Magnesium in PDB 2j17: Ptyr Bound Form of Sdp-1

All present enzymatic activity of Ptyr Bound Form of Sdp-1:
3.1.3.48;

The structure of Ptyr Bound Form of Sdp-1, PDB code: 2j17 was solved by D.C.Briggs, N.Q.Mcdonald, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.34 / 2.84
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.661, 61.661, 217.562, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 26.9

The binding sites of Magnesium atom in the Ptyr Bound Form of Sdp-1 (pdb code 2j17). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Ptyr Bound Form of Sdp-1, PDB code: 2j17:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Ptyr Bound Form of Sdp-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ptyr Bound Form of Sdp-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1197 b:65.8 occ:1.00 OD1 A:ASN93 2.0 58.5 1.0 OE2 A:GLU73 2.6 55.2 1.0 OE1 A:GLU73 2.7 55.0 1.0 CD A:GLU73 2.9 54.4 1.0 CG A:ASN93 3.2 58.4 1.0 ND2 A:ASN93 3.9 58.9 1.0 N A:ASN93 4.3 56.3 1.0 CB A:ASN93 4.3 57.2 1.0 CG A:GLU73 4.4 51.9 1.0 O A:GLU91 4.7 54.5 1.0 OE1 A:GLN141 4.8 54.0 1.0 CA A:ASN93 4.9 57.0 1.0

Magnesium binding site 2 out of 5 in the Ptyr Bound Form of Sdp-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ptyr Bound Form of Sdp-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1198 b:88.2 occ:1.00 OE1 A:GLU110 2.9 66.3 1.0 O A:HOH2009 3.0 73.7 1.0 O A:HOH2010 3.1 57.0 1.0 OD2 A:ASP112 3.2 59.9 1.0 OD1 A:ASP112 3.3 58.1 1.0 CG A:ASP112 3.7 59.2 1.0 O A:HOH2011 3.8 62.5 1.0 CD A:GLU110 3.9 64.3 1.0 OE2 A:GLU110 4.4 64.6 1.0 CB A:GLU110 4.7 59.7 1.0 CG A:GLU110 4.9 61.6 1.0

Magnesium binding site 3 out of 5 in the Ptyr Bound Form of Sdp-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ptyr Bound Form of Sdp-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1197 b:49.4 occ:1.00 ND2 B:ASN93 2.2 59.5 1.0 OE2 B:GLU73 2.4 50.3 1.0 OE1 B:GLU73 2.7 50.3 1.0 CD B:GLU73 2.9 50.2 1.0 CG B:ASN93 3.5 58.3 1.0 OD1 B:ASN93 4.3 60.3 1.0 CB B:ASN93 4.4 56.9 1.0 CG B:GLU73 4.4 49.6 1.0 N B:ASN93 4.5 56.1 1.0 OE1 B:GLN141 4.6 51.2 1.0 NE2 B:GLN141 4.8 51.6 1.0 O B:GLU91 4.9 55.9 1.0

Magnesium binding site 4 out of 5 in the Ptyr Bound Form of Sdp-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ptyr Bound Form of Sdp-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1198 b:27.4 occ:0.50 O B:HOH2005 2.6 33.8 1.0 OE2 B:GLU134 2.6 53.3 1.0 CD B:GLU134 3.5 50.9 1.0 OE1 B:GLU103 3.9 49.4 1.0 OE1 B:GLU134 3.9 52.2 1.0 CB B:ASP83 4.0 43.7 1.0 CB B:GLU103 4.1 47.9 1.0 O B:ASP83 4.1 44.1 1.0 C B:ASP83 4.4 43.7 1.0 CG B:GLU134 4.6 50.0 1.0 CG2 B:VAL84 4.6 43.5 1.0 CA B:ASP83 4.6 43.6 1.0 N B:GLU103 4.8 48.3 1.0 CD B:GLU103 4.8 48.1 1.0 NZ B:LYS132 5.0 55.5 1.0 CG B:GLU103 5.0 48.1 1.0

Magnesium binding site 5 out of 5 in the Ptyr Bound Form of Sdp-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ptyr Bound Form of Sdp-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1199 b:48.6 occ:0.50 O B:PRO100 2.8 52.8 1.0 O B:VAL102 3.4 48.8 1.0 C B:PRO100 3.6 52.7 1.0 CA B:PRO100 3.8 53.1 1.0 O B:VAL99 4.5 54.2 1.0 C B:VAL102 4.6 48.9 1.0 CB B:PRO100 4.6 53.2 1.0 N B:ALA101 4.9 52.2 1.0 N B:PRO100 5.0 53.6 1.0 N B:VAL102 5.0 50.3 1.0

G.C.Fox, M.Shafiq, D.C.Briggs, P.P.Knowles, M.Collister, M.J.Didmon, V.Makrantoni, R.J.Dickinson, S.Hanrahan, N.Totty, M.J.Stark, S.M.Keyse, N.Q.Mcdonald. Redox-Mediated Substrate Recognition By SDP1 Defines A New Group of Tyrosine Phosphatases. Nature V. 447 487 2007.
ISSN: ESSN 1476-4687
PubMed: 17495930
DOI: 10.1038/NATURE05804