Magnesium in PDB 2wef: Human 3'(2'), 5'-Bisphosphate Nucleotidase 1 (BPNT1) in Complex with Amp, PO4 and Magnesium

All present enzymatic activity of Human 3'(2'), 5'-Bisphosphate Nucleotidase 1 (BPNT1) in Complex with Amp, PO4 and Magnesium:
3.1.3.7;

The structure of Human 3'(2'), 5'-Bisphosphate Nucleotidase 1 (BPNT1) in Complex with Amp, PO4 and Magnesium, PDB code: 2wef was solved by M.Moche, P.Schutz, C.H.Arrowsmith, H.Berglund, C.Bountra, R.Collins, L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, A.Johansson, I.Johansson, T.Karlberg, T.Kotenyova, M.E.Nilsson, T.Nyman, C.Persson, J.Sagemark, H.Schueler, M.I.Siponen, A.G.Thorsell, L.Tresaugues, S.Van Der Berg, J.Weigelt, M.Welin, 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)	19.52 / 1.80
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.980, 67.664, 100.394, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 18.9

The binding sites of Magnesium atom in the Human 3'(2'), 5'-Bisphosphate Nucleotidase 1 (BPNT1) in Complex with Amp, PO4 and Magnesium (pdb code 2wef). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human 3'(2'), 5'-Bisphosphate Nucleotidase 1 (BPNT1) in Complex with Amp, PO4 and Magnesium, PDB code: 2wef:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human 3'(2'), 5'-Bisphosphate Nucleotidase 1 (BPNT1) in Complex with Amp, PO4 and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human 3'(2'), 5'-Bisphosphate Nucleotidase 1 (BPNT1) in Complex with Amp, PO4 and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:2.0 occ:1.00 O3 A:PO4501 2.0 7.3 1.0 OD1 A:ASP247 2.0 9.4 1.0 OD1 A:ASP120 2.0 10.2 1.0 OD2 A:ASP117 2.1 7.7 1.0 O A:HOH2206 2.3 12.2 1.0 O3' A:AMP601 2.3 14.2 1.0 CG A:ASP247 3.1 8.7 1.0 CG A:ASP120 3.2 8.6 1.0 CG A:ASP117 3.2 10.4 1.0 P A:PO4501 3.2 8.5 1.0 C3' A:AMP601 3.5 15.4 1.0 OD2 A:ASP247 3.6 9.6 1.0 OD1 A:ASP117 3.7 9.0 1.0 CB A:ASP120 3.7 8.1 1.0 O1 A:PO4501 3.7 9.7 1.0 MG A:MG402 3.7 2.0 1.0 CA A:ASP120 3.9 6.3 1.0 O2 A:PO4501 3.9 7.8 1.0 C4' A:AMP601 4.0 12.7 1.0 OE1 A:GLU74 4.1 7.8 1.0 OD2 A:ASP120 4.3 10.2 1.0 CB A:ASP247 4.3 7.5 1.0 CB A:ASP117 4.4 6.6 1.0 CD1 A:TRP246 4.4 6.7 1.0 O4 A:PO4501 4.4 6.2 1.0 O4' A:AMP601 4.5 16.1 1.0 C2' A:AMP601 4.5 18.6 1.0 CD A:GLU74 4.6 10.2 1.0 C1' A:AMP601 4.6 17.1 1.0 NE1 A:TRP246 4.6 8.4 1.0 O2' A:AMP601 4.6 20.5 1.0 OE2 A:GLU74 4.7 11.5 1.0 CA A:ASP247 4.7 8.0 1.0 O A:LEU119 4.7 8.4 1.0 N A:GLY121 4.7 6.0 1.0 O A:HOH2249 4.8 14.4 1.0 C A:ASP120 4.8 6.5 1.0 N A:ASP120 4.9 7.3 1.0

Magnesium binding site 2 out of 3 in the Human 3'(2'), 5'-Bisphosphate Nucleotidase 1 (BPNT1) in Complex with Amp, PO4 and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human 3'(2'), 5'-Bisphosphate Nucleotidase 1 (BPNT1) in Complex with Amp, PO4 and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:2.0 occ:1.00 OE1 A:GLU74 2.1 7.8 1.0 OD1 A:ASP117 2.1 9.0 1.0 O A:LEU119 2.1 8.4 1.0 O A:HOH2038 2.1 7.8 1.0 O3 A:PO4501 2.1 7.3 1.0 O4 A:PO4501 2.2 6.2 1.0 P A:PO4501 2.7 8.5 1.0 CG A:ASP117 3.0 10.4 1.0 C A:LEU119 3.1 6.8 1.0 CD A:GLU74 3.2 10.2 1.0 OD2 A:ASP117 3.3 7.7 1.0 OE2 A:GLU74 3.7 11.5 1.0 MG A:MG401 3.7 2.0 1.0 O1 A:PO4501 3.7 9.7 1.0 N A:ASP120 3.9 7.3 1.0 O2 A:PO4501 3.9 7.8 1.0 N A:LEU119 3.9 7.4 1.0 CA A:ASP120 3.9 6.3 1.0 OD2 A:ASP51 4.0 12.3 1.0 OE2 A:GLU75 4.0 12.1 1.0 OG1 A:THR122 4.1 8.8 1.0 CA A:LEU119 4.1 8.0 1.0 O A:HOH2206 4.2 12.2 1.0 CD A:PRO118 4.3 7.7 1.0 O A:HOH2064 4.3 15.0 1.0 CG A:GLU74 4.4 7.6 1.0 CB A:ASP117 4.4 6.6 1.0 MG A:MG403 4.5 6.0 1.0 N A:PRO118 4.6 7.6 1.0 CB A:GLU74 4.6 9.1 1.0 CA A:ASP117 4.7 7.5 1.0 C A:ASP117 4.7 7.6 1.0 CB A:LEU119 4.7 7.5 1.0 CB A:ASP120 4.7 8.1 1.0 OD1 A:ASP120 4.8 10.2 1.0 CG A:PRO118 4.8 7.3 1.0 O3' A:AMP601 5.0 14.2 1.0

Magnesium binding site 3 out of 3 in the Human 3'(2'), 5'-Bisphosphate Nucleotidase 1 (BPNT1) in Complex with Amp, PO4 and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human 3'(2'), 5'-Bisphosphate Nucleotidase 1 (BPNT1) in Complex with Amp, PO4 and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:6.0 occ:1.00 O1 A:PO4501 2.0 9.7 1.0 OE2 A:GLU74 2.0 11.5 1.0 O A:HOH2033 2.1 17.9 1.0 O A:HOH2035 2.1 19.2 1.0 O A:HOH2064 2.1 15.0 1.0 O A:HOH2249 2.2 14.4 1.0 CD A:GLU74 3.2 10.2 1.0 P A:PO4501 3.2 8.5 1.0 O4 A:PO4501 3.3 6.2 1.0 OD1 A:ASP45 3.8 19.8 1.0 OE1 A:GLU74 3.8 7.8 1.0 O A:HOH2203 4.0 19.8 1.0 O A:HOH2206 4.0 12.2 1.0 O3 A:PO4501 4.1 7.3 1.0 O2' A:AMP601 4.1 20.5 1.0 NZ A:LYS40 4.1 18.8 1.0 CG A:GLU74 4.3 7.6 1.0 O2 A:PO4501 4.4 7.8 1.0 OE2 A:GLU75 4.5 12.1 1.0 MG A:MG402 4.5 2.0 1.0 O3' A:AMP601 4.5 14.2 1.0 CE A:LYS40 4.5 20.2 1.0 O A:LEU46 4.5 12.0 1.0 O A:HOH2032 4.5 16.3 1.0 N3 A:AMP601 4.5 27.4 1.0 O A:HOH2202 4.9 32.2 1.0

M.Moche, P.Schutz, C.H.Arrowsmith, H.Berglund, C.Bountra, R.Collins, L.G.Dahlgren, A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, A.Johansson, I.Johansson, T.Karlberg, T.Kotenyova, M.E.Nilsson, T.Nyman, C.Persson, J.Sagemark, H.Schueler, M.I.Siponen, A.G.Thorsell, L.Tresaugues, S.Van Den Berg, J.Weigelt, M.Welin, M.Wisniewska, P.Nordlund. Human 3'(2'), 5'-Bisphosphate Nucleotidase 1 ( BPNT1) in Complex with Amp, PO4 and Magnesium To Be Published.