Zinc in PDB 1w7v: Znmg Substituted Aminopeptidase P From E. Coli

All present enzymatic activity of Znmg Substituted Aminopeptidase P From E. Coli:
3.4.11.9;

The structure of Znmg Substituted Aminopeptidase P From E. Coli, PDB code: 1w7v was solved by S.C.Graham, C.S.Bond, H.C.Freeman, J.M.Guss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.80 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.731, 236.527, 137.997, 90.00, 106.34, 90.00
R / Rfree (%)	15.6 / 18

The structure of Znmg Substituted Aminopeptidase P From E. Coli also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Znmg Substituted Aminopeptidase P From E. Coli (pdb code 1w7v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Znmg Substituted Aminopeptidase P From E. Coli, PDB code: 1w7v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Znmg Substituted Aminopeptidase P From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Znmg Substituted Aminopeptidase P From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1440 b:50.9 occ:1.00 O A:HOH2270 2.1 32.1 1.0 OE2 A:GLU406 2.1 43.3 1.0 OD2 A:ASP271 2.2 35.7 1.0 NE2 A:HIS354 2.2 31.7 1.0 OE2 A:GLU383 2.6 47.5 1.0 CG A:ASP271 3.0 34.1 1.0 CD A:GLU406 3.1 40.3 1.0 CD2 A:HIS354 3.2 30.1 1.0 OE1 A:GLU383 3.2 53.4 1.0 MG A:MG1441 3.2 32.4 1.0 CE1 A:HIS354 3.2 32.3 1.0 CD A:GLU383 3.2 49.4 1.0 OD1 A:ASP271 3.2 33.4 1.0 O E:HOH2001 3.2 51.6 1.0 OE1 A:GLU406 3.4 35.9 1.0 CG2 A:THR381 3.8 31.9 1.0 O A:HOH2193 3.9 35.0 1.0 OG1 A:THR381 3.9 32.1 1.0 CB A:THR381 4.1 34.5 1.0 ND1 A:HIS354 4.3 29.5 1.0 CG A:HIS354 4.3 34.5 1.0 CB A:ASP271 4.3 30.8 1.0 CG A:GLU406 4.5 35.3 1.0 N E:PRO1 4.5 61.7 0.7 CG A:GLU383 4.6 37.8 1.0 CA E:PRO1 4.6 61.4 0.7 NE2 A:HIS361 4.7 39.1 1.0 CD2 A:HIS361 4.9 44.0 1.0 CG2 A:VAL360 5.0 38.8 1.0

Zinc binding site 2 out of 4 in the Znmg Substituted Aminopeptidase P From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Znmg Substituted Aminopeptidase P From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1440 b:44.0 occ:1.00 O B:HOH2344 2.1 29.6 1.0 OD2 B:ASP271 2.1 32.2 1.0 NE2 B:HIS354 2.2 30.9 1.0 OE2 B:GLU406 2.2 41.9 1.0 OE2 B:GLU383 2.5 46.5 1.0 CG B:ASP271 3.0 33.1 1.0 CE1 B:HIS354 3.1 30.7 1.0 CD B:GLU406 3.1 39.0 1.0 CD2 B:HIS354 3.2 27.0 1.0 MG B:MG1441 3.2 27.6 1.0 CD B:GLU383 3.2 49.9 1.0 OE1 B:GLU383 3.2 52.1 1.0 OD1 B:ASP271 3.2 30.9 1.0 O F:HOH2001 3.3 55.3 1.0 OE1 B:GLU406 3.5 36.4 1.0 CG2 B:THR381 3.8 32.9 1.0 O B:HOH2230 3.9 28.6 1.0 OG1 B:THR381 3.9 34.6 1.0 CB B:THR381 4.1 33.0 1.0 ND1 B:HIS354 4.2 28.5 1.0 CB B:ASP271 4.2 31.0 1.0 CG B:HIS354 4.3 31.1 1.0 N F:PRO1 4.4 56.3 0.7 CG B:GLU406 4.5 34.3 1.0 CA F:PRO1 4.5 54.6 0.7 CG B:GLU383 4.6 36.8 1.0 NE2 B:HIS361 4.8 39.0 1.0 CG2 B:VAL360 4.9 39.3 1.0 CD2 B:HIS361 4.9 44.0 1.0 OD2 B:ASP260 5.0 32.4 1.0

Zinc binding site 3 out of 4 in the Znmg Substituted Aminopeptidase P From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Znmg Substituted Aminopeptidase P From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1440 b:67.8 occ:1.00 OD2 C:ASP271 2.1 30.6 1.0 OE2 C:GLU406 2.2 42.5 1.0 NE2 C:HIS354 2.2 29.7 1.0 O C:HOH2137 2.5 57.2 1.0 OE2 C:GLU383 2.6 46.9 1.0 CG C:ASP271 3.1 34.8 1.0 MG C:MG1441 3.1 49.2 1.0 CD C:GLU406 3.1 37.6 1.0 CD2 C:HIS354 3.2 29.8 1.0 CE1 C:HIS354 3.2 31.5 1.0 CD C:GLU383 3.2 48.5 1.0 OE1 C:GLU406 3.4 33.4 1.0 OE1 C:GLU383 3.4 54.7 1.0 OD1 C:ASP271 3.4 31.3 1.0 CG2 C:THR381 3.8 33.5 1.0 OG1 C:THR381 3.8 31.6 1.0 O C:HOH2110 4.1 51.7 1.0 CB C:THR381 4.1 32.9 1.0 ND1 C:HIS354 4.3 28.4 1.0 CG C:HIS354 4.3 33.8 1.0 CA G:PRO1 4.3 67.0 0.7 N G:PRO1 4.3 67.5 0.7 CB C:ASP271 4.3 30.7 1.0 CG C:GLU406 4.5 34.9 1.0 CG C:GLU383 4.5 36.2 1.0 NE2 C:HIS361 4.8 37.3 1.0 OD2 C:ASP260 4.9 30.4 1.0 CD2 C:HIS361 5.0 44.5 1.0

Zinc binding site 4 out of 4 in the Znmg Substituted Aminopeptidase P From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Znmg Substituted Aminopeptidase P From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1440 b:48.1 occ:1.00 O D:HOH2337 2.0 27.5 1.0 OD2 D:ASP271 2.1 36.4 1.0 OE2 D:GLU406 2.2 42.8 1.0 NE2 D:HIS354 2.2 29.4 1.0 OE2 D:GLU383 2.5 44.9 1.0 CG D:ASP271 3.0 34.4 1.0 CE1 D:HIS354 3.1 29.9 1.0 MG D:MG1441 3.1 26.9 1.0 CD D:GLU406 3.1 40.4 1.0 CD D:GLU383 3.2 48.7 1.0 CD2 D:HIS354 3.2 28.3 1.0 OD1 D:ASP271 3.3 32.5 1.0 OE1 D:GLU383 3.3 52.6 1.0 O H:HOH2001 3.4 59.3 1.0 OE1 D:GLU406 3.4 34.5 1.0 CG2 D:THR381 3.8 34.4 1.0 OG1 D:THR381 3.9 31.8 1.0 O D:HOH2237 4.0 26.0 1.0 CB D:THR381 4.1 33.3 1.0 ND1 D:HIS354 4.3 28.2 1.0 CB D:ASP271 4.3 31.1 1.0 CG D:HIS354 4.3 34.9 1.0 N H:PRO1 4.3 57.8 0.7 CG D:GLU406 4.5 34.6 1.0 CG D:GLU383 4.5 38.3 1.0 CA H:PRO1 4.5 57.4 0.7 NE2 D:HIS361 4.8 38.2 1.0 CG2 D:VAL360 4.9 40.1 1.0 CD2 D:HIS361 5.0 45.4 1.0 O H:HOH2002 5.0 48.8 1.0

S.C.Graham, C.S.Bond, H.C.Freeman, J.M.Guss. Structural and Functional Implications of Metal Ion Selection in Aminopeptidase P, A Metalloprotease with A Dinuclear Metal Center. Biochemistry V. 44 13820 2005.
ISSN: ISSN 0006-2960
PubMed: 16229471
DOI: 10.1021/BI0512849