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Magnesium in PDB 1wbq: 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: 1wbq 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) 29.97 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.974, 236.703, 137.637, 90.00, 106.14, 90.00
R / Rfree (%) 16.7 / 19.7

Other elements in 1wbq:

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 1wbq). 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: 1wbq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1wbq

Go back to Magnesium Binding Sites List in 1wbq
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:32.0
occ:1.00
OD1 A:ASP271 2.1 29.9 1.0
OE1 A:GLU406 2.1 32.2 1.0
OD2 A:ASP260 2.2 30.6 1.0
O A:HOH2191 2.2 37.8 1.0
OD1 A:ASP260 2.2 33.0 1.0
O A:HOH2134 2.3 34.0 1.0
CG A:ASP260 2.5 38.3 1.0
CD A:GLU406 3.0 33.5 1.0
CG A:ASP271 3.1 32.7 1.0
OE2 A:GLU406 3.3 44.6 1.0
ZN A:ZN1440 3.3 53.9 1.0
OG1 A:THR273 3.5 31.9 1.0
OD2 A:ASP271 3.5 35.7 1.0
OH A:TYR229 3.7 30.4 1.0
O A:HOH2155 3.9 45.7 1.0
OE1 A:GLU383 4.0 40.1 1.0
CB A:ASP260 4.0 32.4 1.0
CZ A:TYR229 4.2 32.1 1.0
CG A:GLU406 4.4 35.0 1.0
CB A:ASP271 4.5 32.7 1.0
O A:ILE272 4.5 31.0 1.0
C A:ASP271 4.5 33.5 1.0
CE2 A:TYR229 4.5 31.0 1.0
C A:ILE272 4.6 31.3 1.0
N A:ILE272 4.7 29.8 1.0
O A:ASP271 4.7 33.0 1.0
CA A:ASP271 4.8 32.4 1.0
CD A:GLU383 4.8 36.4 1.0
CA A:ASP260 4.8 34.2 1.0
NE A:ARG404 4.8 33.7 1.0
CB A:THR273 4.9 32.0 1.0
N A:THR273 4.9 32.0 1.0
CB A:GLU406 4.9 28.7 1.0
CE1 A:TYR229 4.9 35.0 1.0
NH2 A:ARG404 5.0 34.8 1.0
OE2 A:GLU383 5.0 41.5 1.0

Magnesium binding site 2 out of 6 in 1wbq

Go back to Magnesium Binding Sites List in 1wbq
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:26.7
occ:1.00
OD1 B:ASP271 2.0 32.0 1.0
OE1 B:GLU406 2.1 31.6 1.0
O B:HOH2198 2.1 25.8 1.0
OD1 B:ASP260 2.2 29.3 1.0
OD2 B:ASP260 2.2 32.6 1.0
O B:HOH2285 2.3 24.2 1.0
CG B:ASP260 2.5 37.7 1.0
CG B:ASP271 3.1 31.2 1.0
CD B:GLU406 3.1 34.9 1.0
ZN B:ZN1440 3.2 44.1 1.0
OE2 B:GLU406 3.4 43.0 1.0
OD2 B:ASP271 3.4 32.5 1.0
OG1 B:THR273 3.6 29.1 1.0
OH B:TYR229 3.6 29.6 1.0
OE1 B:GLU383 4.0 40.6 1.0
O B:HOH2235 4.0 34.9 1.0
CZ B:TYR229 4.1 33.0 1.0
CB B:ASP260 4.1 33.6 1.0
CE2 B:TYR229 4.4 30.0 1.0
CB B:ASP271 4.4 33.8 1.0
C B:ASP271 4.4 33.5 1.0
CG B:GLU406 4.4 34.7 1.0
O B:ILE272 4.5 31.1 1.0
O B:ASP271 4.6 33.0 1.0
N B:ILE272 4.6 29.8 1.0
C B:ILE272 4.6 31.4 1.0
CA B:ASP271 4.6 32.3 1.0
CE1 B:TYR229 4.8 30.3 1.0
CD B:GLU383 4.8 37.3 1.0
CA B:ASP260 4.8 34.3 1.0
NE B:ARG404 4.8 32.0 1.0
CB B:GLU406 4.9 29.1 1.0
N B:THR273 4.9 32.1 1.0
CB B:THR273 4.9 30.2 1.0
NH2 B:ARG404 4.9 35.6 1.0

Magnesium binding site 3 out of 6 in 1wbq

Go back to Magnesium Binding Sites List in 1wbq
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:37.1
occ:1.00
O B:HOH2255 2.0 33.7 1.0
O B:HOH2257 2.0 32.9 1.0
O B:HOH2254 2.1 29.5 1.0
O B:HOH2258 2.2 23.2 1.0
O B:HOH2188 3.7 34.6 1.0
O B:ARG399 3.8 31.7 1.0
OE2 B:GLU396 4.1 29.8 1.0
O B:GLN397 4.4 26.2 1.0
O B:HOH2207 4.5 30.4 1.0
O B:HOH2260 4.6 36.3 1.0
O B:HOH2176 4.6 34.0 1.0
O B:GLU396 4.6 28.8 1.0
C B:GLN397 4.9 27.8 1.0

Magnesium binding site 4 out of 6 in 1wbq

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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:60.4
occ:1.00
OD1 C:ASP271 2.2 32.6 1.0
OE1 C:GLU406 2.3 31.2 1.0
OD2 C:ASP260 2.4 30.6 1.0
OD1 C:ASP260 2.4 31.8 1.0
CG C:ASP260 2.7 38.0 1.0
CG C:ASP271 3.1 31.8 1.0
ZN C:ZN1440 3.1 67.0 1.0
CD C:GLU406 3.2 33.7 1.0
OD2 C:ASP271 3.3 30.5 1.0
OE2 C:GLU406 3.4 43.1 1.0
OG1 C:THR273 3.7 29.3 1.0
OH C:TYR229 3.7 29.7 1.0
OE1 C:GLU383 3.9 42.8 1.0
CZ C:TYR229 4.1 32.7 1.0
CB C:ASP260 4.2 33.3 1.0
CE2 C:TYR229 4.5 30.6 1.0
CB C:ASP271 4.5 30.9 1.0
CG C:GLU406 4.5 34.8 1.0
CD C:GLU383 4.7 36.5 1.0
C C:ASP271 4.7 33.5 1.0
OE2 C:GLU383 4.7 42.3 1.0
NE C:ARG404 4.8 33.8 1.0
O C:ILE272 4.8 31.0 1.0
O C:ASP271 4.8 33.1 1.0
CA C:ASP271 4.9 32.2 1.0
CE1 C:TYR229 4.9 32.8 1.0
N C:ILE272 4.9 29.6 1.0
C C:ILE272 4.9 31.3 1.0
NH2 C:ARG404 5.0 36.6 1.0

Magnesium binding site 5 out of 6 in 1wbq

Go back to Magnesium Binding Sites List in 1wbq
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:29.7
occ:1.00
O D:HOH2256 2.0 25.0 1.0
OD1 D:ASP271 2.0 30.4 1.0
OD1 D:ASP260 2.1 30.7 1.0
O D:HOH2172 2.2 25.5 1.0
OD2 D:ASP260 2.2 31.6 1.0
OE1 D:GLU406 2.2 31.3 1.0
CG D:ASP260 2.5 37.9 1.0
CG D:ASP271 3.1 31.1 1.0
CD D:GLU406 3.2 35.4 1.0
ZN D:ZN1440 3.3 46.7 1.0
OD2 D:ASP271 3.4 35.8 1.0
OE2 D:GLU406 3.4 44.5 1.0
OH D:TYR229 3.6 26.8 1.0
OG1 D:THR273 3.6 31.0 1.0
CB D:ASP260 4.0 32.3 1.0
CZ D:TYR229 4.0 31.4 1.0
OE1 D:GLU383 4.1 40.9 1.0
CE2 D:TYR229 4.3 29.4 1.0
CB D:ASP271 4.4 32.3 1.0
C D:ASP271 4.5 33.5 1.0
O D:ILE272 4.5 30.9 1.0
CG D:GLU406 4.5 33.9 1.0
N D:ILE272 4.7 29.7 1.0
CA D:ASP271 4.7 32.2 1.0
O D:ASP271 4.7 32.9 1.0
C D:ILE272 4.7 31.2 1.0
CE1 D:TYR229 4.8 32.6 1.0
CA D:ASP260 4.8 34.1 1.0
NE D:ARG404 4.9 30.7 1.0
NH2 D:ARG404 4.9 36.4 1.0
CD D:GLU383 4.9 34.8 1.0
CB D:THR273 5.0 30.7 1.0
N D:THR273 5.0 32.1 1.0

Magnesium binding site 6 out of 6 in 1wbq

Go back to Magnesium Binding Sites List in 1wbq
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:38.8
occ:1.00
O D:HOH2228 2.0 31.2 1.0
O D:HOH2062 2.1 34.6 1.0
O D:HOH2225 2.1 30.1 1.0
O D:HOH2231 2.1 26.7 1.0
O D:HOH2232 2.1 38.9 1.0
O D:HOH2161 3.8 36.9 1.0
O D:ARG399 3.9 36.9 1.0
OE2 D:GLU396 4.1 31.8 1.0
O D:GLN397 4.2 27.0 1.0
O D:GLU396 4.6 27.2 1.0
O D:HOH2233 4.6 41.2 1.0
O D:HOH2179 4.7 28.3 1.0
C D:GLN397 4.8 28.3 1.0
O D:HOH2150 4.8 41.2 1.0
CA D:GLN397 4.9 29.4 1.0
CD D:GLU396 5.0 31.6 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: Mon Dec 14 07:01:59 2020

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