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Calcium in PDB 1w2m: Ca-Substituted Form of E. Coli Aminopeptidase P

Enzymatic activity of Ca-Substituted Form of E. Coli Aminopeptidase P

All present enzymatic activity of Ca-Substituted Form of E. Coli Aminopeptidase P:
3.4.11.9;

Protein crystallography data

The structure of Ca-Substituted Form of E. Coli Aminopeptidase P, PDB code: 1w2m 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) 182.57 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 208.359, 312.688, 160.198, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20

Other elements in 1w2m:

The structure of Ca-Substituted Form of E. Coli Aminopeptidase P also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Ca-Substituted Form of E. Coli Aminopeptidase P (pdb code 1w2m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Ca-Substituted Form of E. Coli Aminopeptidase P, PDB code: 1w2m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1w2m

Go back to Calcium Binding Sites List in 1w2m
Calcium binding site 1 out of 6 in the Ca-Substituted Form of E. Coli Aminopeptidase P


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ca-Substituted Form of E. Coli Aminopeptidase P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1442

b:32.9
occ:1.00
 OD2 A:ASP271 2.2 19.0 1.0
OE2 A:GLU406 2.3 26.4 1.0
O A:HOH2163 2.5 27.6 1.0
NE2 A:HIS354 2.5 20.2 1.0
OE2 A:GLU383 2.5 34.9 1.0
OE1 A:GLU383 2.8 37.4 1.0
CD A:GLU383 3.0 31.4 1.0
CG A:ASP271 3.1 19.7 1.0
CD A:GLU406 3.2 24.2 1.0
OD1 A:ASP271 3.3 21.6 1.0
OE1 A:GLU406 3.4 27.6 1.0
CE1 A:HIS354 3.5 20.8 1.0
CD2 A:HIS354 3.5 18.5 1.0
OG1 A:THR381 4.2 18.7 1.0
CG2 A:THR381 4.2 17.9 1.0
CG A:GLU383 4.3 26.1 1.0
CB A:THR381 4.5 18.4 1.0
CB A:ASP271 4.5 19.4 1.0
CG A:GLU406 4.6 23.7 1.0
ND1 A:HIS354 4.6 19.0 1.0
CG A:HIS354 4.6 19.0 1.0
NE2 A:HIS361 4.7 26.2 1.0
CB A:GLU383 4.8 22.7 1.0
OD1 A:ASP260 4.9 28.4 1.0
OD2 A:ASP260 5.0 26.6 1.0

Calcium binding site 2 out of 6 in 1w2m

Go back to Calcium Binding Sites List in 1w2m
Calcium binding site 2 out of 6 in the Ca-Substituted Form of E. Coli Aminopeptidase P


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ca-Substituted Form of E. Coli Aminopeptidase P within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1441

b:34.6
occ:1.00
 OD2 B:ASP271 2.1 20.4 1.0
OE2 B:GLU406 2.2 25.6 1.0
NE2 B:HIS354 2.5 19.7 1.0
O B:HOH2136 2.5 29.7 1.0
OE2 B:GLU383 2.6 33.8 1.0
OE1 B:GLU383 2.9 37.0 1.0
CD B:GLU383 3.1 30.9 1.0
CG B:ASP271 3.1 19.9 1.0
CD B:GLU406 3.2 23.8 1.0
OD1 B:ASP271 3.4 21.1 1.0
CD2 B:HIS354 3.4 19.1 1.0
CE1 B:HIS354 3.4 21.8 1.0
OE1 B:GLU406 3.5 28.2 1.0
OG1 B:THR381 4.2 17.2 1.0
CG2 B:THR381 4.2 18.1 1.0
CB B:ASP271 4.4 19.6 1.0
CB B:THR381 4.4 17.8 1.0
CG B:GLU383 4.5 26.7 1.0
ND1 B:HIS354 4.6 20.1 1.0
CG B:HIS354 4.6 19.7 1.0
CG B:GLU406 4.6 23.0 1.0
NE2 B:HIS361 4.6 27.8 1.0
CB B:GLU383 4.9 22.3 1.0
OD2 B:ASP260 5.0 25.8 1.0
CD2 B:HIS361 5.0 26.4 1.0
OD1 B:ASP260 5.0 27.1 1.0

Calcium binding site 3 out of 6 in 1w2m

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Calcium binding site 3 out of 6 in the Ca-Substituted Form of E. Coli Aminopeptidase P


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ca-Substituted Form of E. Coli Aminopeptidase P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1441

b:29.3
occ:1.00
 OD2 C:ASP271 2.1 21.4 1.0
OE2 C:GLU406 2.3 24.5 1.0
O C:HOH2140 2.4 37.1 1.0
NE2 C:HIS354 2.5 19.9 1.0
O C:HOH2143 2.5 32.3 1.0
OE2 C:GLU383 2.7 37.8 1.0
OE1 C:GLU383 2.8 37.1 1.0
CG C:ASP271 3.1 20.4 1.0
CD C:GLU383 3.1 31.9 1.0
CD C:GLU406 3.2 24.5 1.0
OD1 C:ASP271 3.3 22.3 1.0
CE1 C:HIS354 3.4 21.7 1.0
CD2 C:HIS354 3.4 19.2 1.0
OE1 C:GLU406 3.5 28.8 1.0
OG1 C:THR381 4.1 18.8 1.0
CG2 C:THR381 4.2 17.6 1.0
CB C:ASP271 4.4 19.7 1.0
CB C:THR381 4.4 17.8 1.0
CG C:GLU383 4.5 26.7 1.0
ND1 C:HIS354 4.5 20.2 1.0
CG C:HIS354 4.6 19.9 1.0
CG C:GLU406 4.6 23.2 1.0
O C:HOH2110 4.6 45.4 1.0
NE2 C:HIS361 4.7 26.4 1.0
CB C:GLU383 4.9 23.1 1.0
OD2 C:ASP260 5.0 25.5 1.0
CD2 C:HIS361 5.0 25.3 1.0

Calcium binding site 4 out of 6 in 1w2m

Go back to Calcium Binding Sites List in 1w2m
Calcium binding site 4 out of 6 in the Ca-Substituted Form of E. Coli Aminopeptidase P


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ca-Substituted Form of E. Coli Aminopeptidase P within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1444

b:35.2
occ:1.00
 OD2 D:ASP271 2.1 22.6 1.0
OE2 D:GLU406 2.3 26.9 1.0
NE2 D:HIS354 2.5 20.4 1.0
O D:HOH2157 2.5 27.7 1.0
OE2 D:GLU383 2.7 34.4 1.0
OE1 D:GLU383 2.8 35.0 1.0
CD D:GLU383 3.0 30.4 1.0
CG D:ASP271 3.1 21.3 1.0
CD D:GLU406 3.2 24.8 1.0
OD1 D:ASP271 3.4 25.4 1.0
CE1 D:HIS354 3.4 21.5 1.0
CD2 D:HIS354 3.4 19.6 1.0
OE1 D:GLU406 3.5 29.1 1.0
OG1 D:THR381 4.1 17.6 1.0
CG2 D:THR381 4.2 17.0 1.0
CB D:ASP271 4.4 19.6 1.0
CB D:THR381 4.4 18.3 1.0
CG D:GLU383 4.5 26.2 1.0
ND1 D:HIS354 4.5 20.1 1.0
CG D:GLU406 4.6 23.2 1.0
CG D:HIS354 4.6 20.6 1.0
NE2 D:HIS361 4.8 26.4 1.0
CB D:GLU383 4.8 22.1 1.0
OD1 D:ASP260 5.0 24.9 1.0

Calcium binding site 5 out of 6 in 1w2m

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Calcium binding site 5 out of 6 in the Ca-Substituted Form of E. Coli Aminopeptidase P


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ca-Substituted Form of E. Coli Aminopeptidase P within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1442

b:26.7
occ:1.00
 OD2 E:ASP271 2.2 22.6 1.0
OE2 E:GLU406 2.2 22.8 1.0
NE2 E:HIS354 2.5 20.3 1.0
OE2 E:GLU383 2.5 36.2 1.0
O E:HOH2204 2.5 28.6 1.0
O E:HOH2183 2.6 40.6 1.0
OE1 E:GLU383 3.1 37.9 1.0
CD E:GLU383 3.1 31.3 1.0
CG E:ASP271 3.2 20.4 1.0
CD E:GLU406 3.2 23.2 1.0
CD2 E:HIS354 3.4 19.9 1.0
OE1 E:GLU406 3.4 30.0 1.0
OD1 E:ASP271 3.4 24.0 1.0
CE1 E:HIS354 3.5 21.6 1.0
OG1 E:THR381 4.1 17.4 1.0
CG2 E:THR381 4.1 17.9 1.0
CB E:THR381 4.4 17.8 1.0
CG E:GLU383 4.4 26.6 1.0
CB E:ASP271 4.4 19.4 1.0
CG E:GLU406 4.5 22.2 1.0
CG E:HIS354 4.6 20.0 1.0
ND1 E:HIS354 4.6 19.6 1.0
NE2 E:HIS361 4.8 26.3 1.0
CB E:GLU383 4.9 22.6 1.0
OD2 E:ASP260 4.9 25.8 1.0
O E:HOH2148 4.9 39.9 1.0
CG2 E:VAL360 5.0 20.4 1.0
OD1 E:ASP260 5.0 24.6 1.0

Calcium binding site 6 out of 6 in 1w2m

Go back to Calcium Binding Sites List in 1w2m
Calcium binding site 6 out of 6 in the Ca-Substituted Form of E. Coli Aminopeptidase P


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Ca-Substituted Form of E. Coli Aminopeptidase P within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1443

b:30.1
occ:1.00
 OD2 F:ASP271 2.2 22.2 1.0
OE2 F:GLU406 2.4 25.4 1.0
NE2 F:HIS354 2.5 19.8 1.0
OE2 F:GLU383 2.5 34.6 1.0
O F:HOH2172 2.7 30.8 1.0
OE1 F:GLU383 2.7 35.7 1.0
CD F:GLU383 3.0 29.9 1.0
CG F:ASP271 3.2 20.9 1.0
CD F:GLU406 3.3 24.1 1.0
CD2 F:HIS354 3.4 17.8 1.0
CE1 F:HIS354 3.5 20.7 1.0
OD1 F:ASP271 3.5 25.6 1.0
OE1 F:GLU406 3.5 29.7 1.0
OG1 F:THR381 4.2 16.5 1.0
CG2 F:THR381 4.2 17.6 1.0
CG F:GLU383 4.4 26.4 1.0
CB F:THR381 4.5 18.2 1.0
CB F:ASP271 4.5 19.4 1.0
ND1 F:HIS354 4.6 19.6 1.0
CG F:HIS354 4.6 19.8 1.0
CG F:GLU406 4.7 22.7 1.0
O F:HOH2126 4.7 37.4 1.0
NE2 F:HIS361 4.7 25.9 1.0
CB F:GLU383 4.9 22.5 1.0
CG2 F:VAL360 5.0 20.4 1.0
CD2 F:HIS361 5.0 25.7 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 Jul 8 03:04:38 2025

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