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Chlorine 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:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6dws

Go back to Chlorine Binding Sites List in 6dws
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl501

b:61.0
occ:1.00
 CL A:HFY501 0.0 61.0 1.0
C16 A:HFY501 1.7 51.9 1.0
C15 A:HFY501 2.7 50.0 1.0
C11 A:HFY501 2.7 46.2 1.0
H18 A:HFY501 2.8 48.8 1.0
H1 A:HFY501 2.9 28.2 1.0
H14 A:HFY501 2.9 36.8 1.0
C10 A:HFY501 3.1 38.0 1.0
H6 A:HFY501 3.1 29.0 1.0
N5 A:HFY501 3.2 32.5 1.0
H12 A:HFY501 3.4 32.6 1.0
O1 A:HFY501 3.6 29.4 1.0
O A:HOH712 3.7 45.3 1.0
OH A:TYR39 3.8 36.5 1.0
OE1 A:GLU293 3.8 48.8 1.0
C14 A:HFY501 4.0 48.6 1.0
C12 A:HFY501 4.0 46.8 1.0
C1 A:HFY501 4.0 28.4 1.0
CD1 A:ILE61 4.0 23.8 1.0
CZ A:TYR39 4.1 32.5 1.0
H13 A:HFY501 4.1 38.2 1.0
C5 A:HFY501 4.1 27.6 1.0
CE2 A:TYR39 4.3 26.3 1.0
H2 A:HFY501 4.3 25.6 1.0
NE A:ARG297 4.4 50.2 1.0
CD A:ARG297 4.5 37.2 1.0
C13 A:HFY501 4.5 48.6 1.0
H8 A:HFY501 4.5 30.0 1.0
O3 A:HFY501 4.6 30.8 1.0
C2 A:HFY501 4.7 25.6 1.0
CE1 A:TYR39 4.7 26.5 1.0
H17 A:HFY501 4.8 48.5 1.0
N A:HFY501 4.8 24.6 1.0
H15 A:HFY501 4.9 46.8 1.0
C A:HFY501 4.9 27.0 1.0
C4 A:HFY501 4.9 27.9 1.0
N1 A:HFY501 4.9 27.0 1.0
CD A:GLU293 5.0 72.1 1.0

Chlorine binding site 2 out of 2 in 6dws

Go back to Chlorine Binding Sites List in 6dws
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl501

b:54.5
occ:1.00
 CL B:HFY501 0.0 54.5 1.0
C16 B:HFY501 1.7 46.7 1.0
C15 B:HFY501 2.7 44.2 1.0
C11 B:HFY501 2.7 40.5 1.0
H18 B:HFY501 2.8 43.5 1.0
H1 B:HFY501 2.9 28.1 1.0
H14 B:HFY501 3.0 32.7 1.0
C10 B:HFY501 3.1 33.7 1.0
N5 B:HFY501 3.1 33.0 1.0
H12 B:HFY501 3.2 33.1 1.0
O1 B:HFY501 3.3 33.1 1.0
H6 B:HFY501 3.5 34.0 1.0
OH B:TYR39 3.7 54.8 1.0
OE1 B:GLU293 3.8 44.0 1.0
CD1 B:ILE61 3.9 37.8 1.0
C14 B:HFY501 4.0 43.7 1.0
C12 B:HFY501 4.0 42.5 1.0
CZ B:TYR39 4.0 46.2 1.0
C1 B:HFY501 4.0 28.6 1.0
H13 B:HFY501 4.1 33.9 1.0
C5 B:HFY501 4.2 30.2 1.0
H8 B:HFY501 4.3 30.4 1.0
CD B:ARG297 4.3 30.8 1.0
CE2 B:TYR39 4.3 34.6 1.0
H2 B:HFY501 4.3 27.2 1.0
NE B:ARG297 4.4 37.0 1.0
C13 B:HFY501 4.5 42.7 1.0
CE1 B:TYR39 4.6 37.2 1.0
O3 B:HFY501 4.7 30.6 1.0
C4 B:HFY501 4.7 29.2 1.0
C2 B:HFY501 4.7 27.6 1.0
H17 B:HFY501 4.8 44.0 1.0
N B:HFY501 4.9 27.4 1.0
H15 B:HFY501 4.9 42.7 1.0
CD B:GLU293 4.9 52.8 1.0
C B:HFY501 4.9 26.3 1.0
N1 B:HFY501 4.9 28.3 1.0
CG1 B:ILE61 5.0 33.3 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: Sat Jul 27 21:51:26 2024

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