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

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