Manganese in PDB 7obe: 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: 7obe
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 (°)
|
51.58,
103.01,
95.06,
90,
95.56,
90
|
R / Rfree (%)
|
21 /
24.3
|
Other elements in 7obe:
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 7obe). 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: 7obe:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 7obe
Go back to
Manganese Binding Sites List in 7obe
Manganese binding site 1 out
of 4 in the X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana
![](/pictures/MN/pdb/ob/7obe-MN-sphere_01.jpg) Mono view
![](/pictures/MN/pdb/ob/7obe-MN-sphere_01_stereo.jpg) 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:3.1
occ:1.00
|
OD2
|
A:ASP228
|
1.9
|
18.5
|
1.0
|
NE2
|
A:HIS230
|
2.3
|
18.9
|
1.0
|
O
|
A:HOH611
|
2.3
|
21.8
|
1.0
|
OD2
|
A:ASP257
|
2.4
|
19.2
|
1.0
|
CL
|
A:CL503
|
2.6
|
21.8
|
1.0
|
MN
|
A:MN502
|
3.1
|
3.1
|
1.0
|
CG
|
A:ASP228
|
3.1
|
18.5
|
1.0
|
CE1
|
A:HIS230
|
3.2
|
18.7
|
1.0
|
CD2
|
A:HIS230
|
3.4
|
19.2
|
1.0
|
CG
|
A:ASP257
|
3.5
|
18.8
|
1.0
|
O
|
A:HIS413
|
3.7
|
19.4
|
1.0
|
O
|
A:HOH603
|
3.7
|
7.6
|
1.0
|
O
|
A:HOH604
|
3.9
|
7.6
|
1.0
|
CB
|
A:ASP228
|
4.0
|
18.6
|
1.0
|
CB
|
A:ASP257
|
4.0
|
18.6
|
1.0
|
OD1
|
A:ASP228
|
4.0
|
18.5
|
1.0
|
C
|
A:HIS413
|
4.2
|
19.5
|
1.0
|
CA
|
A:HIS413
|
4.2
|
19.2
|
1.0
|
ND1
|
A:HIS230
|
4.3
|
19.1
|
1.0
|
CG
|
A:HIS230
|
4.5
|
19.4
|
1.0
|
CE1
|
A:HIS338
|
4.5
|
18.1
|
1.0
|
NE2
|
A:HIS338
|
4.5
|
18.6
|
1.0
|
CD2
|
A:HIS290
|
4.5
|
19.6
|
1.0
|
OD1
|
A:ASP257
|
4.6
|
18.6
|
1.0
|
ND1
|
A:HIS413
|
4.6
|
18.6
|
1.0
|
CE2
|
A:PHE432
|
4.6
|
20.0
|
1.0
|
OH
|
A:TYR437
|
4.6
|
21.5
|
1.0
|
OD1
|
A:ASN289
|
4.8
|
19.7
|
1.0
|
N
|
A:HIS413
|
4.9
|
19.0
|
1.0
|
|
Manganese binding site 2 out
of 4 in 7obe
Go back to
Manganese Binding Sites List in 7obe
Manganese binding site 2 out
of 4 in the X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana
![](/pictures/MN/pdb/ob/7obe-MN-sphere_02.jpg) Mono view
![](/pictures/MN/pdb/ob/7obe-MN-sphere_02_stereo.jpg) 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:3.1
occ:1.00
|
NE2
|
A:HIS338
|
2.1
|
18.6
|
1.0
|
OD1
|
A:ASN289
|
2.1
|
19.7
|
1.0
|
ND1
|
A:HIS413
|
2.2
|
18.6
|
1.0
|
OD2
|
A:ASP257
|
2.3
|
19.2
|
1.0
|
CL
|
A:CL503
|
2.6
|
21.8
|
1.0
|
CE1
|
A:HIS338
|
2.9
|
18.1
|
1.0
|
MN
|
A:MN501
|
3.1
|
3.1
|
1.0
|
CG
|
A:ASN289
|
3.1
|
19.5
|
1.0
|
CG
|
A:ASP257
|
3.2
|
18.8
|
1.0
|
CE1
|
A:HIS413
|
3.2
|
18.9
|
1.0
|
CD2
|
A:HIS338
|
3.2
|
19.2
|
1.0
|
CG
|
A:HIS413
|
3.2
|
19.3
|
1.0
|
CA
|
A:HIS413
|
3.3
|
19.2
|
1.0
|
ND2
|
A:ASN289
|
3.4
|
19.5
|
1.0
|
CB
|
A:HIS413
|
3.5
|
19.2
|
1.0
|
OD2
|
A:ASP228
|
3.6
|
18.5
|
1.0
|
OD1
|
A:ASP257
|
3.6
|
18.6
|
1.0
|
O
|
A:HIS413
|
3.8
|
19.4
|
1.0
|
C
|
A:HIS413
|
4.0
|
19.5
|
1.0
|
ND1
|
A:HIS338
|
4.1
|
18.2
|
1.0
|
CG
|
A:HIS338
|
4.3
|
19.0
|
1.0
|
CB
|
A:ASP257
|
4.3
|
18.6
|
1.0
|
N
|
A:HIS413
|
4.3
|
19.0
|
1.0
|
NE2
|
A:HIS413
|
4.3
|
19.7
|
1.0
|
CD2
|
A:HIS413
|
4.4
|
19.9
|
1.0
|
N
|
A:ASN289
|
4.4
|
20.5
|
1.0
|
CG
|
A:ASP228
|
4.5
|
18.5
|
1.0
|
CB
|
A:ASN289
|
4.5
|
19.4
|
1.0
|
OD1
|
A:ASP228
|
4.5
|
18.5
|
1.0
|
CD2
|
A:HIS290
|
4.8
|
19.6
|
1.0
|
NE2
|
A:HIS230
|
4.9
|
18.9
|
1.0
|
O
|
A:LEU371
|
4.9
|
20.7
|
1.0
|
|
Manganese binding site 3 out
of 4 in 7obe
Go back to
Manganese Binding Sites List in 7obe
Manganese binding site 3 out
of 4 in the X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana
![](/pictures/MN/pdb/ob/7obe-MN-sphere_03.jpg) Mono view
![](/pictures/MN/pdb/ob/7obe-MN-sphere_03_stereo.jpg) 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:3.1
occ:1.00
|
OD2
|
B:ASP228
|
2.0
|
17.7
|
1.0
|
NE2
|
B:HIS230
|
2.2
|
15.7
|
1.0
|
OD2
|
B:ASP257
|
2.3
|
16.2
|
1.0
|
O
|
B:HOH610
|
2.6
|
21.8
|
1.0
|
CL
|
B:CL503
|
2.9
|
21.8
|
1.0
|
CE1
|
B:HIS230
|
3.0
|
16.2
|
1.0
|
MN
|
B:MN502
|
3.1
|
3.1
|
1.0
|
CG
|
B:ASP228
|
3.2
|
17.4
|
1.0
|
O
|
B:HOH604
|
3.3
|
26.8
|
1.0
|
CD2
|
B:HIS230
|
3.3
|
15.8
|
1.0
|
CG
|
B:ASP257
|
3.4
|
16.3
|
1.0
|
O
|
B:HOH606
|
3.7
|
26.8
|
1.0
|
O
|
B:HIS413
|
3.7
|
16.8
|
1.0
|
CB
|
B:ASP257
|
4.0
|
15.9
|
1.0
|
CB
|
B:ASP228
|
4.0
|
17.7
|
1.0
|
OD1
|
B:ASP228
|
4.1
|
17.1
|
1.0
|
ND1
|
B:HIS230
|
4.2
|
16.5
|
1.0
|
C
|
B:HIS413
|
4.3
|
16.4
|
1.0
|
CA
|
B:HIS413
|
4.3
|
15.8
|
1.0
|
CD2
|
B:HIS290
|
4.3
|
16.6
|
1.0
|
CG
|
B:HIS230
|
4.4
|
16.3
|
1.0
|
OD1
|
B:ASP257
|
4.5
|
17.0
|
1.0
|
OH
|
B:TYR437
|
4.6
|
20.9
|
1.0
|
CE1
|
B:HIS338
|
4.6
|
14.9
|
1.0
|
NE2
|
B:HIS338
|
4.6
|
15.6
|
1.0
|
CE2
|
B:PHE432
|
4.6
|
16.7
|
1.0
|
ND1
|
B:HIS413
|
4.7
|
16.4
|
1.0
|
OD1
|
B:ASN289
|
4.8
|
15.9
|
1.0
|
ND2
|
B:ASN289
|
4.9
|
16.8
|
1.0
|
NE2
|
B:HIS290
|
4.9
|
17.3
|
1.0
|
|
Manganese binding site 4 out
of 4 in 7obe
Go back to
Manganese Binding Sites List in 7obe
Manganese binding site 4 out
of 4 in the X-Ray Structure of the Phosphatase PAPP5 From Arabidopsis Thaliana
![](/pictures/MN/pdb/ob/7obe-MN-sphere_04.jpg) Mono view
![](/pictures/MN/pdb/ob/7obe-MN-sphere_04_stereo.jpg) 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:3.1
occ:1.00
|
NE2
|
B:HIS338
|
2.1
|
15.6
|
1.0
|
OD1
|
B:ASN289
|
2.1
|
15.9
|
1.0
|
ND1
|
B:HIS413
|
2.2
|
16.4
|
1.0
|
OD2
|
B:ASP257
|
2.3
|
16.2
|
1.0
|
CL
|
B:CL503
|
2.7
|
21.8
|
1.0
|
CE1
|
B:HIS338
|
2.9
|
14.9
|
1.0
|
CG
|
B:ASN289
|
3.0
|
16.7
|
1.0
|
MN
|
B:MN501
|
3.1
|
3.1
|
1.0
|
CE1
|
B:HIS413
|
3.1
|
17.2
|
1.0
|
CG
|
B:ASP257
|
3.1
|
16.3
|
1.0
|
CG
|
B:HIS413
|
3.2
|
16.3
|
1.0
|
CD2
|
B:HIS338
|
3.2
|
15.9
|
1.0
|
CA
|
B:HIS413
|
3.2
|
15.8
|
1.0
|
ND2
|
B:ASN289
|
3.3
|
16.8
|
1.0
|
CB
|
B:HIS413
|
3.5
|
15.6
|
1.0
|
OD1
|
B:ASP257
|
3.5
|
17.0
|
1.0
|
OD2
|
B:ASP228
|
3.6
|
17.7
|
1.0
|
O
|
B:HIS413
|
3.6
|
16.8
|
1.0
|
C
|
B:HIS413
|
3.9
|
16.4
|
1.0
|
ND1
|
B:HIS338
|
4.1
|
14.7
|
1.0
|
NE2
|
B:HIS413
|
4.2
|
17.6
|
1.0
|
CG
|
B:HIS338
|
4.3
|
15.3
|
1.0
|
CD2
|
B:HIS413
|
4.3
|
17.0
|
1.0
|
N
|
B:HIS413
|
4.3
|
15.4
|
1.0
|
CB
|
B:ASP257
|
4.3
|
15.9
|
1.0
|
CB
|
B:ASN289
|
4.4
|
17.9
|
1.0
|
N
|
B:ASN289
|
4.4
|
16.1
|
1.0
|
CG
|
B:ASP228
|
4.5
|
17.4
|
1.0
|
OD1
|
B:ASP228
|
4.6
|
17.1
|
1.0
|
CD2
|
B:HIS290
|
4.7
|
16.6
|
1.0
|
NE2
|
B:HIS230
|
4.9
|
15.7
|
1.0
|
O
|
B:HOH606
|
4.9
|
26.8
|
1.0
|
O
|
B:LEU371
|
4.9
|
17.0
|
1.0
|
|
Reference:
S.Von Horsten,
L.-O.Essen.
Partial Unfolding of Tpr Domain Triggers Phytochrome-Associated Protein Phosphatase 5 To Be Published.
Page generated: Mon Jul 12 15:28:28 2021
|