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Manganese in PDB 3zk4: Structure of Purple Acid Phosphatase PPD1 Isolated From Yellow Lupin (Lupinus Luteus) Seeds

Enzymatic activity of Structure of Purple Acid Phosphatase PPD1 Isolated From Yellow Lupin (Lupinus Luteus) Seeds

All present enzymatic activity of Structure of Purple Acid Phosphatase PPD1 Isolated From Yellow Lupin (Lupinus Luteus) Seeds:
3.1.3.2;

Protein crystallography data

The structure of Structure of Purple Acid Phosphatase PPD1 Isolated From Yellow Lupin (Lupinus Luteus) Seeds, PDB code: 3zk4 was solved by S.V.Antonyuk, R.W.Strange, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.62 / 1.65
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 223.925, 223.925, 111.904, 90.00, 90.00, 90.00
R / Rfree (%) 14.959 / 17.459

Other elements in 3zk4:

The structure of Structure of Purple Acid Phosphatase PPD1 Isolated From Yellow Lupin (Lupinus Luteus) Seeds also contains other interesting chemical elements:

Iron (Fe) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Purple Acid Phosphatase PPD1 Isolated From Yellow Lupin (Lupinus Luteus) Seeds (pdb code 3zk4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Structure of Purple Acid Phosphatase PPD1 Isolated From Yellow Lupin (Lupinus Luteus) Seeds, PDB code: 3zk4:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 3zk4

Go back to Manganese Binding Sites List in 3zk4
Manganese binding site 1 out of 3 in the Structure of Purple Acid Phosphatase PPD1 Isolated From Yellow Lupin (Lupinus Luteus) Seeds


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Purple Acid Phosphatase PPD1 Isolated From Yellow Lupin (Lupinus Luteus) Seeds within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:14.1
occ:1.00
 OD1 A:ASN346 2.1 12.8 1.0
NE2 A:HIS435 2.2 11.8 1.0
ND1 A:HIS477 2.2 12.6 1.0
OD2 A:ASP313 2.3 13.8 1.0
O2 A:PO4999 2.5 19.0 1.0
O3 A:PO4999 2.5 23.5 1.0
P A:PO4999 3.1 22.9 1.0
CE1 A:HIS477 3.1 13.1 1.0
CG A:ASP313 3.1 12.7 1.0
CG A:ASN346 3.1 12.7 1.0
CE1 A:HIS435 3.1 11.7 1.0
CD2 A:HIS435 3.2 11.1 1.0
CG A:HIS477 3.3 12.6 1.0
OD1 A:ASP313 3.3 12.6 1.0
ND2 A:ASN346 3.5 13.4 1.0
CA A:HIS477 3.6 12.7 1.0
FE A:FE800 3.6 17.8 1.0
CB A:HIS477 3.7 12.5 1.0
OD2 A:ASP272 3.9 12.8 1.0
O1 A:PO4999 3.9 18.7 1.0
NE2 A:HIS477 4.2 13.3 1.0
O4 A:PO4999 4.3 22.1 1.0
ND1 A:HIS435 4.3 11.9 1.0
O A:HIS477 4.3 12.4 1.0
CD2 A:HIS347 4.3 14.4 1.0
CG A:HIS435 4.3 11.9 1.0
CB A:ASP313 4.4 13.1 1.0
CD2 A:HIS477 4.4 13.3 1.0
N A:ASN346 4.4 11.2 1.0
CB A:ASN346 4.5 12.4 1.0
C A:HIS477 4.5 11.6 1.0
N A:HIS477 4.6 13.2 1.0
NE2 A:HIS347 5.0 15.5 1.0
CG A:ASP272 5.0 12.9 1.0
CA A:ASN346 5.0 10.8 1.0

Manganese binding site 2 out of 3 in 3zk4

Go back to Manganese Binding Sites List in 3zk4
Manganese binding site 2 out of 3 in the Structure of Purple Acid Phosphatase PPD1 Isolated From Yellow Lupin (Lupinus Luteus) Seeds


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Purple Acid Phosphatase PPD1 Isolated From Yellow Lupin (Lupinus Luteus) Seeds within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn801

b:14.4
occ:1.00
 OD1 B:ASN346 2.1 15.0 1.0
NE2 B:HIS435 2.2 12.5 1.0
ND1 B:HIS477 2.2 14.6 1.0
OD2 B:ASP313 2.2 13.7 1.0
O1 B:PO4999 2.4 18.7 1.0
O4 B:PO4999 2.5 22.7 1.0
CG B:ASP313 3.0 12.6 1.0
P B:PO4999 3.1 23.4 1.0
CE1 B:HIS477 3.1 14.6 1.0
CG B:ASN346 3.1 13.1 1.0
CE1 B:HIS435 3.2 12.3 1.0
CD2 B:HIS435 3.2 12.6 1.0
CG B:HIS477 3.3 12.6 1.0
OD1 B:ASP313 3.3 13.0 1.0
ND2 B:ASN346 3.5 14.2 1.0
CA B:HIS477 3.6 12.7 1.0
FE B:FE800 3.6 19.3 1.0
CB B:HIS477 3.6 11.9 1.0
OD2 B:ASP272 3.8 14.7 1.0
O2 B:PO4999 3.9 20.9 1.0
O3 B:PO4999 4.2 21.5 1.0
NE2 B:HIS477 4.2 14.0 1.0
O B:HIS477 4.3 13.8 1.0
CD2 B:HIS347 4.3 14.6 1.0
ND1 B:HIS435 4.3 11.8 1.0
CG B:HIS435 4.3 12.7 1.0
CB B:ASP313 4.3 13.2 1.0
CD2 B:HIS477 4.3 13.1 1.0
CB B:ASN346 4.4 12.3 1.0
C B:HIS477 4.5 12.4 1.0
N B:ASN346 4.5 12.6 1.0
N B:HIS477 4.6 12.4 1.0
CG B:ASP272 4.9 15.1 1.0
NE2 B:HIS347 4.9 16.4 1.0
CA B:ASN346 5.0 12.9 1.0

Manganese binding site 3 out of 3 in 3zk4

Go back to Manganese Binding Sites List in 3zk4
Manganese binding site 3 out of 3 in the Structure of Purple Acid Phosphatase PPD1 Isolated From Yellow Lupin (Lupinus Luteus) Seeds


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Purple Acid Phosphatase PPD1 Isolated From Yellow Lupin (Lupinus Luteus) Seeds within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn801

b:17.3
occ:1.00
 OD1 C:ASN346 2.0 16.5 1.0
NE2 C:HIS435 2.2 14.9 1.0
ND1 C:HIS477 2.2 14.4 1.0
OD2 C:ASP313 2.3 17.3 1.0
O3 C:PO4999 2.5 19.0 1.0
O1 C:PO4999 2.6 28.0 1.0
P C:PO4999 3.0 29.3 1.0
CG C:ASN346 3.0 16.1 1.0
CG C:ASP313 3.1 18.6 1.0
CD2 C:HIS435 3.1 16.1 1.0
CE1 C:HIS477 3.1 15.9 1.0
CE1 C:HIS435 3.2 14.7 1.0
CG C:HIS477 3.3 14.6 1.0
OD1 C:ASP313 3.3 17.6 1.0
ND2 C:ASN346 3.4 16.8 1.0
FE C:FE800 3.6 21.7 1.0
CA C:HIS477 3.6 15.3 1.0
CB C:HIS477 3.7 13.6 1.0
O2 C:PO4999 3.8 24.5 1.0
OD2 C:ASP272 3.8 19.0 1.0
O4 C:PO4999 4.2 26.4 1.0
NE2 C:HIS477 4.3 15.3 1.0
O C:HIS477 4.3 17.3 1.0
CG C:HIS435 4.3 14.9 1.0
ND1 C:HIS435 4.3 15.7 1.0
CD2 C:HIS347 4.3 20.6 1.0
CB C:ASP313 4.3 19.9 1.0
CD2 C:HIS477 4.4 14.2 1.0
N C:ASN346 4.4 14.8 1.0
CB C:ASN346 4.4 16.1 1.0
C C:HIS477 4.5 15.0 1.0
N C:HIS477 4.6 14.6 1.0
CG C:ASP272 4.9 16.2 1.0
CA C:ASN346 5.0 15.4 1.0

Reference:

S.V.Antonyuk, M.Olczak, T.Olczak, J.Ciuraszkiewicz, R.W.Strange. The Structure of A Purple Acid Phosphatase Involved in Plant Growth and Pathogen Defence Exhibits A Novel Immunoglobulin-Like Fold Iucrj V. 1 101 2014.
ISSN: ISSN 2052-2525
PubMed: 25075326
DOI: 10.1107/S205225251400400X
Page generated: Tue Dec 15 04:17:58 2020

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