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

Enzymatic activity of Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and Gastrin Peptide

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

Protein crystallography data

The structure of Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and Gastrin Peptide, PDB code: 5wrj 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) 48.99 / 2.31
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 51.668, 93.263, 93.012, 90.60, 93.39, 103.39
R / Rfree (%) 24.1 / 26.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and Gastrin Peptide (pdb code 5wrj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and Gastrin Peptide, PDB code: 5wrj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5wrj

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and Gastrin 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 Gastrin Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:46.6
occ:1.00
 O A:ILE95 2.4 37.4 1.0
O A:ASP90 2.4 38.9 1.0
O A:HIS92 2.4 39.3 1.0
O A:GLY276 2.6 49.6 1.0
C A:GLY276 3.3 49.0 1.0
C A:ASP90 3.4 39.3 1.0
C A:HIS92 3.4 39.8 1.0
C A:ILE95 3.5 37.6 1.0
O A:PRO93 3.7 43.4 1.0
CA A:PRO93 3.8 41.9 1.0
C A:PRO93 3.9 41.7 1.0
CA A:ASP90 4.0 39.8 1.0
N A:GLY277 4.0 48.4 1.0
N A:ILE95 4.0 39.6 1.0
O A:GLY277 4.1 45.6 1.0
N A:PRO93 4.1 41.5 1.0
CA A:GLY276 4.1 50.1 1.0
CA A:GLY277 4.2 46.0 1.0
CA A:ILE95 4.3 38.5 1.0
N A:HIS92 4.4 38.1 1.0
N A:ALA91 4.4 38.2 1.0
C A:ALA91 4.4 38.6 1.0
N A:ARG96 4.5 36.8 1.0
C A:GLY277 4.5 44.7 1.0
O A:LEU89 4.5 39.6 1.0
CA A:HIS92 4.5 38.5 1.0
CA A:ARG96 4.7 36.4 1.0
N A:ASP94 4.7 41.8 1.0
OD1 A:ASP90 4.7 44.0 1.0
CA A:ALA91 4.7 38.2 1.0
CB A:ASP90 4.8 41.1 1.0
O A:ALA91 4.8 39.9 1.0
CB A:ILE95 4.9 39.5 1.0

Magnesium binding site 2 out of 4 in 5wrj

Go back to Magnesium Binding Sites List in 5wrj
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and Gastrin 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 Gastrin Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:53.1
occ:1.00
 O B:ILE95 2.1 41.8 1.0
O B:HIS92 2.3 44.0 1.0
O B:ASP90 2.4 39.0 1.0
O B:GLY276 2.9 57.2 1.0
C B:ILE95 3.3 40.6 1.0
C B:ASP90 3.4 39.4 1.0
C B:HIS92 3.5 43.3 1.0
C B:GLY276 3.5 58.7 1.0
O B:PRO93 3.7 47.5 1.0
CA B:PRO93 3.9 45.6 1.0
C B:PRO93 3.9 45.9 1.0
N B:ILE95 3.9 42.6 1.0
CA B:ASP90 4.0 38.8 1.0
N B:PRO93 4.1 44.4 1.0
CA B:ILE95 4.2 41.1 1.0
N B:GLY277 4.2 55.7 1.0
N B:ARG96 4.2 39.8 1.0
CA B:GLY276 4.3 60.6 1.0
O B:GLY277 4.3 52.5 1.0
CA B:ARG96 4.4 39.7 1.0
N B:HIS92 4.5 41.5 1.0
CA B:GLY277 4.5 53.8 1.0
N B:ALA91 4.5 40.2 1.0
C B:ALA91 4.5 40.1 1.0
CA B:HIS92 4.6 42.0 1.0
O B:LEU89 4.6 38.3 1.0
N B:ASP94 4.7 45.5 1.0
OD1 B:ASP90 4.7 41.7 1.0
C B:GLY277 4.7 53.0 1.0
CB B:ILE95 4.8 41.6 1.0
O B:ALA91 4.9 41.4 1.0
CA B:ALA91 4.9 39.6 1.0
CB B:ASP90 4.9 39.9 1.0
CB B:ARG96 4.9 40.2 1.0
C B:ASP94 5.0 44.5 1.0

Magnesium binding site 3 out of 4 in 5wrj

Go back to Magnesium Binding Sites List in 5wrj
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and Gastrin Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and Gastrin Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:39.0
occ:1.00
 O C:HIS92 2.2 42.1 1.0
O C:ILE95 2.3 40.1 1.0
O C:ASP90 2.5 39.4 1.0
O C:HOH512 2.5 36.1 1.0
O C:GLY276 2.6 63.0 1.0
C C:HIS92 3.3 42.4 1.0
C C:GLY276 3.4 65.5 1.0
C C:ILE95 3.5 41.8 1.0
C C:ASP90 3.5 40.8 1.0
O C:PRO93 3.6 46.0 1.0
C C:PRO93 3.7 44.6 1.0
CA C:PRO93 3.7 44.5 1.0
N C:ILE95 4.0 43.4 1.0
N C:PRO93 4.0 43.7 1.0
N C:GLY277 4.0 64.1 1.0
CA C:ASP90 4.1 42.7 1.0
CA C:GLY277 4.1 62.5 1.0
O C:GLY277 4.2 63.1 1.0
CA C:ILE95 4.3 42.2 1.0
CA C:GLY276 4.4 67.1 1.0
N C:HIS92 4.4 41.8 1.0
N C:ARG96 4.4 42.1 1.0
CA C:HIS92 4.4 42.2 1.0
C C:ALA91 4.5 42.2 1.0
C C:GLY277 4.5 63.1 1.0
N C:ASP94 4.5 44.9 1.0
N C:ALA91 4.6 40.5 1.0
O C:LEU89 4.6 42.4 1.0
CA C:ARG96 4.7 42.5 1.0
OD1 C:ASP90 4.7 46.9 1.0
O C:ALA91 4.9 44.1 1.0
C C:ASP94 4.9 43.5 1.0
CB C:ASP90 4.9 44.3 1.0
CA C:ALA91 4.9 41.5 1.0
CB C:ILE95 4.9 42.4 1.0

Magnesium binding site 4 out of 4 in 5wrj

Go back to Magnesium Binding Sites List in 5wrj
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and Gastrin Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Tyrosylprotein Sulfotransferase-1 Complexed with Pap and Gastrin Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:46.3
occ:1.00
 O D:ILE95 2.1 44.0 1.0
O D:ASP90 2.4 38.7 1.0
O D:GLY276 2.5 53.5 1.0
O D:HIS92 2.5 45.2 1.0
C D:GLY276 3.3 55.6 1.0
C D:ILE95 3.4 43.0 1.0
C D:ASP90 3.4 40.5 1.0
C D:HIS92 3.7 44.9 1.0
CA D:ASP90 3.9 40.8 1.0
N D:GLY277 4.0 53.3 1.0
O D:GLY277 4.2 49.7 1.0
N D:ILE95 4.2 42.6 1.0
CA D:GLY276 4.2 58.0 1.0
CA D:GLY277 4.2 51.7 1.0
O D:PRO93 4.2 46.9 1.0
N D:ARG96 4.2 42.3 1.0
CA D:PRO93 4.3 46.7 1.0
OD1 D:ASP90 4.3 42.0 1.0
C D:PRO93 4.3 46.3 1.0
CA D:ILE95 4.3 42.3 1.0
CA D:ARG96 4.3 42.0 1.0
N D:PRO93 4.5 46.5 1.0
C D:GLY277 4.5 50.3 1.0
N D:ALA91 4.6 40.4 1.0
N D:HIS92 4.6 42.1 1.0
CB D:ASP90 4.6 41.3 1.0
O D:LEU89 4.6 39.6 1.0
C D:ALA91 4.7 41.2 1.0
CA D:HIS92 4.8 43.8 1.0
CB D:ARG96 4.9 41.5 1.0
CB D:ILE95 4.9 42.0 1.0
CG D:ASP90 5.0 42.5 1.0
CA D:ALA91 5.0 40.2 1.0

Reference:

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
Page generated: Mon Sep 30 06:49:13 2024

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