Magnesium in PDB 5okn: Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant

Enzymatic activity of Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant

All present enzymatic activity of Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant:
3.1.3.86;

Protein crystallography data

The structure of Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant, PDB code: 5okn was solved by J.Le Coq, D.Lietha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.17 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 137.065, 177.143, 177.371, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant (pdb code 5okn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant, PDB code: 5okn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5okn

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Magnesium binding site 1 out of 6 in the Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg902

b:83.0
occ:1.00
 O C:HOH1005 2.2 71.9 1.0
O2 C:PO4901 2.5 0.9 1.0
O C:HOH1015 3.2 48.1 1.0
P C:PO4901 3.9 0.2 1.0
OD1 C:ASN432 3.9 40.4 1.0
CG C:GLU473 4.0 49.5 1.0
NE2 C:HIS718 4.2 40.7 1.0
ND2 C:ASN432 4.2 40.1 1.0
O1 C:PO4901 4.3 0.6 1.0
OD1 C:ASP717 4.3 43.6 1.0
OD2 C:ASP717 4.3 44.5 1.0
CG C:ASN432 4.5 39.9 1.0
O3 C:PO4901 4.5 0.2 1.0
CD C:GLU473 4.6 52.5 1.0
CD2 C:HIS718 4.7 40.8 1.0
CA C:GLY434 4.7 43.6 1.0
CB C:GLU473 4.8 47.8 1.0
CG C:ASP717 4.8 44.0 1.0
OE1 C:GLU473 4.8 55.5 1.0
O4 C:PO4901 5.0 0.5 1.0

Magnesium binding site 2 out of 6 in 5okn

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Magnesium binding site 2 out of 6 in the Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg902

b:50.6
occ:1.00
 O2 D:PO4901 2.0 61.7 1.0
O D:HOH1002 2.2 55.0 1.0
O D:HOH1021 2.2 51.7 1.0
OE2 D:GLU473 2.4 41.0 1.0
CD D:GLU473 3.2 41.1 1.0
OE1 D:GLU473 3.3 42.3 1.0
P D:PO4901 3.5 62.3 1.0
O D:HOH1034 3.5 56.3 1.0
ND2 D:ASN432 3.9 39.0 1.0
OD2 D:ASP717 3.9 45.6 1.0
NE2 D:HIS718 3.9 39.7 1.0
OD1 D:ASP717 4.0 45.0 1.0
O4 D:PO4901 4.1 60.8 1.0
O3 D:PO4901 4.1 61.3 1.0
OD1 D:ASN432 4.1 40.5 1.0
CG D:ASN432 4.3 39.5 1.0
CG D:ASP717 4.4 45.0 1.0
CD2 D:HIS718 4.4 40.1 1.0
O1 D:PO4901 4.4 61.4 1.0
CG D:GLU473 4.6 40.2 1.0
CE1 D:TYR661 4.7 44.5 1.0

Magnesium binding site 3 out of 6 in 5okn

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Magnesium binding site 3 out of 6 in the Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg902

b:78.9
occ:1.00
 O4 E:PO4901 2.4 0.1 1.0
O E:HOH1028 2.8 53.6 1.0
OE2 E:GLU473 3.1 46.8 1.0
O E:HOH1024 3.2 59.9 1.0
CD E:GLU473 3.4 45.5 1.0
OD1 E:ASN432 3.6 34.6 1.0
CG E:GLU473 3.8 43.1 1.0
P E:PO4901 3.9 0.0 1.0
OE1 E:GLU473 4.0 48.3 1.0
ND2 E:ASN432 4.1 34.3 1.0
CG E:ASN432 4.2 34.1 1.0
OD1 E:ASP717 4.3 38.0 1.0
NE2 E:HIS718 4.4 34.9 1.0
CA E:GLY434 4.5 37.9 1.0
OD2 E:ASP717 4.5 38.2 1.0
O2 E:PO4901 4.6 0.4 1.0
CB E:GLU473 4.6 42.2 1.0
O3 E:PO4901 4.7 0.3 1.0
CD2 E:HIS718 4.7 34.9 1.0
O1 E:PO4901 4.7 0.7 1.0
CG E:ASP717 4.9 37.7 1.0

Magnesium binding site 4 out of 6 in 5okn

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Magnesium binding site 4 out of 6 in the Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg902

b:58.2
occ:1.00
 O F:HOH1021 1.9 59.1 1.0
O2 F:PO4901 2.3 85.5 1.0
OE2 F:GLU473 2.4 42.1 1.0
CD F:GLU473 3.2 42.2 1.0
OE1 F:GLU473 3.2 43.5 1.0
P F:PO4901 3.6 83.6 1.0
O1 F:PO4901 3.9 85.9 1.0
OD2 F:ASP717 4.0 47.0 1.0
OD1 F:ASN432 4.2 41.5 1.0
ND2 F:ASN432 4.2 40.1 1.0
NE2 F:HIS718 4.3 40.8 1.0
O3 F:PO4901 4.3 82.8 1.0
OD1 F:ASP717 4.4 45.9 1.0
CG F:ASN432 4.6 40.6 1.0
CG F:GLU473 4.6 41.2 1.0
CG F:ASP717 4.6 46.6 1.0
O4 F:PO4901 4.7 84.7 1.0
CD2 F:HIS718 4.7 41.3 1.0

Magnesium binding site 5 out of 6 in 5okn

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Magnesium binding site 5 out of 6 in the Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg902

b:75.0
occ:1.00
 O4 G:PO4901 1.9 0.8 1.0
O G:HOH1007 2.8 58.5 1.0
P G:PO4901 3.4 0.7 1.0
OE1 G:GLU473 3.7 57.5 1.0
ND2 G:ASN432 3.8 40.1 1.0
OD1 G:ASN432 3.8 40.8 1.0
O1 G:PO4901 4.0 0.8 1.0
CG G:GLU473 4.0 52.7 1.0
NE2 G:HIS718 4.0 39.8 1.0
CG G:ASN432 4.2 40.3 1.0
O2 G:PO4901 4.2 0.7 1.0
O3 G:PO4901 4.3 0.6 1.0
CD G:GLU473 4.3 55.9 1.0
CD2 G:HIS718 4.5 39.7 1.0
OD1 G:ASP717 4.5 42.6 1.0
OD2 G:ASP717 4.8 43.9 1.0
CB G:GLU473 4.9 51.4 1.0

Magnesium binding site 6 out of 6 in 5okn

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Magnesium binding site 6 out of 6 in the Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human SHIP2 Phosphatase-C2 D607A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg902

b:60.3
occ:1.00
 O2 H:PO4901 2.1 72.8 1.0
O H:HOH1024 2.1 54.1 1.0
OE2 H:GLU473 2.4 47.8 1.0
O H:HOH1006 2.4 62.3 1.0
CD H:GLU473 3.2 47.8 1.0
OE1 H:GLU473 3.3 49.2 1.0
P H:PO4901 3.6 74.3 1.0
ND2 H:ASN432 4.2 43.7 1.0
O3 H:PO4901 4.2 72.0 1.0
O1 H:PO4901 4.3 74.9 1.0
OD1 H:ASP717 4.3 54.3 1.0
OD2 H:ASP717 4.3 54.1 1.0
NE2 H:HIS718 4.4 45.9 1.0
O4 H:PO4901 4.4 71.5 1.0
OD1 H:ASN432 4.4 45.3 1.0
CG H:GLU473 4.7 46.4 1.0
CG H:ASN432 4.7 44.1 1.0
CD2 H:HIS718 4.8 46.5 1.0
CG H:ASP717 4.8 54.0 1.0

Reference:

J.Le Coq, M.Camacho-Artacho, J.V.Velazquez, C.M.Santiveri, L.H.Gallego, R.Campos-Olivas, N.Dolker, D.Lietha. Structural Basis For Interdomain Communication in SHIP2 Providing High Phosphatase Activity. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28792888
DOI: 10.7554/ELIFE.26640
Page generated: Mon Dec 14 21:00:15 2020

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