Magnesium in PDB 6dws: Crystal Structure of Human GRP78 in Complex with (2R,3R,4S,5R)-2-(6- Amino-8-((2-Chlorobenzyl)Amino)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol

Enzymatic activity of Crystal Structure of Human GRP78 in Complex with (2R,3R,4S,5R)-2-(6- Amino-8-((2-Chlorobenzyl)Amino)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol

All present enzymatic activity of Crystal Structure of Human GRP78 in Complex with (2R,3R,4S,5R)-2-(6- Amino-8-((2-Chlorobenzyl)Amino)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol:
3.6.4.10;

Protein crystallography data

The structure of Crystal Structure of Human GRP78 in Complex with (2R,3R,4S,5R)-2-(6- Amino-8-((2-Chlorobenzyl)Amino)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol, PDB code: 6dws was solved by Y.Chen, T.Antoshchenko, D.Smil, C.Zepeda, Y.Huang, H.W.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.82 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.916, 74.611, 86.848, 90.00, 98.10, 90.00
R / Rfree (%) 21.3 / 24.8

Other elements in 6dws:

The structure of Crystal Structure of Human GRP78 in Complex with (2R,3R,4S,5R)-2-(6- Amino-8-((2-Chlorobenzyl)Amino)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human GRP78 in Complex with (2R,3R,4S,5R)-2-(6- Amino-8-((2-Chlorobenzyl)Amino)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol (pdb code 6dws). 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 GRP78 in Complex with (2R,3R,4S,5R)-2-(6- Amino-8-((2-Chlorobenzyl)Amino)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol, PDB code: 6dws:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6dws

Go back to Magnesium Binding Sites List in 6dws
Magnesium binding site 1 out of 2 in the Crystal Structure of Human GRP78 in Complex with (2R,3R,4S,5R)-2-(6- Amino-8-((2-Chlorobenzyl)Amino)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol


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 GRP78 in Complex with (2R,3R,4S,5R)-2-(6- Amino-8-((2-Chlorobenzyl)Amino)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:51.2
occ:1.00
O A:HOH687 1.9 32.6 1.0
O A:HOH690 2.2 26.8 1.0
O A:HOH604 2.2 24.0 1.0
O A:HOH638 2.3 22.6 1.0
OD2 A:ASP224 3.9 32.1 1.0
OD1 A:ASP224 4.0 28.6 1.0
OD2 A:ASP34 4.1 21.6 1.0
OD1 A:ASP34 4.2 21.0 1.0
O A:HOH766 4.3 19.9 1.0
OE1 A:GLU201 4.3 22.4 1.0
CG A:ASP224 4.4 29.2 1.0
O A:HOH728 4.5 28.3 1.0
CG A:ASP34 4.6 22.9 1.0
O A:HOH779 4.6 33.9 1.0
CD A:GLU201 4.8 26.9 1.0
CG1 A:VAL362 4.9 26.7 1.0
O A:HOH650 4.9 34.7 1.0
CA A:GLY36 5.0 14.3 1.0

Magnesium binding site 2 out of 2 in 6dws

Go back to Magnesium Binding Sites List in 6dws
Magnesium binding site 2 out of 2 in the Crystal Structure of Human GRP78 in Complex with (2R,3R,4S,5R)-2-(6- Amino-8-((2-Chlorobenzyl)Amino)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol


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 GRP78 in Complex with (2R,3R,4S,5R)-2-(6- Amino-8-((2-Chlorobenzyl)Amino)-9H-Purin-9-Yl)-5-(Hydroxymethyl) Tetrahydrofuran-3,4-Diol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:74.8
occ:1.00
O B:HOH680 1.9 41.7 1.0
O B:HOH652 1.9 33.5 1.0
O B:HOH614 2.3 37.1 1.0
O B:HOH632 2.6 32.0 1.0
O B:HOH720 3.6 47.1 1.0
O B:HOH711 3.9 46.8 1.0
OD2 B:ASP224 3.9 41.4 1.0
OD1 B:ASP224 3.9 36.6 1.0
O B:HOH705 4.1 25.3 1.0
OD2 B:ASP34 4.1 32.2 1.0
CG B:ASP224 4.4 38.1 1.0
OD1 B:ASP34 4.4 35.3 1.0
OE1 B:GLU201 4.5 35.2 1.0
O B:HOH718 4.5 38.3 1.0
O B:HOH660 4.7 38.3 1.0
CG B:ASP34 4.7 30.7 1.0
O B:HOH691 4.8 43.3 1.0
CG1 B:VAL362 4.9 35.0 1.0

Reference:

Y.Chen, T.Antoshchenko, D.Smil, C.Zepeda, Y.Huang, H.W.Park. Crystal Structure of Human GRP78 in Complex with (2R,3R,4S,5R)-2-(6-Amino-8-((2-Chlorobenzyl)Amino) -9H-Purin-9-Yl)-5-(Hydroxymethyl)Tetrahydrofuran-3,4-Diol To Be Published.
Page generated: Mon Dec 14 22:37:32 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy