0 CD A:GLU212 4.2 38.6 1.0 CB A:ASP235 4.3 37.3 1.0 CG A:HIS68 4.3 36.7 1.0 OE2 A:GLU212 4.3 39.1 1.0 CB A:ASP182 4.3 38.4 1.0 CG2 A:VAL236 4.3 37.1 1.0 ND1 A:HIS68 4.3 36.7 1.0 OD1 A:ASP183 4.5 39.8 1.0 OD2 A:ASP183 4.5 38.6 1.0 CA A:ASP183 4.6 37.9 1.0 CA A:ASP182 4.6 37.8 1.0 N A:ASP183 4.7 37.9 1.0 C A:ASP182 4.7 38.1 1.0 N A:VAL236 4.7 36.9 1.0 CD A:GLU213 4.7 38.0 1.0 O A:HOH392 4.8 28.9 1.0 CA A:ASP235 5.0 37.1 1.0 OE1 A:GLU213 5.0 38.4 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of An Archaeal Aminopeptidase


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 An Archaeal Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn382 b:61.0 occ:1.00 NE2 A:HIS323 2.1 41.4 1.0 OD2 A:ASP182 2.2 40.6 1.0 OE2 A:GLU213 2.3 39.6 1.0 OE1 A:GLU213 2.5 38.4 1.0 O A:HOH465 2.6 41.1 1.0 CD A:GLU213 2.7 38.0 1.0 CG A:ASP182 3.0 39.1 1.0 CE1 A:HIS323 3.0 40.7 1.0 CD2 A:HIS323 3.1 40.4 1.0 OD1 A:ASP182 3.3 40.4 1.0 ZN A:ZN354 3.6 39.9 1.0 ND1 A:HIS323 4.1 40.8 1.0 CG A:HIS323 4.2 39.5 1.0 O A:HOH478 4.2 28.8 1.0 CG A:GLU213 4.2 37.5 1.0 CB A:ASP182 4.2 38.4 1.0 OE1 A:GLU212 4.4 38.4 1.0 NE2 A:HIS68 4.5 36.6 1.0 CE1 A:HIS68 4.6 36.9 1.0 O A:HOH462 4.6 27.2 1.0 CG2 A:ILE72 4.8 35.9 1.0 CG2 A:ILE322 4.9 37.2 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of An Archaeal Aminopeptidase


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 An Archaeal Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn354 b:66.7 occ:1.00 OD2 B:ASP182 2.1 38.8 1.0 NE2 B:HIS323 2.2 41.1 1.0 OE2 B:GLU213 2.4 38.9 1.0 O B:HOH426 2.6 47.4 1.0 OE1 B:GLU213 2.6 38.2 1.0 CD B:GLU213 2.8 38.0 1.0 CG B:ASP182 2.9 38.0 1.0 CD2 B:HIS323 3.1 40.4 1.0 CE1 B:HIS323 3.2 40.6 1.0 OD1 B:ASP182 3.2 38.3 1.0 ZN B:ZN371 3.5 41.5 1.0 CB B:ASP182 4.2 37.6 1.0 O B:HOH433 4.2 27.6 1.0 CG B:HIS323 4.2 39.4 1.0 ND1 B:HIS323 4.2 40.7 1.0 CG B:GLU213 4.3 37.7 1.0 OE1 B:GLU212 4.4 39.5 1.0 NE2 B:HIS68 4.5 36.6 1.0 CE1 B:HIS68 4.7 36.8 1.0 O B:HOH405 4.8 29.6 1.0 CG2 B:ILE322 4.8 37.9 1.0 CG2 B:ILE72 4.9 35.8 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of An Archaeal Aminopeptidase


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 An Archaeal Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn371 b:41.5 occ:1.00 OD1 B:ASP182 2.0 38.3 1.0 OD1 B:ASP235 2.2 38.5 1.0 NE2 B:HIS68 2.2 36.6 1.0 O B:HOH426 2.4 47.4 1.0 OD2 B:ASP235 2.6 39.1 1.0 CG B:ASP235 2.7 38.2 1.0 CG B:ASP182 3.0 38.0 1.0 CD2 B:HIS68 3.1 36.9 1.0 CE1 B:HIS68 3.2 36.8 1.0 OD2 B:ASP182 3.3 38.8 1.0 ZN B:ZN354 3.5 66.7 1.0 CB B:ASP183 3.8 38.1 1.0 OE1 B:GLU212 3.8 39.5 1.0 OE2 B:GLU213 4.1 38.9 1.0 CG B:ASP183 4.1 38.5 1.0 CD B:GLU212 4.2 38.8 1.0 CB B:ASP235 4.3 37.5 1.0 OE2 B:GLU212 4.3 39.6 1.0 CG B:HIS68 4.3 36.6 1.0 CB B:ASP182 4.3 37.6 1.0 ND1 B:HIS68 4.3 36.7 1.0 CG2 B:VAL236 4.4 36.8 1.0 OD2 B:ASP183 4.5 38.4 1.0 OD1 B:ASP183 4.5 38.7 1.0 CA B:ASP182 4.6 37.5 1.0 CA B:ASP183 4.6 37.8 1.0 CD B:GLU213 4.7 38.0 1.0 N B:VAL236 4.7 36.9 1.0 C B:ASP182 4.7 37.5 1.0 N B:ASP183 4.7 37.7 1.0 O B:HOH434 4.8 33.0 1.0 O B:HOH443 4.8 51.2 1.0 CA B:ASP235 4.9 37.2 1.0 OE1 B:GLU213 4.9 38.2 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of An Archaeal Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of An Archaeal Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn354 b:41.8 occ:1.00 OD1 C:ASP182 2.0 39.4 1.0 OD1 C:ASP235 2.1 38.9 1.0 NE2 C:HIS68 2.2 36.6 1.0 O C:HOH415 2.4 43.9 1.0 OD2 C:ASP235 2.6 38.1 1.0 CG C:ASP235 2.7 37.9 1.0 CD2 C:HIS68 3.0 36.6 1.0 CG C:ASP182 3.1 38.9 1.0 CE1 C:HIS68 3.2 36.6 1.0 ZN C:ZN355 3.4 69.8 1.0 OD2 C:ASP182 3.5 40.2 1.0 CB C:ASP183 3.8 38.0 1.0 OE1 C:GLU212 3.9 38.9 1.0 OE2 C:GLU213 4.1 38.9 1.0 CG C:ASP183 4.1 38.2 1.0 CD C:GLU212 4.2 38.7 1.0 CB C:ASP235 4.2 36.8 1.0 OE2 C:GLU212 4.2 39.5 1.0 CG C:HIS68 4.2 36.2 1.0 ND1 C:HIS68 4.3 36.8 1.0 CG2 C:VAL236 4.4 36.9 1.0 CB C:ASP182 4.4 38.2 1.0 OD2 C:ASP183 4.5 37.3 1.0 OD1 C:ASP183 4.6 38.5 1.0 CA C:ASP183 4.6 37.7 1.0 CA C:ASP182 4.6 38.0 1.0 O C:HOH419 4.7 32.3 1.0 N C:VAL236 4.7 36.7 1.0 C C:ASP182 4.7 37.9 1.0 N C:ASP183 4.7 37.9 1.0 CD C:GLU213 4.7 38.2 1.0 CA C:ASP235 4.9 36.9 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of An Archaeal Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of An Archaeal Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn355 b:69.8 occ:1.00 OD2 C:ASP182 2.1 40.2 1.0 NE2 C:HIS323 2.3 40.6 1.0 OE2 C:GLU213 2.3 38.9 1.0 O C:HOH415 2.3 43.9 1.0 OE1 C:GLU213 2.7 38.0 1.0 CD C:GLU213 2.8 38.2 1.0 CG C:ASP182 2.8 38.9 1.0 OD1 C:ASP182 3.0 39.4 1.0 CE1 C:HIS323 3.2 40.2 1.0 CD2 C:HIS323 3.2 39.9 1.0 ZN C:ZN354 3.4 41.8 1.0 O C:HOH376 4.2 29.1 1.0 CB C:ASP182 4.2 38.2 1.0 ND1 C:HIS323 4.3 40.9 1.0 CG C:GLU213 4.3 37.5 1.0 NE2 C:HIS68 4.3 36.6 1.0 CG C:HIS323 4.3 39.2 1.0 OE1 C:GLU212 4.4 38.9 1.0 CE1 C:HIS68 4.5 36.6 1.0 O C:HOH418 4.8 32.6 1.0 CG2 C:ILE322 4.9 37.3 1.0 CG2 C:ILE72 5.0 35.8 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of An Archaeal Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of An Archaeal Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn354 b:34.5 occ:1.00 OD1 D:ASP182 2.0 38.8 1.0 O D:HOH435 2.1 28.8 1.0 OD1 D:ASP235 2.2 39.0 1.0 NE2 D:HIS68 2.2 37.1 1.0 OD2 D:ASP235 2.6 39.1 1.0 CG D:ASP235 2.7 38.2 1.0 CG D:ASP182 3.0 38.7 1.0 CD2 D:HIS68 3.1 36.8 1.0 CE1 D:HIS68 3.2 37.1 1.0 OD2 D:ASP182 3.4 39.4 1.0 ZN D:ZN355 3.5 55.5 1.0 CB D:ASP183 3.7 38.7 1.0 OE1 D:GLU212 3.9 38.3 1.0 OE2 D:GLU213 4.1 39.3 1.0 CG D:ASP183 4.1 38.9 1.0 CD D:GLU212 4.2 39.1 1.0 CB D:ASP235 4.3 37.2 1.0 CG D:HIS68 4.3 36.5 1.0 ND1 D:HIS68 4.3 36.7 1.0 CB D:ASP182 4.3 38.2 1.0 OE2 D:GLU212 4.3 39.7 1.0 O D:HOH500 4.4 49.3 1.0 CG2 D:VAL236 4.4 37.5 1.0 OD2 D:ASP183 4.5 38.8 1.0 CA D:ASP183 4.6 38.2 1.0 CA D:ASP182 4.6 38.0 1.0 OD1 D:ASP183 4.6 39.4 1.0 N D:ASP183 4.7 38.4 1.0 C D:ASP182 4.7 38.2 1.0 N D:VAL236 4.7 36.7 1.0 CD D:GLU213 4.7 38.1 1.0 O D:HOH372 4.8 24.3 1.0 OE1 D:GLU213 4.9 38.2 1.0 CA D:ASP235 4.9 36.8 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of An Archaeal Aminopeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of An Archaeal Aminopeptidase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn355 b:55.5 occ:1.00 OD2 D:ASP182 2.0 39.4 1.0 NE2 D:HIS323 2.1 42.0 1.0 OE2 D:GLU213 2.3 39.3 1.0 O D:HOH435 2.4 28.8 1.0 OE1 D:GLU213 2.7 38.2 1.0 CD D:GLU213 2.8 38.1 1.0 CG D:ASP182 2.9 38.7 1.0 CD2 D:HIS323 3.0 41.5 1.0 CE1 D:HIS323 3.1 41.7 1.0 OD1 D:ASP182 3.2 38.8 1.0 ZN D:ZN354 3.5 34.5 1.0 O D:HOH356 4.1 24.4 1.0 ND1 D:HIS323 4.1 41.8 1.0 CG D:HIS323 4.2 40.1 1.0 CB D:ASP182 4.2 38.2 1.0 CG D:GLU213 4.3 37.2 1.0 OE1 D:GLU212 4.5 38.3 1.0 NE2 D:HIS68 4.5 37.1 1.0 CE1 D:HIS68 4.7 37.1 1.0 O D:HOH420 4.8 23.8 1.0 CG2 D:ILE322 4.8 37.8 1.0 CG2 D:ILE72 4.9 35.9 1.0

S.Russo, U.Baumann. Crystal Structure of A Dodecameric Tetrahedral Shaped Aminopeptidase J.Biol.Chem. V. 279 51275 2004.
ISSN: ISSN 0021-9258
PubMed: 15375159
DOI: 10.1074/JBC.M409455200