Magnesium in PDB 5iuc: Crystal Structure of the Gspb Siglec Domain with Sialyl T Antigen Bound

The structure of Crystal Structure of the Gspb Siglec Domain with Sialyl T Antigen Bound, PDB code: 5iuc was solved by L.V.Loukachevitch, K.P.Fialkowski, Z.Wawrzak, T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.86 / 1.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.670, 66.547, 55.854, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 17.8

The binding sites of Magnesium atom in the Crystal Structure of the Gspb Siglec Domain with Sialyl T Antigen Bound (pdb code 5iuc). 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 the Gspb Siglec Domain with Sialyl T Antigen Bound, PDB code: 5iuc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Gspb Siglec Domain with Sialyl T Antigen Bound


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 the Gspb Siglec Domain with Sialyl T Antigen Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:14.5 occ:1.00 OD2 A:ASP399 2.1 41.8 1.0 O A:GLU401 2.1 15.9 1.0 OD1 A:ASP399 2.1 51.0 1.0 OD2 A:ASP490 2.1 15.8 1.0 OD1 A:ASN428 2.1 19.0 1.0 OD1 A:ASP427 2.1 13.7 1.0 OD2 A:ASP427 2.2 14.1 1.0 CG A:ASP399 2.4 22.2 1.0 CG A:ASP427 2.5 13.1 1.0 C A:GLU401 3.2 13.7 1.0 CG A:ASP490 3.3 10.6 1.0 HD22 A:ASN494 3.3 19.4 1.0 CG A:ASN428 3.3 18.8 1.0 HB3 A:GLU401 3.5 19.9 1.0 H A:SER429 3.6 15.6 1.0 HD21 A:ASN428 3.7 25.6 1.0 HB3 A:ASP490 3.7 15.8 1.0 HB2 A:ASP490 3.7 15.8 1.0 HG A:SER429 3.8 17.8 1.0 CB A:ASP490 3.8 13.2 1.0 H A:ASN428 3.8 17.1 1.0 HB3 A:SER429 3.8 18.4 1.0 ND2 A:ASN428 3.9 21.3 1.0 CB A:ASP399 4.0 39.0 1.0 H A:GLU401 4.0 27.5 1.0 ND2 A:ASN494 4.1 16.2 1.0 CB A:ASP427 4.1 12.6 1.0 CA A:GLU401 4.1 17.1 1.0 HD3 A:PRO403 4.1 14.0 1.0 HA A:ARG402 4.1 14.8 1.0 HB2 A:ASN494 4.1 16.7 1.0 CB A:GLU401 4.2 16.6 1.0 O A:HOH703 4.2 16.4 1.0 C A:ARG402 4.2 9.9 1.0 HG2 A:GLU401 4.2 27.9 1.0 N A:ARG402 4.2 13.3 1.0 N A:GLU401 4.2 22.9 1.0 N A:ASN428 4.3 14.3 1.0 OD1 A:ASP490 4.3 14.5 1.0 HB3 A:ASP399 4.3 46.8 1.0 N A:SER429 4.3 13.0 1.0 OG A:SER429 4.4 14.8 1.0 CA A:ARG402 4.4 12.3 1.0 HD21 A:ASN494 4.4 19.4 1.0 HB2 A:ASP399 4.4 46.8 1.0 N A:PRO403 4.4 10.7 1.0 HB2 A:ASP427 4.5 15.2 1.0 HB3 A:ASP427 4.5 15.2 1.0 O A:ARG402 4.5 11.8 1.0 CB A:SER429 4.5 15.4 1.0 HA A:ASP427 4.6 14.9 1.0 CB A:ASN428 4.6 15.4 1.0 O A:HOH753 4.6 16.6 1.0 HA A:ASP399 4.7 66.4 1.0 HA A:PRO403 4.7 13.8 1.0 CG A:GLU401 4.7 23.2 1.0 CA A:ASP427 4.8 12.4 1.0 CD A:PRO403 4.8 11.7 1.0 HD22 A:ASN428 4.8 25.6 1.0 HB3 A:ASN428 4.8 18.5 1.0 CA A:ASP399 4.8 55.3 1.0 C A:ASP427 4.8 12.9 1.0 CA A:ASN428 4.9 13.6 1.0 CB A:ASN494 4.9 13.9 1.0 CG A:ASN494 5.0 15.1 1.0 HA A:GLU401 5.0 20.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Gspb Siglec Domain with Sialyl T Antigen Bound


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 the Gspb Siglec Domain with Sialyl T Antigen Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:13.9 occ:1.00 OD2 B:ASP399 2.1 43.9 1.0 OD1 B:ASP399 2.1 43.5 1.0 O B:GLU401 2.1 16.9 1.0 OD2 B:ASP490 2.1 14.1 1.0 OD1 B:ASP427 2.1 12.5 1.0 OD1 B:ASN428 2.2 18.9 1.0 OD2 B:ASP427 2.2 13.5 1.0 CG B:ASP399 2.4 21.4 1.0 CG B:ASP427 2.6 12.4 1.0 HD21 B:ASN494 3.2 19.7 1.0 CG B:ASP490 3.3 13.7 1.0 C B:GLU401 3.3 13.9 1.0 CG B:ASN428 3.4 17.4 1.0 H B:SER429 3.6 13.4 1.0 HB3 B:GLU401 3.6 25.0 1.0 HB3 B:ASP490 3.7 13.5 1.0 HD21 B:ASN428 3.7 27.9 1.0 HB2 B:ASP490 3.8 13.5 1.0 HG B:SER429 3.8 17.5 1.0 CB B:ASP490 3.9 11.2 1.0 H B:ASN428 3.9 13.7 1.0 HB3 B:SER429 3.9 16.9 1.0 CB B:ASP399 4.0 38.2 1.0 ND2 B:ASN428 4.0 23.3 1.0 ND2 B:ASN494 4.0 16.4 1.0 H B:GLU401 4.0 30.7 1.0 HD3 B:PRO403 4.1 13.1 1.0 CB B:ASP427 4.1 10.4 1.0 HB2 B:ASN494 4.1 15.7 1.0 CA B:GLU401 4.1 19.6 1.0 HA B:ARG402 4.2 16.2 1.0 O B:HOH705 4.2 15.0 1.0 N B:GLU401 4.3 25.6 1.0 N B:ARG402 4.3 14.0 1.0 HB3 B:ASP399 4.3 45.9 1.0 CB B:GLU401 4.3 20.8 1.0 C B:ARG402 4.3 12.3 1.0 N B:ASN428 4.3 11.4 1.0 OD1 B:ASP490 4.3 12.8 1.0 HD22 B:ASN494 4.3 19.7 1.0 N B:SER429 4.3 11.2 1.0 OG B:SER429 4.3 14.6 1.0 HG2 B:GLU401 4.4 27.8 1.0 HB2 B:ASP399 4.4 45.9 1.0 CA B:ARG402 4.5 13.5 1.0 N B:PRO403 4.5 11.2 1.0 HB2 B:ASP427 4.5 12.5 1.0 CB B:SER429 4.5 14.1 1.0 HB3 B:ASP427 4.5 12.5 1.0 HA B:ASP427 4.6 13.3 1.0 O B:ARG402 4.6 12.6 1.0 O B:HOH784 4.6 16.7 1.0 HA B:ASP399 4.7 63.5 1.0 CB B:ASN428 4.7 15.7 1.0 HA B:PRO403 4.8 12.8 1.0 CD B:PRO403 4.8 10.9 1.0 CA B:ASP427 4.8 11.1 1.0 CA B:ASP399 4.8 52.9 1.0 HD22 B:ASN428 4.8 27.9 1.0 CG B:GLU401 4.9 23.2 1.0 CB B:ASN494 4.9 13.1 1.0 C B:ASP427 4.9 10.7 1.0 CG B:ASN494 4.9 16.1 1.0 HB3 B:ASN428 4.9 18.8 1.0 CA B:ASN428 5.0 13.4 1.0 HB3 B:ALA492 5.0 23.2 1.0

T.M.Pyburn, B.A.Bensing, Y.Q.Xiong, B.J.Melancon, T.M.Tomasiak, N.J.Ward, V.Yankovskaya, K.M.Oliver, G.Cecchini, G.A.Sulikowski, M.J.Tyska, P.M.Sullam, T.M.Iverson. A Structural Model For Binding of the Serine-Rich Repeat Adhesin Gspb to Host Carbohydrate Receptors. Plos Pathog. V. 7 02112 2011.
ISSN: ESSN 1553-7374
PubMed: 21765814
DOI: 10.1371/JOURNAL.PPAT.1002112