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:

Chlorine (Cl) 2 atoms

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

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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: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

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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: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

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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: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


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: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

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