Magnesium in PDB 5wri: Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and C4 Peptide

All present enzymatic activity of Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and C4 Peptide:
2.8.2.20;

The structure of Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and C4 Peptide, PDB code: 5wri was solved by S.Tanaka, T.Nishiyori, H.Kojo, R.Otsubo, Y.Kakuta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.34 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.576, 155.972, 48.892, 90.00, 90.00, 90.00
R / Rfree (%)	13.3 / 17.8

The structure of Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and C4 Peptide also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and C4 Peptide (pdb code 5wri). 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 Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and C4 Peptide, PDB code: 5wri:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and C4 Peptide


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 Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and C4 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:15.7 occ:1.00 O A:ILE95 2.3 14.5 1.0 O A:GLY276 2.3 17.9 1.0 O A:HIS92 2.3 14.8 0.5 O A:ASP90 2.4 12.7 1.0 O A:HIS92 2.4 14.8 0.5 O A:HOH527 2.4 14.9 1.0 O A:HOH577 2.5 20.0 1.0 C A:GLY276 3.3 16.3 1.0 C A:ASP90 3.4 13.9 1.0 C A:ILE95 3.4 15.4 1.0 C A:HIS92 3.5 14.7 0.5 C A:HIS92 3.5 14.7 0.5 CA A:ASP90 3.9 14.6 1.0 N A:ILE95 3.9 14.1 1.0 C A:PRO93 4.1 14.4 1.0 N A:GLY277 4.1 16.6 1.0 CA A:GLY276 4.1 16.1 1.0 CA A:PRO93 4.2 16.8 1.0 O A:PRO93 4.2 16.6 1.0 N A:HIS92 4.2 13.9 0.5 N A:HIS92 4.2 13.8 0.5 CA A:ILE95 4.2 15.2 1.0 O A:GLY277 4.3 17.1 1.0 N A:PRO93 4.3 15.6 1.0 CA A:GLY277 4.4 17.5 1.0 O A:HOH566 4.4 28.1 1.0 O A:LEU89 4.4 12.9 1.0 N A:ARG96 4.4 14.8 1.0 OD1 A:ASP90 4.4 16.1 1.0 N A:ALA91 4.4 13.3 1.0 O A:HOH749 4.5 20.3 1.0 CA A:HIS92 4.5 14.3 0.5 CA A:HIS92 4.5 14.5 0.5 C A:ALA91 4.5 13.9 1.0 N A:ASP94 4.6 17.4 1.0 CA A:ARG96 4.6 14.6 1.0 C A:GLY277 4.7 15.5 1.0 CB A:ASP90 4.7 15.0 1.0 CB A:ILE95 4.8 15.7 1.0 CA A:ALA91 4.8 14.6 1.0 O A:HOH544 4.9 21.2 1.0 C A:ASP94 4.9 15.8 1.0 O A:ALA91 5.0 15.3 1.0 N A:ASP90 5.0 13.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and C4 Peptide


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 Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and C4 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:17.2 occ:1.00 O B:ILE95 2.3 13.9 1.0 O B:HOH533 2.4 13.0 1.0 O B:HIS92 2.4 15.2 1.0 O B:ASP90 2.4 14.6 1.0 O B:HOH639 2.4 21.2 1.0 O B:GLY276 2.5 18.3 1.0 C B:GLY276 3.3 19.1 1.0 C B:ASP90 3.4 13.7 1.0 C B:ILE95 3.5 13.3 1.0 C B:HIS92 3.5 14.9 1.0 CA B:ASP90 3.9 14.3 1.0 N B:ILE95 4.1 13.0 1.0 O B:HOH515 4.1 35.9 1.0 N B:GLY277 4.1 16.8 1.0 CA B:GLY276 4.2 20.1 1.0 C B:PRO93 4.2 16.9 1.0 N B:HIS92 4.2 13.5 1.0 CA B:PRO93 4.2 16.4 1.0 O B:PRO93 4.3 19.4 1.0 O B:GLY277 4.3 17.7 1.0 O B:HOH767 4.3 16.5 1.0 CA B:GLY277 4.4 16.4 1.0 CA B:ILE95 4.4 12.7 1.0 OD1 B:ASP90 4.4 14.6 1.0 N B:PRO93 4.4 16.6 1.0 O B:LEU89 4.4 13.7 1.0 CA B:HIS92 4.5 15.0 1.0 N B:ALA91 4.5 13.2 1.0 N B:ARG96 4.5 12.8 1.0 C B:ALA91 4.5 14.4 1.0 CA B:ARG96 4.6 13.2 1.0 CB B:ASP90 4.6 14.1 1.0 C B:GLY277 4.7 16.4 1.0 N B:ASP94 4.7 16.4 1.0 O B:HOH585 4.8 20.1 1.0 CA B:ALA91 4.8 14.3 1.0 CB B:ILE95 4.9 13.9 1.0

S.Tanaka, T.Nishiyori, H.Kojo, R.Otsubo, M.Tsuruta, K.Kurogi, M.C.Liu, M.Suiko, Y.Sakakibara, Y.Kakuta. Structural Basis For the Broad Substrate Specificity of the Human Tyrosylprotein Sulfotransferase-1. Sci Rep V. 7 8776 2017.
ISSN: ESSN 2045-2322
PubMed: 28821720
DOI: 10.1038/S41598-017-07141-8