Magnesium in PDB 3n9v: Crystal Structure of INPP5B

All present enzymatic activity of Crystal Structure of INPP5B:
3.1.3.36;

The structure of Crystal Structure of INPP5B, PDB code: 3n9v was solved by L.Tresaugues, M.Welin, C.H.Arrowsmith, H.Berglund, C.Bountra, R.Collins, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, I.Johansson, T.Karlberg, S.Kol, T.Kotenyova, M.Moche, T.Nyman, C.Persson, H.Schuler, P.Schutz, M.I.Siponen, A.G.Thorsell, S.Van Der Berg, E.Wahlberg, J.Weigelt, M.Wisniewska, P.Nordlund, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.66 / 2.65
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.160, 110.660, 159.380, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.1

The structure of Crystal Structure of INPP5B also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of INPP5B (pdb code 3n9v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of INPP5B, PDB code: 3n9v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of INPP5B


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 INPP5B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg61 b:59.0 occ:1.00 O A:HOH18 2.1 49.4 1.0 OD1 A:ASN275 2.1 64.6 1.0 O A:HOH17 2.4 54.3 1.0 OE1 A:GLU303 2.4 70.4 1.0 CD A:GLU303 3.3 65.9 1.0 CG A:ASN275 3.3 61.2 1.0 OE2 A:GLU303 3.4 68.4 1.0 OD2 A:ASP548 3.7 57.2 1.0 CB A:ASN275 4.2 61.0 1.0 CD1 A:LEU306 4.3 47.4 1.0 CA A:ASN275 4.3 60.2 1.0 OD1 A:ASP548 4.3 57.9 1.0 ND2 A:ASN275 4.3 56.3 1.0 CG A:ASP548 4.5 59.9 1.0 CG A:GLU303 4.8 58.8 1.0 OD1 A:ASN273 4.8 62.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of INPP5B


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 INPP5B within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg62 b:89.0 occ:1.00 OE1 B:GLU303 2.3 82.4 1.0 OD1 B:ASN275 2.5 86.4 1.0 CD B:GLU303 3.0 78.6 1.0 OE2 B:GLU303 3.1 81.6 1.0 CG B:ASN275 3.7 85.1 1.0 OD2 B:ASP548 4.2 86.8 1.0 OD1 B:ASN273 4.4 75.2 1.0 CB B:ASN275 4.5 82.7 1.0 CG B:GLU303 4.5 72.4 1.0 ND2 B:ASN273 4.5 69.8 1.0 CA B:ASN275 4.6 81.1 1.0 ND2 B:ASN275 4.6 84.5 1.0 OD1 B:ASP548 4.7 84.3 1.0 CG B:ASN273 4.9 72.4 1.0 CG B:ASP548 4.9 84.9 1.0 NE2 B:HIS549 5.0 80.8 1.0

L.Tresaugues, C.Silvander, S.Flodin, M.Welin, T.Nyman, S.Graslund, M.Hammarstrom, H.Berglund, P.Nordlund. Structural Basis For Phosphoinositide Substrate Recognition, Catalysis, and Membrane Interactions in Human Inositol Polyphosphate 5-Phosphatases Structure V. 22 744 2014.
ISSN: ISSN 0969-2126
PubMed: 24704254
DOI: 10.1016/J.STR.2014.01.013