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Magnesium in PDB 1jp4: Crystal Structure of An Enzyme Displaying Both Inositol-Polyphosphate 1-Phosphatase and 3'-Phosphoadenosine-5'-Phosphate Phosphatase Activities

Enzymatic activity of Crystal Structure of An Enzyme Displaying Both Inositol-Polyphosphate 1-Phosphatase and 3'-Phosphoadenosine-5'-Phosphate Phosphatase Activities

All present enzymatic activity of Crystal Structure of An Enzyme Displaying Both Inositol-Polyphosphate 1-Phosphatase and 3'-Phosphoadenosine-5'-Phosphate Phosphatase Activities:
3.1.3.57; 3.1.3.7;

Protein crystallography data

The structure of Crystal Structure of An Enzyme Displaying Both Inositol-Polyphosphate 1-Phosphatase and 3'-Phosphoadenosine-5'-Phosphate Phosphatase Activities, PDB code: 1jp4 was solved by S.Patel, L.Yenush, P.L.Rodriguez, R.Serrano, T.L.Blundell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.94 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.635, 74.493, 92.827, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 18

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of An Enzyme Displaying Both Inositol-Polyphosphate 1-Phosphatase and 3'-Phosphoadenosine-5'-Phosphate Phosphatase Activities (pdb code 1jp4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of An Enzyme Displaying Both Inositol-Polyphosphate 1-Phosphatase and 3'-Phosphoadenosine-5'-Phosphate Phosphatase Activities, PDB code: 1jp4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1jp4

Go back to Magnesium Binding Sites List in 1jp4
Magnesium binding site 1 out of 3 in the Crystal Structure of An Enzyme Displaying Both Inositol-Polyphosphate 1-Phosphatase and 3'-Phosphoadenosine-5'-Phosphate Phosphatase Activities


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 An Enzyme Displaying Both Inositol-Polyphosphate 1-Phosphatase and 3'-Phosphoadenosine-5'-Phosphate Phosphatase Activities within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:11.3
occ:1.00
 OD1 A:ASP247 2.0 11.3 1.0
OD2 A:ASP117 2.0 9.1 1.0
OD1 A:ASP120 2.0 10.8 1.0
O3 A:PO4501 2.0 10.1 1.0
O3' A:AMP601 2.2 21.5 1.0
O A:HOH840 2.5 14.7 1.0
CG A:ASP120 3.2 12.2 1.0
CG A:ASP117 3.2 10.2 1.0
CG A:ASP247 3.2 13.6 1.0
P A:PO4501 3.3 13.0 1.0
C3' A:AMP601 3.5 22.6 1.0
OD1 A:ASP117 3.6 7.3 1.0
CB A:ASP120 3.6 6.5 1.0
MG A:MG702 3.7 10.0 1.0
OD2 A:ASP247 3.7 10.1 1.0
O1 A:PO4501 3.7 10.7 1.0
C4' A:AMP601 3.8 17.1 1.0
CA A:ASP120 3.8 7.8 1.0
O2 A:PO4501 3.9 11.8 1.0
OE1 A:GLU74 4.2 10.0 1.0
OD2 A:ASP120 4.2 12.6 1.0
CB A:ASP247 4.3 10.1 1.0
CB A:ASP117 4.4 6.5 1.0
O4 A:PO4501 4.4 12.1 1.0
O4' A:AMP601 4.5 15.3 1.0
CD1 A:TRP246 4.5 10.0 1.0
C2' A:AMP601 4.6 22.6 1.0
O A:VAL119 4.6 9.4 1.0
CA A:ASP247 4.6 10.2 1.0
N A:GLY121 4.7 11.0 1.0
C1' A:AMP601 4.7 20.9 1.0
NE1 A:TRP246 4.7 10.7 1.0
C A:ASP120 4.8 9.7 1.0
O2' A:AMP601 4.8 21.6 1.0
CD A:GLU74 4.8 15.2 1.0
N A:ASP120 4.9 7.7 1.0
OE2 A:GLU74 4.9 14.1 1.0

Magnesium binding site 2 out of 3 in 1jp4

Go back to Magnesium Binding Sites List in 1jp4
Magnesium binding site 2 out of 3 in the Crystal Structure of An Enzyme Displaying Both Inositol-Polyphosphate 1-Phosphatase and 3'-Phosphoadenosine-5'-Phosphate Phosphatase Activities


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 An Enzyme Displaying Both Inositol-Polyphosphate 1-Phosphatase and 3'-Phosphoadenosine-5'-Phosphate Phosphatase Activities within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:10.0
occ:1.00
 OE1 A:GLU74 2.0 10.0 1.0
OD1 A:ASP117 2.1 7.3 1.0
O A:VAL119 2.1 9.4 1.0
O3 A:PO4501 2.1 10.1 1.0
O A:HOH811 2.1 9.5 1.0
O4 A:PO4501 2.2 12.1 1.0
P A:PO4501 2.8 13.0 1.0
CG A:ASP117 3.1 10.2 1.0
CD A:GLU74 3.1 15.2 1.0
C A:VAL119 3.2 10.7 1.0
OD2 A:ASP117 3.3 9.1 1.0
OE2 A:GLU74 3.6 14.1 1.0
MG A:MG701 3.7 11.3 1.0
O1 A:PO4501 3.8 10.7 1.0
O2 A:PO4501 3.9 11.8 1.0
N A:ASP120 3.9 7.7 1.0
CA A:ASP120 3.9 7.8 1.0
OD2 A:ASP51 4.0 14.8 1.0
N A:VAL119 4.0 9.7 1.0
OG1 A:THR122 4.1 11.5 1.0
OE2 A:GLU75 4.1 15.7 1.0
O A:HOH840 4.1 14.7 1.0
CA A:VAL119 4.2 8.2 1.0
O A:HOH1216 4.3 19.4 1.0
CG A:GLU74 4.4 8.7 1.0
CB A:ASP117 4.4 6.5 1.0
MG A:MG703 4.4 22.4 1.0
CD A:PRO118 4.4 10.2 1.0
N A:PRO118 4.6 7.5 1.0
CB A:GLU74 4.6 8.9 1.0
C A:ASP117 4.7 8.3 1.0
CA A:ASP117 4.7 7.2 1.0
CB A:ASP120 4.7 6.5 1.0
CB A:VAL119 4.8 8.0 1.0
O3' A:AMP601 4.8 21.5 1.0
CG A:PRO118 4.8 9.8 1.0
OD1 A:ASP120 4.8 10.8 1.0

Magnesium binding site 3 out of 3 in 1jp4

Go back to Magnesium Binding Sites List in 1jp4
Magnesium binding site 3 out of 3 in the Crystal Structure of An Enzyme Displaying Both Inositol-Polyphosphate 1-Phosphatase and 3'-Phosphoadenosine-5'-Phosphate Phosphatase Activities


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 An Enzyme Displaying Both Inositol-Polyphosphate 1-Phosphatase and 3'-Phosphoadenosine-5'-Phosphate Phosphatase Activities within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:22.4
occ:1.00
 O A:HOH1217 2.0 19.1 1.0
O A:HOH1218 2.1 27.9 1.0
OE2 A:GLU74 2.1 14.1 1.0
O1 A:PO4501 2.1 10.7 1.0
O A:HOH1216 2.4 19.4 1.0
O A:HOH1219 2.4 30.8 1.0
O A:HOH929 2.6 24.6 1.0
O4 A:PO4501 3.2 12.1 1.0
P A:PO4501 3.2 13.0 1.0
CD A:GLU74 3.2 15.2 1.0
O A:HOH1033 3.6 40.2 1.0
OD1 A:ASP45 3.7 20.3 1.0
OE1 A:GLU74 3.8 10.0 1.0
NZ A:LYS40 3.9 16.1 1.0
O A:HOH840 4.0 14.7 1.0
O2' A:AMP601 4.1 21.6 1.0
O3 A:PO4501 4.1 10.1 1.0
O2 A:PO4501 4.3 11.8 1.0
CE A:LYS40 4.3 17.0 1.0
CG A:GLU74 4.4 8.7 1.0
MG A:MG702 4.4 10.0 1.0
O A:LEU46 4.4 12.6 1.0
O A:HOH895 4.5 22.7 1.0
OE2 A:GLU75 4.6 15.7 1.0
N3 A:AMP601 4.7 24.3 1.0
O3' A:AMP601 4.7 21.5 1.0
CG A:ASP45 5.0 20.5 1.0

Reference:

S.Patel, L.Yenush, P.L.Rodriguez, R.Serrano, T.L.Blundell. Crystal Structure of An Enzyme Displaying Both Inositol-Polyphosphate-1-Phosphatase and 3'-Phosphoadenosine-5'-Phosphate Phosphatase Activities: A Novel Target of Lithium Therapy. J.Mol.Biol. V. 315 677 2002.
ISSN: ISSN 0022-2836
PubMed: 11812139
DOI: 10.1006/JMBI.2001.5271
Page generated: Sat Aug 9 23:23:30 2025

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