Magnesium in PDB 4pv4: Proline Aminopeptidase P II From Yersinia Pestis
Enzymatic activity of Proline Aminopeptidase P II From Yersinia Pestis
All present enzymatic activity of Proline Aminopeptidase P II From Yersinia Pestis:
3.4.11.9;
Protein crystallography data
The structure of Proline Aminopeptidase P II From Yersinia Pestis, PDB code: 4pv4
was solved by
J.Osipiuk,
N.Maltseva,
S.Shatsman,
W.F.Anderson,
A.Joachimiak,
Center Forstructural Genomics Of Infectious Diseases (Csgid),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.40 /
1.76
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
124.299,
82.865,
110.091,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16 /
19.8
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Proline Aminopeptidase P II From Yersinia Pestis
(pdb code 4pv4). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Proline Aminopeptidase P II From Yersinia Pestis, PDB code: 4pv4:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 4pv4
Go back to
Magnesium Binding Sites List in 4pv4
Magnesium binding site 1 out
of 4 in the Proline Aminopeptidase P II From Yersinia Pestis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Proline Aminopeptidase P II From Yersinia Pestis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:24.6
occ:1.00
|
OD1
|
A:ASP269
|
2.1
|
23.9
|
1.0
|
OE1
|
A:GLU405
|
2.2
|
21.2
|
1.0
|
O
|
A:HOH1083
|
2.2
|
39.9
|
1.0
|
OD1
|
A:ASP258
|
2.3
|
18.4
|
1.0
|
OD2
|
A:ASP258
|
2.3
|
18.5
|
1.0
|
CG
|
A:ASP258
|
2.7
|
17.5
|
1.0
|
CG
|
A:ASP269
|
3.0
|
23.9
|
1.0
|
MG
|
A:MG502
|
3.1
|
20.9
|
0.7
|
CD
|
A:GLU405
|
3.1
|
21.6
|
1.0
|
OE2
|
A:GLU405
|
3.2
|
19.4
|
1.0
|
OD2
|
A:ASP269
|
3.3
|
29.7
|
1.0
|
OG1
|
A:THR271
|
3.5
|
17.7
|
1.0
|
OH
|
A:TYR227
|
3.9
|
19.4
|
1.0
|
CB
|
A:ASP258
|
4.2
|
16.5
|
1.0
|
OE1
|
A:GLU382
|
4.2
|
30.6
|
1.0
|
C24
|
A:1PE503
|
4.2
|
46.1
|
1.0
|
CZ
|
A:TYR227
|
4.4
|
20.4
|
1.0
|
CB
|
A:ASP269
|
4.4
|
17.8
|
1.0
|
CG
|
A:GLU405
|
4.5
|
17.8
|
1.0
|
O
|
A:HOH837
|
4.5
|
34.7
|
1.0
|
OH4
|
A:1PE503
|
4.6
|
47.1
|
1.0
|
NE
|
A:ARG403
|
4.6
|
17.3
|
1.0
|
C
|
A:ASP269
|
4.6
|
18.5
|
1.0
|
O
|
A:ILE270
|
4.7
|
15.7
|
1.0
|
CE2
|
A:TYR227
|
4.7
|
20.4
|
1.0
|
C23
|
A:1PE503
|
4.7
|
36.2
|
1.0
|
C14
|
A:1PE503
|
4.8
|
48.3
|
1.0
|
C
|
A:ILE270
|
4.8
|
16.9
|
1.0
|
OE2
|
A:GLU382
|
4.8
|
29.0
|
1.0
|
N
|
A:ILE270
|
4.8
|
17.2
|
1.0
|
CA
|
A:ASP269
|
4.8
|
17.0
|
1.0
|
CD
|
A:GLU382
|
4.8
|
27.5
|
1.0
|
NH1
|
A:ARG403
|
4.8
|
21.6
|
1.0
|
CB
|
A:THR271
|
4.9
|
17.7
|
1.0
|
O
|
A:ASP269
|
4.9
|
18.6
|
1.0
|
CA
|
A:ASP258
|
5.0
|
16.4
|
1.0
|
CB
|
A:GLU405
|
5.0
|
18.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 4pv4
Go back to
Magnesium Binding Sites List in 4pv4
Magnesium binding site 2 out
of 4 in the Proline Aminopeptidase P II From Yersinia Pestis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Proline Aminopeptidase P II From Yersinia Pestis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg502
b:20.9
occ:0.70
|
O
|
A:HOH1083
|
2.0
|
39.9
|
1.0
|
OE2
|
A:GLU405
|
2.1
|
19.4
|
1.0
|
NE2
|
A:HIS352
|
2.2
|
20.1
|
1.0
|
OD2
|
A:ASP269
|
2.3
|
29.7
|
1.0
|
OE2
|
A:GLU382
|
2.4
|
29.0
|
1.0
|
MG
|
A:MG501
|
3.1
|
24.6
|
1.0
|
CD
|
A:GLU405
|
3.1
|
21.6
|
1.0
|
CE1
|
A:HIS352
|
3.1
|
20.3
|
1.0
|
CG
|
A:ASP269
|
3.2
|
23.9
|
1.0
|
CD
|
A:GLU382
|
3.2
|
27.5
|
1.0
|
CD2
|
A:HIS352
|
3.2
|
20.8
|
1.0
|
OE1
|
A:GLU382
|
3.3
|
30.6
|
1.0
|
OE1
|
A:GLU405
|
3.4
|
21.2
|
1.0
|
OD1
|
A:ASP269
|
3.4
|
23.9
|
1.0
|
O
|
A:HOH837
|
3.5
|
34.7
|
1.0
|
CG2
|
A:THR380
|
3.7
|
18.8
|
1.0
|
OG1
|
A:THR380
|
3.8
|
19.9
|
1.0
|
CB
|
A:THR380
|
4.0
|
17.8
|
1.0
|
OH2
|
A:1PE503
|
4.1
|
55.2
|
1.0
|
ND1
|
A:HIS352
|
4.2
|
19.7
|
1.0
|
CG
|
A:HIS352
|
4.3
|
20.3
|
1.0
|
CB
|
A:ASP269
|
4.3
|
17.8
|
1.0
|
CG
|
A:GLU405
|
4.4
|
17.8
|
1.0
|
CG
|
A:GLU382
|
4.5
|
20.2
|
1.0
|
CB
|
A:GLU382
|
4.9
|
18.9
|
1.0
|
CG2
|
A:VAL358
|
5.0
|
21.6
|
1.0
|
NE2
|
A:HIS359
|
5.0
|
21.5
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 4pv4
Go back to
Magnesium Binding Sites List in 4pv4
Magnesium binding site 3 out
of 4 in the Proline Aminopeptidase P II From Yersinia Pestis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Proline Aminopeptidase P II From Yersinia Pestis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg501
b:26.8
occ:1.00
|
OE2
|
B:GLU405
|
2.2
|
19.0
|
1.0
|
NE2
|
B:HIS352
|
2.2
|
20.2
|
1.0
|
OD2
|
B:ASP269
|
2.3
|
29.2
|
1.0
|
OE2
|
B:GLU382
|
2.5
|
26.7
|
1.0
|
O
|
B:HOH844
|
2.5
|
38.8
|
1.0
|
MG
|
B:MG502
|
3.1
|
24.8
|
1.0
|
CD
|
B:GLU405
|
3.1
|
20.8
|
1.0
|
CD2
|
B:HIS352
|
3.1
|
19.8
|
1.0
|
CG
|
B:ASP269
|
3.1
|
25.2
|
1.0
|
CD
|
B:GLU382
|
3.2
|
27.7
|
1.0
|
CE1
|
B:HIS352
|
3.2
|
19.8
|
1.0
|
OE1
|
B:GLU382
|
3.3
|
29.7
|
1.0
|
OE1
|
B:GLU405
|
3.4
|
23.2
|
1.0
|
OD1
|
B:ASP269
|
3.5
|
23.8
|
1.0
|
O
|
B:HOH781
|
3.6
|
33.7
|
1.0
|
CG2
|
B:THR380
|
3.6
|
17.8
|
1.0
|
OG1
|
B:THR380
|
3.8
|
18.9
|
1.0
|
CB
|
B:THR380
|
4.0
|
18.4
|
1.0
|
ND1
|
B:HIS352
|
4.3
|
19.7
|
1.0
|
CG
|
B:HIS352
|
4.3
|
19.1
|
1.0
|
CB
|
B:ASP269
|
4.3
|
19.9
|
1.0
|
CG
|
B:GLU405
|
4.5
|
18.9
|
1.0
|
CG
|
B:GLU382
|
4.5
|
21.2
|
1.0
|
C11
|
B:P6G503
|
4.8
|
44.6
|
1.0
|
CB
|
B:GLU382
|
4.9
|
20.1
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 4pv4
Go back to
Magnesium Binding Sites List in 4pv4
Magnesium binding site 4 out
of 4 in the Proline Aminopeptidase P II From Yersinia Pestis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Proline Aminopeptidase P II From Yersinia Pestis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:24.8
occ:1.00
|
OD1
|
B:ASP269
|
2.2
|
23.8
|
1.0
|
O
|
B:HOH844
|
2.2
|
38.8
|
1.0
|
OE1
|
B:GLU405
|
2.2
|
23.2
|
1.0
|
OD2
|
B:ASP258
|
2.3
|
19.7
|
1.0
|
OD1
|
B:ASP258
|
2.4
|
20.4
|
1.0
|
CG
|
B:ASP258
|
2.7
|
19.9
|
1.0
|
CG
|
B:ASP269
|
3.0
|
25.2
|
1.0
|
CD
|
B:GLU405
|
3.1
|
20.8
|
1.0
|
MG
|
B:MG501
|
3.1
|
26.8
|
1.0
|
OE2
|
B:GLU405
|
3.2
|
19.0
|
1.0
|
OD2
|
B:ASP269
|
3.3
|
29.2
|
1.0
|
OG1
|
B:THR271
|
3.5
|
17.9
|
1.0
|
C12
|
B:P6G503
|
3.8
|
46.1
|
1.0
|
OH
|
B:TYR227
|
3.9
|
17.8
|
1.0
|
C11
|
B:P6G503
|
4.1
|
44.6
|
1.0
|
O13
|
B:P6G503
|
4.1
|
36.2
|
1.0
|
CB
|
B:ASP258
|
4.2
|
18.7
|
1.0
|
OE1
|
B:GLU382
|
4.2
|
29.7
|
1.0
|
CZ
|
B:TYR227
|
4.4
|
20.0
|
1.0
|
CB
|
B:ASP269
|
4.4
|
19.9
|
1.0
|
O
|
B:HOH781
|
4.5
|
33.7
|
1.0
|
CG
|
B:GLU405
|
4.5
|
18.9
|
1.0
|
C14
|
B:P6G503
|
4.5
|
41.0
|
1.0
|
NE
|
B:ARG403
|
4.6
|
19.4
|
1.0
|
C
|
B:ASP269
|
4.7
|
17.7
|
1.0
|
O
|
B:ILE270
|
4.7
|
17.8
|
1.0
|
CE2
|
B:TYR227
|
4.7
|
19.7
|
1.0
|
C
|
B:ILE270
|
4.8
|
17.0
|
1.0
|
O16
|
B:P6G503
|
4.8
|
40.7
|
1.0
|
CA
|
B:ASP269
|
4.8
|
18.3
|
1.0
|
CD
|
B:GLU382
|
4.9
|
27.7
|
1.0
|
N
|
B:ILE270
|
4.9
|
17.3
|
1.0
|
OE2
|
B:GLU382
|
4.9
|
26.7
|
1.0
|
O
|
B:ASP269
|
4.9
|
18.0
|
1.0
|
CB
|
B:THR271
|
4.9
|
18.1
|
1.0
|
NH1
|
B:ARG403
|
4.9
|
23.3
|
1.0
|
CB
|
B:GLU405
|
5.0
|
18.4
|
1.0
|
CA
|
B:ASP258
|
5.0
|
18.1
|
1.0
|
|
Reference:
J.Osipiuk,
N.Maltseva,
S.Shatsman,
W.F.Anderson,
A.Joachimiak.
Proline Aminopeptidase P II From Yersinia Pestis To Be Published.
Page generated: Tue Aug 20 01:41:11 2024
|