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

Go back to Magnesium Binding Sites List in 5wrj
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 Dec 14 21:24:08 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy