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

Enzymatic activity of Znmg Substituted Aminopeptidase P From E. Coli

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

Protein crystallography data

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

Other elements in 1w7v:

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

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

Zinc Binding Sites:

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 1w7v

Go back to Zinc Binding Sites List in 1w7v
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 1w7v

Go back to Zinc Binding Sites List in 1w7v
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 1w7v

Go back to Zinc Binding Sites List in 1w7v
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 1w7v

Go back to Zinc Binding Sites List in 1w7v
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

Reference:

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
Page generated: Wed Dec 16 03:08:31 2020

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