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Magnesium 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:

Chlorine (Cl) 4 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Znmg Substituted Aminopeptidase P From E. Coli (pdb code 1w7v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Znmg Substituted Aminopeptidase P From E. Coli, PDB code: 1w7v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1w7v

Go back to Magnesium Binding Sites List in 1w7v
Magnesium binding site 1 out of 6 in the Znmg Substituted Aminopeptidase P From E. Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Znmg Substituted Aminopeptidase P From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1441

b:32.4
occ:1.00
 OD1 A:ASP271 2.0 33.4 1.0
O A:HOH2270 2.1 32.1 1.0
OE1 A:GLU406 2.1 35.9 1.0
O A:HOH2193 2.2 35.0 1.0
OD1 A:ASP260 2.2 31.4 1.0
OD2 A:ASP260 2.3 31.9 1.0
CG A:ASP260 2.6 33.3 1.0
CD A:GLU406 3.0 40.3 1.0
CG A:ASP271 3.1 34.1 1.0
ZN A:ZN1440 3.2 50.9 1.0
OE2 A:GLU406 3.3 43.3 1.0
OD2 A:ASP271 3.4 35.7 1.0
OG1 A:THR273 3.6 30.7 1.0
OH A:TYR229 3.7 33.7 1.0
O E:HOH2001 3.8 51.6 1.0
OE1 A:GLU383 3.9 53.4 1.0
CB A:ASP260 4.1 29.9 1.0
CZ A:TYR229 4.2 32.8 1.0
CB A:ASP271 4.4 30.8 1.0
CG A:GLU406 4.4 35.3 1.0
CE2 A:TYR229 4.5 33.5 1.0
C A:ASP271 4.5 31.9 1.0
N E:PRO1 4.7 61.7 0.7
O A:ILE272 4.7 28.1 1.0
N A:ILE272 4.7 30.6 1.0
CA A:ASP271 4.7 30.2 1.0
O A:ASP271 4.8 32.1 1.0
CD A:GLU383 4.8 49.4 1.0
CD E:PRO1 4.8 61.6 0.7
C A:ILE272 4.8 29.8 1.0
CE1 A:TYR229 4.9 33.0 1.0
CA A:ASP260 4.9 29.8 1.0
NE A:ARG404 4.9 31.8 1.0
CB A:GLU406 5.0 32.3 1.0
OE2 A:GLU383 5.0 47.5 1.0
CB A:THR273 5.0 31.1 1.0

Magnesium binding site 2 out of 6 in 1w7v

Go back to Magnesium Binding Sites List in 1w7v
Magnesium binding site 2 out of 6 in the Znmg Substituted Aminopeptidase P From E. Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Znmg Substituted Aminopeptidase P From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1441

b:27.6
occ:1.00
 OD1 B:ASP271 2.0 30.9 1.0
O B:HOH2344 2.0 29.6 1.0
O B:HOH2230 2.1 28.6 1.0
OD1 B:ASP260 2.2 28.8 1.0
OE1 B:GLU406 2.2 36.4 1.0
OD2 B:ASP260 2.2 32.4 1.0
CG B:ASP260 2.5 31.2 1.0
CG B:ASP271 3.0 33.1 1.0
CD B:GLU406 3.1 39.0 1.0
ZN B:ZN1440 3.2 44.0 1.0
OE2 B:GLU406 3.3 41.9 1.0
OD2 B:ASP271 3.3 32.2 1.0
OG1 B:THR273 3.6 31.1 1.0
OH B:TYR229 3.7 32.6 1.0
O F:HOH2001 3.8 55.3 1.0
OE1 B:GLU383 4.0 52.1 1.0
CB B:ASP260 4.1 32.0 1.0
CZ B:TYR229 4.1 31.9 1.0
CB B:ASP271 4.4 31.0 1.0
CG B:GLU406 4.4 34.3 1.0
CE2 B:TYR229 4.5 31.9 1.0
C B:ASP271 4.5 32.2 1.0
N F:PRO1 4.5 56.3 0.7
N B:ILE272 4.7 30.4 1.0
CA B:ASP271 4.7 30.4 1.0
O B:ILE272 4.7 28.5 1.0
C B:ILE272 4.8 29.8 1.0
CD B:GLU383 4.8 49.9 1.0
O B:ASP271 4.8 32.5 1.0
CD F:PRO1 4.9 56.0 0.7
NE B:ARG404 4.9 31.5 1.0
CE1 B:TYR229 4.9 31.4 1.0
CA B:ASP260 4.9 29.9 1.0
OE2 B:GLU383 4.9 46.5 1.0
NH2 B:ARG404 5.0 34.6 1.0
CB B:GLU406 5.0 33.3 1.0
CB B:THR273 5.0 30.9 1.0

Magnesium binding site 3 out of 6 in 1w7v

Go back to Magnesium Binding Sites List in 1w7v
Magnesium binding site 3 out of 6 in the Znmg Substituted Aminopeptidase P From E. Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Znmg Substituted Aminopeptidase P From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1442

b:44.1
occ:1.00
 O B:HOH2306 2.0 41.0 1.0
O B:HOH2304 2.1 38.7 1.0
O B:HOH2310 2.1 41.7 1.0
O B:HOH2309 2.1 31.0 1.0
O B:HOH2226 3.7 52.0 1.0
O B:ARG399 3.8 34.8 1.0
OE2 B:GLU396 4.0 41.4 1.0
O B:GLN397 4.2 29.8 1.0
O B:HOH2247 4.4 36.6 1.0
O B:GLU396 4.5 27.8 1.0
O B:HOH2311 4.6 47.3 1.0
C B:GLN397 4.8 30.6 1.0
O B:HOH2217 4.9 51.5 1.0
CD B:GLU396 5.0 42.8 1.0
CA B:GLN397 5.0 30.7 1.0

Magnesium binding site 4 out of 6 in 1w7v

Go back to Magnesium Binding Sites List in 1w7v
Magnesium binding site 4 out of 6 in the Znmg Substituted Aminopeptidase P From E. Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Znmg Substituted Aminopeptidase P From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1441

b:49.2
occ:1.00
 O C:HOH2137 2.1 57.2 1.0
OD1 C:ASP271 2.1 31.3 1.0
OD2 C:ASP260 2.2 30.4 1.0
O C:HOH2110 2.2 51.7 1.0
OE1 C:GLU406 2.2 33.4 1.0
OD1 C:ASP260 2.4 29.5 1.0
CG C:ASP260 2.6 32.7 1.0
CG C:ASP271 3.0 34.8 1.0
ZN C:ZN1440 3.1 67.8 1.0
CD C:GLU406 3.1 37.6 1.0
OD2 C:ASP271 3.2 30.6 1.0
OE2 C:GLU406 3.4 42.5 1.0
OH C:TYR229 3.7 33.2 1.0
OG1 C:THR273 3.7 29.8 1.0
CZ C:TYR229 4.1 34.2 1.0
CB C:ASP260 4.1 30.4 1.0
OE1 C:GLU383 4.1 54.7 1.0
CB C:ASP271 4.4 30.7 1.0
N G:PRO1 4.4 67.5 0.7
CG C:GLU406 4.5 34.9 1.0
CE2 C:TYR229 4.5 32.9 1.0
C C:ASP271 4.6 32.0 1.0
CD G:PRO1 4.7 67.7 0.7
CA C:ASP271 4.8 30.2 1.0
N C:ILE272 4.8 30.4 1.0
O C:ASP271 4.8 32.2 1.0
CE1 C:TYR229 4.8 30.8 1.0
O C:ILE272 4.8 28.7 1.0
CD C:GLU383 4.9 48.5 1.0
NE C:ARG404 4.9 32.2 1.0
C C:ILE272 4.9 29.9 1.0
OE2 C:GLU383 4.9 46.9 1.0
CA C:ASP260 5.0 29.8 1.0

Magnesium binding site 5 out of 6 in 1w7v

Go back to Magnesium Binding Sites List in 1w7v
Magnesium binding site 5 out of 6 in the Znmg Substituted Aminopeptidase P From E. Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Znmg Substituted Aminopeptidase P From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1441

b:26.9
occ:1.00
 O D:HOH2337 2.0 27.5 1.0
OD1 D:ASP271 2.0 32.5 1.0
O D:HOH2237 2.1 26.0 1.0
OE1 D:GLU406 2.2 34.5 1.0
OD1 D:ASP260 2.2 30.2 1.0
OD2 D:ASP260 2.3 33.2 1.0
CG D:ASP260 2.6 35.0 1.0
CG D:ASP271 3.0 34.4 1.0
CD D:GLU406 3.1 40.4 1.0
ZN D:ZN1440 3.1 48.1 1.0
OD2 D:ASP271 3.3 36.4 1.0
OE2 D:GLU406 3.4 42.8 1.0
OG1 D:THR273 3.7 32.8 1.0
OH D:TYR229 3.7 32.4 1.0
O H:HOH2001 3.8 59.3 1.0
OE1 D:GLU383 4.0 52.6 1.0
CB D:ASP260 4.1 32.3 1.0
CZ D:TYR229 4.1 34.4 1.0
CB D:ASP271 4.4 31.1 1.0
N H:PRO1 4.4 57.8 0.7
CE2 D:TYR229 4.5 33.1 1.0
CG D:GLU406 4.5 34.6 1.0
C D:ASP271 4.6 31.7 1.0
CD H:PRO1 4.7 56.3 0.7
CA D:ASP271 4.8 30.1 1.0
O D:ILE272 4.8 28.4 1.0
CD D:GLU383 4.8 48.7 1.0
N D:ILE272 4.8 30.5 1.0
CE1 D:TYR229 4.8 31.6 1.0
O D:ASP271 4.8 32.8 1.0
NE D:ARG404 4.8 31.7 1.0
OE2 D:GLU383 4.9 44.9 1.0
C D:ILE272 4.9 29.9 1.0
CA D:ASP260 5.0 29.8 1.0

Magnesium binding site 6 out of 6 in 1w7v

Go back to Magnesium Binding Sites List in 1w7v
Magnesium binding site 6 out of 6 in the Znmg Substituted Aminopeptidase P From E. Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Znmg Substituted Aminopeptidase P From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1442

b:43.6
occ:1.00
 O D:HOH2306 1.9 40.5 1.0
O D:HOH2096 2.0 44.0 1.0
O D:HOH2304 2.1 36.4 1.0
O D:HOH2311 2.1 37.5 1.0
O D:HOH2310 2.1 32.6 1.0
O D:HOH2232 3.6 54.2 1.0
O D:ARG399 3.9 38.0 1.0
OE2 D:GLU396 4.1 38.5 1.0
O D:GLN397 4.3 32.5 1.0
O D:HOH2251 4.5 35.2 1.0
O D:HOH2312 4.6 48.1 1.0
O D:GLU396 4.6 29.3 1.0
C D:GLN397 4.8 33.0 1.0
CA D:GLN397 5.0 31.7 1.0
O D:HOH2231 5.0 30.6 1.0
CD D:GLU396 5.0 39.5 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: Tue Aug 13 17:10:39 2024

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