Atomistry » Magnesium » PDB 1w56-1wdt » 1w7v
Atomistry »
  Magnesium »
    PDB 1w56-1wdt »
      1w7v »

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

Last articles

Ca in 5VPH
Ca in 5VMS
Ca in 5VPG
Ca in 5VOF
Ca in 5VMA
Ca in 5VOE
Ca in 5VLL
Ca in 5VMQ
Ca in 5V5X
Ca in 5VH2
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy