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:

Chlorine (Cl) 1 atom

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

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