Manganese in PDB 5obl: X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana
Enzymatic activity of X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana
All present enzymatic activity of X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana:
3.1.3.16;
Protein crystallography data
The structure of X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana, PDB code: 5obl
was solved by
S.Von Horsten,
L.-O.Essen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
34.84 /
3.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.580,
103.010,
95.060,
90.00,
95.56,
90.00
|
R / Rfree (%)
|
18.1 /
25.4
|
Other elements in 5obl:
The structure of X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana
(pdb code 5obl). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana, PDB code: 5obl:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 5obl
Go back to
Manganese Binding Sites List in 5obl
Manganese binding site 1 out
of 4 in the X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn501
b:8.2
occ:1.00
|
OD2
|
A:ASP228
|
2.0
|
7.4
|
1.0
|
NE2
|
A:HIS230
|
2.1
|
6.9
|
1.0
|
OD2
|
A:ASP257
|
2.1
|
5.8
|
1.0
|
CE1
|
A:HIS230
|
3.0
|
6.6
|
1.0
|
CL
|
A:CL503
|
3.1
|
32.2
|
1.0
|
MN
|
A:MN502
|
3.1
|
5.1
|
1.0
|
CG
|
A:ASP228
|
3.1
|
10.6
|
1.0
|
CD2
|
A:HIS230
|
3.2
|
6.1
|
1.0
|
CG
|
A:ASP257
|
3.3
|
6.6
|
1.0
|
CB
|
A:ASP228
|
3.8
|
9.3
|
1.0
|
O
|
A:HIS413
|
3.9
|
7.4
|
1.0
|
CB
|
A:ASP257
|
4.1
|
9.3
|
1.0
|
OD1
|
A:ASP228
|
4.1
|
18.4
|
1.0
|
ND1
|
A:HIS230
|
4.2
|
7.0
|
1.0
|
OD1
|
A:ASP257
|
4.2
|
6.4
|
1.0
|
CG
|
A:HIS230
|
4.3
|
8.1
|
1.0
|
CA
|
A:HIS413
|
4.3
|
6.3
|
1.0
|
C
|
A:HIS413
|
4.3
|
5.9
|
1.0
|
CD2
|
A:HIS290
|
4.5
|
7.7
|
1.0
|
CE2
|
A:PHE432
|
4.5
|
5.0
|
1.0
|
NE2
|
A:HIS338
|
4.5
|
4.2
|
1.0
|
CE1
|
A:HIS338
|
4.6
|
4.5
|
1.0
|
OH
|
A:TYR437
|
4.6
|
15.4
|
1.0
|
ND1
|
A:HIS413
|
4.8
|
6.7
|
1.0
|
OD1
|
A:ASN289
|
4.9
|
7.0
|
1.0
|
N
|
A:HIS413
|
5.0
|
6.3
|
1.0
|
|
Manganese binding site 2 out
of 4 in 5obl
Go back to
Manganese Binding Sites List in 5obl
Manganese binding site 2 out
of 4 in the X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn502
b:5.1
occ:1.00
|
ND1
|
A:HIS413
|
2.2
|
6.7
|
1.0
|
NE2
|
A:HIS338
|
2.2
|
4.2
|
1.0
|
OD1
|
A:ASN289
|
2.2
|
7.0
|
1.0
|
OD2
|
A:ASP257
|
2.5
|
5.8
|
1.0
|
CL
|
A:CL503
|
2.9
|
32.2
|
1.0
|
CE1
|
A:HIS338
|
3.1
|
4.5
|
1.0
|
CE1
|
A:HIS413
|
3.1
|
6.7
|
1.0
|
MN
|
A:MN501
|
3.1
|
8.2
|
1.0
|
CG
|
A:ASN289
|
3.1
|
7.6
|
1.0
|
CG
|
A:HIS413
|
3.2
|
6.8
|
1.0
|
CG
|
A:ASP257
|
3.2
|
6.6
|
1.0
|
CD2
|
A:HIS338
|
3.3
|
6.0
|
1.0
|
CA
|
A:HIS413
|
3.3
|
6.3
|
1.0
|
ND2
|
A:ASN289
|
3.3
|
7.3
|
1.0
|
OD1
|
A:ASP257
|
3.4
|
6.4
|
1.0
|
CB
|
A:HIS413
|
3.5
|
5.7
|
1.0
|
OD2
|
A:ASP228
|
3.6
|
7.4
|
1.0
|
O
|
A:HIS413
|
3.7
|
7.4
|
1.0
|
C
|
A:HIS413
|
4.0
|
5.9
|
1.0
|
ND1
|
A:HIS338
|
4.2
|
4.9
|
1.0
|
NE2
|
A:HIS413
|
4.2
|
4.5
|
1.0
|
CD2
|
A:HIS413
|
4.3
|
6.6
|
1.0
|
CG
|
A:HIS338
|
4.4
|
5.0
|
1.0
|
N
|
A:HIS413
|
4.4
|
6.3
|
1.0
|
CG
|
A:ASP228
|
4.4
|
10.6
|
1.0
|
CB
|
A:ASN289
|
4.5
|
4.6
|
1.0
|
N
|
A:ASN289
|
4.5
|
4.3
|
1.0
|
CB
|
A:ASP257
|
4.5
|
9.3
|
1.0
|
CD2
|
A:HIS290
|
4.6
|
7.7
|
1.0
|
OD1
|
A:ASP228
|
4.6
|
18.4
|
1.0
|
NE2
|
A:HIS230
|
4.8
|
6.9
|
1.0
|
O
|
A:LEU371
|
5.0
|
5.2
|
1.0
|
|
Manganese binding site 3 out
of 4 in 5obl
Go back to
Manganese Binding Sites List in 5obl
Manganese binding site 3 out
of 4 in the X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn501
b:2.7
occ:1.00
|
OD2
|
B:ASP228
|
2.0
|
5.4
|
1.0
|
NE2
|
B:HIS230
|
2.3
|
6.3
|
1.0
|
OD2
|
B:ASP257
|
2.3
|
6.5
|
1.0
|
MN
|
B:MN502
|
3.0
|
11.7
|
1.0
|
CE1
|
B:HIS230
|
3.2
|
7.5
|
1.0
|
O
|
B:HOH603
|
3.2
|
6.7
|
1.0
|
CG
|
B:ASP228
|
3.2
|
5.8
|
1.0
|
CD2
|
B:HIS230
|
3.3
|
5.5
|
1.0
|
CG
|
B:ASP257
|
3.5
|
7.6
|
1.0
|
O
|
B:HIS413
|
3.9
|
8.9
|
1.0
|
CB
|
B:ASP228
|
4.0
|
6.2
|
1.0
|
CB
|
B:ASP257
|
4.1
|
5.5
|
1.0
|
CA
|
B:HIS413
|
4.1
|
8.4
|
1.0
|
OD1
|
B:ASP228
|
4.1
|
7.8
|
1.0
|
C
|
B:HIS413
|
4.2
|
7.9
|
1.0
|
OH
|
B:TYR437
|
4.2
|
12.1
|
1.0
|
ND1
|
B:HIS230
|
4.3
|
8.2
|
1.0
|
CG
|
B:HIS230
|
4.4
|
7.6
|
1.0
|
ND1
|
B:HIS413
|
4.5
|
7.1
|
1.0
|
NE2
|
B:HIS338
|
4.5
|
7.5
|
1.0
|
CE1
|
B:HIS338
|
4.5
|
6.6
|
1.0
|
OD1
|
B:ASP257
|
4.5
|
6.2
|
1.0
|
CD2
|
B:HIS290
|
4.6
|
9.1
|
1.0
|
CE2
|
B:PHE432
|
4.7
|
9.5
|
1.0
|
OD1
|
B:ASN289
|
4.8
|
5.5
|
1.0
|
N
|
B:HIS413
|
4.9
|
9.5
|
1.0
|
CZ
|
B:TYR437
|
4.9
|
12.2
|
1.0
|
OE1
|
B:GLU61
|
4.9
|
19.1
|
1.0
|
|
Manganese binding site 4 out
of 4 in 5obl
Go back to
Manganese Binding Sites List in 5obl
Manganese binding site 4 out
of 4 in the X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn502
b:11.7
occ:1.00
|
ND1
|
B:HIS413
|
2.1
|
7.1
|
1.0
|
NE2
|
B:HIS338
|
2.1
|
7.5
|
1.0
|
OD1
|
B:ASN289
|
2.3
|
5.5
|
1.0
|
OD2
|
B:ASP257
|
2.5
|
6.5
|
1.0
|
CE1
|
B:HIS338
|
2.9
|
6.6
|
1.0
|
MN
|
B:MN501
|
3.0
|
2.7
|
1.0
|
CG
|
B:HIS413
|
3.0
|
6.5
|
1.0
|
CE1
|
B:HIS413
|
3.1
|
8.7
|
1.0
|
CA
|
B:HIS413
|
3.2
|
8.4
|
1.0
|
CD2
|
B:HIS338
|
3.2
|
8.8
|
1.0
|
CG
|
B:ASP257
|
3.2
|
7.6
|
1.0
|
CB
|
B:HIS413
|
3.3
|
7.9
|
1.0
|
CG
|
B:ASN289
|
3.3
|
7.5
|
1.0
|
OD1
|
B:ASP257
|
3.6
|
6.2
|
1.0
|
OD2
|
B:ASP228
|
3.6
|
5.4
|
1.0
|
O
|
B:HIS413
|
3.7
|
8.9
|
1.0
|
ND2
|
B:ASN289
|
3.8
|
5.7
|
1.0
|
C
|
B:HIS413
|
3.9
|
7.9
|
1.0
|
ND1
|
B:HIS338
|
4.1
|
6.7
|
1.0
|
NE2
|
B:HIS413
|
4.2
|
5.2
|
1.0
|
CD2
|
B:HIS413
|
4.2
|
6.6
|
1.0
|
CG
|
B:HIS338
|
4.2
|
5.7
|
1.0
|
N
|
B:HIS413
|
4.3
|
9.5
|
1.0
|
CB
|
B:ASP257
|
4.4
|
5.5
|
1.0
|
CG
|
B:ASP228
|
4.5
|
5.8
|
1.0
|
N
|
B:ASN289
|
4.5
|
6.6
|
1.0
|
CB
|
B:ASN289
|
4.6
|
6.7
|
1.0
|
OD1
|
B:ASP228
|
4.7
|
7.8
|
1.0
|
CD2
|
B:HIS290
|
4.7
|
9.1
|
1.0
|
NE2
|
B:HIS230
|
4.8
|
6.3
|
1.0
|
O
|
B:HOH603
|
4.9
|
6.7
|
1.0
|
NH2
|
B:ARG386
|
4.9
|
13.8
|
1.0
|
|
Reference:
S.Von Horsten,
L.-O.Essen.
Structural Base For Fatty Acid Control of Phytochrome-Associated Protein Phosphatase 5 To Be Published.
Page generated: Tue Dec 15 04:45:29 2020
|