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Chlorine in PDB 3np7: Glycogen Phosphorylase Complexed with 2,5-Dihydroxy-3-(Beta-D- Glucopyranosyl)-Chlorobenzene and 2,5-Dihydroxy-4-(Beta-D- Glucopyranosyl)-Chlorobenzene

Enzymatic activity of Glycogen Phosphorylase Complexed with 2,5-Dihydroxy-3-(Beta-D- Glucopyranosyl)-Chlorobenzene and 2,5-Dihydroxy-4-(Beta-D- Glucopyranosyl)-Chlorobenzene

All present enzymatic activity of Glycogen Phosphorylase Complexed with 2,5-Dihydroxy-3-(Beta-D- Glucopyranosyl)-Chlorobenzene and 2,5-Dihydroxy-4-(Beta-D- Glucopyranosyl)-Chlorobenzene:
2.4.1.1;

Protein crystallography data

The structure of Glycogen Phosphorylase Complexed with 2,5-Dihydroxy-3-(Beta-D- Glucopyranosyl)-Chlorobenzene and 2,5-Dihydroxy-4-(Beta-D- Glucopyranosyl)-Chlorobenzene, PDB code: 3np7 was solved by K.-M.Alexacou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.05
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.728, 128.728, 116.200, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 22

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Glycogen Phosphorylase Complexed with 2,5-Dihydroxy-3-(Beta-D- Glucopyranosyl)-Chlorobenzene and 2,5-Dihydroxy-4-(Beta-D- Glucopyranosyl)-Chlorobenzene (pdb code 3np7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Glycogen Phosphorylase Complexed with 2,5-Dihydroxy-3-(Beta-D- Glucopyranosyl)-Chlorobenzene and 2,5-Dihydroxy-4-(Beta-D- Glucopyranosyl)-Chlorobenzene, PDB code: 3np7:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 3np7

Go back to Chlorine Binding Sites List in 3np7
Chlorine binding site 1 out of 3 in the Glycogen Phosphorylase Complexed with 2,5-Dihydroxy-3-(Beta-D- Glucopyranosyl)-Chlorobenzene and 2,5-Dihydroxy-4-(Beta-D- Glucopyranosyl)-Chlorobenzene


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Glycogen Phosphorylase Complexed with 2,5-Dihydroxy-3-(Beta-D- Glucopyranosyl)-Chlorobenzene and 2,5-Dihydroxy-4-(Beta-D- Glucopyranosyl)-Chlorobenzene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl997

b:51.3
occ:1.00
 CL5 A:Z15997 0.0 51.3 1.0
C5 A:Z15997 1.7 50.7 1.0
C4 A:Z15997 2.7 50.0 1.0
C6 A:Z15997 2.7 50.5 1.0
O4 A:Z15997 2.9 50.2 1.0
CB A:TYR548 2.9 50.5 1.0
O A:LYS544 3.2 38.3 1.0
CG A:TYR548 3.5 51.1 1.0
CA A:PHE545 3.6 38.9 1.0
CD2 A:TYR548 3.7 51.3 1.0
C A:LYS544 3.7 38.2 1.0
N A:PHE545 3.9 38.5 1.0
C3 A:Z15997 4.0 50.3 1.0
C1 A:Z15997 4.0 50.7 1.0
CD1 A:PHE545 4.1 37.2 1.0
CA A:TYR548 4.1 50.3 1.0
N A:TYR548 4.3 48.9 1.0
CG A:LYS544 4.3 39.4 1.0
CD A:LYS655 4.3 26.8 1.0
CB A:PHE545 4.4 38.4 1.0
CD1 A:TYR548 4.5 51.3 1.0
C2 A:Z15997 4.5 50.7 1.0
C A:PHE545 4.5 39.6 1.0
O A:PHE545 4.5 39.3 1.0
CD A:LYS544 4.6 41.7 1.0
CG A:PHE545 4.7 37.6 1.0
CG A:LYS655 4.7 26.5 1.0
CB A:LYS655 4.8 25.8 1.0
CB A:LYS544 4.8 38.0 1.0
CE2 A:TYR548 4.8 51.6 1.0
CA A:LYS544 4.9 37.9 1.0
CE A:LYS544 4.9 43.2 1.0
CE A:LYS655 4.9 28.5 1.0
CE1 A:PHE545 5.0 37.0 1.0

Chlorine binding site 2 out of 3 in 3np7

Go back to Chlorine Binding Sites List in 3np7
Chlorine binding site 2 out of 3 in the Glycogen Phosphorylase Complexed with 2,5-Dihydroxy-3-(Beta-D- Glucopyranosyl)-Chlorobenzene and 2,5-Dihydroxy-4-(Beta-D- Glucopyranosyl)-Chlorobenzene


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Glycogen Phosphorylase Complexed with 2,5-Dihydroxy-3-(Beta-D- Glucopyranosyl)-Chlorobenzene and 2,5-Dihydroxy-4-(Beta-D- Glucopyranosyl)-Chlorobenzene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl998

b:22.2
occ:0.60
 CL5 A:Z15998 0.0 22.2 0.6
C5 A:Z16999 1.7 20.7 0.4
C5 A:Z15998 1.7 21.0 0.6
C4 A:Z16999 2.6 21.0 0.4
C6 A:Z16999 2.7 20.7 0.4
C6 A:Z15998 2.7 20.5 0.6
C4 A:Z15998 2.7 21.3 0.6
O4 A:Z16999 2.8 21.1 0.4
O4 A:Z15998 3.0 21.4 0.6
CL6 A:Z16999 3.2 22.2 0.4
NE2 A:HIS341 3.7 21.3 1.0
OD2 A:ASP339 3.7 23.4 0.5
N A:ASN284 3.7 31.4 1.0
CE1 A:HIS341 3.8 21.9 1.0
C3 A:Z16999 3.9 20.8 0.4
OD1 A:ASP339 3.9 22.3 0.5
C1 A:Z16999 4.0 20.7 0.4
CA A:ASN284 4.0 32.0 1.0
C1 A:Z15998 4.0 20.9 0.6
C3 A:Z15998 4.0 20.7 0.6
CD1 A:LEU136 4.4 22.4 1.0
C2 A:Z16999 4.4 20.4 0.4
C2 A:Z15998 4.5 20.6 0.6
N A:PHE285 4.7 31.8 1.0
CG A:ASP339 4.8 22.1 0.5
CG A:ASP339 4.8 21.7 0.5
C A:ASN284 4.8 31.9 1.0
C A:ASP283 5.0 30.9 1.0

Chlorine binding site 3 out of 3 in 3np7

Go back to Chlorine Binding Sites List in 3np7
Chlorine binding site 3 out of 3 in the Glycogen Phosphorylase Complexed with 2,5-Dihydroxy-3-(Beta-D- Glucopyranosyl)-Chlorobenzene and 2,5-Dihydroxy-4-(Beta-D- Glucopyranosyl)-Chlorobenzene


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Glycogen Phosphorylase Complexed with 2,5-Dihydroxy-3-(Beta-D- Glucopyranosyl)-Chlorobenzene and 2,5-Dihydroxy-4-(Beta-D- Glucopyranosyl)-Chlorobenzene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl999

b:22.2
occ:0.40
 CL6 A:Z16999 0.0 22.2 0.4
C6 A:Z16999 1.7 20.7 0.4
C6 A:Z15998 1.8 20.5 0.6
OD1 A:ASP283 2.7 30.7 1.0
C1 A:Z15998 2.7 20.9 0.6
C5 A:Z16999 2.7 20.7 0.4
C1 A:Z16999 2.7 20.7 0.4
C5 A:Z15998 2.7 21.0 0.6
O1 A:Z15998 2.9 21.0 0.6
O1 A:Z16999 2.9 20.8 0.4
O A:HOH916 3.0 19.6 1.0
CL5 A:Z15998 3.2 22.2 0.6
CG A:ASP283 3.6 30.6 1.0
N A:ASN284 3.8 31.4 1.0
CA A:ASP283 3.9 30.5 1.0
OE1 A:GLU88 4.0 21.5 1.0
CB A:LEU136 4.0 20.5 1.0
C2 A:Z15998 4.0 20.6 0.6
C4 A:Z16999 4.0 21.0 0.4
C2 A:Z16999 4.0 20.4 0.4
C4 A:Z15998 4.0 21.3 0.6
OE2 A:GLU88 4.2 22.1 1.0
CB A:ASP283 4.3 30.2 1.0
C A:ASP283 4.3 30.9 1.0
O A:ASN282 4.4 30.0 1.0
OD2 A:ASP283 4.4 32.5 1.0
CD A:GLU88 4.4 21.3 1.0
CB A:ASN133 4.5 20.8 1.0
C3 A:Z15998 4.5 20.7 0.6
C3 A:Z16999 4.5 20.8 0.4
CD1 A:LEU136 4.6 22.4 1.0
CG A:LEU136 4.7 21.6 1.0
CD2 A:LEU136 4.7 23.8 1.0
CA A:ASN284 4.8 32.0 1.0
N A:LEU136 4.9 20.1 1.0
ND2 A:ASN284 5.0 36.1 1.0
ND2 A:ASN133 5.0 20.2 1.0

Reference:

K.M.Alexacou, Y.Z.Zhang, J.P.Praly, S.E.Zographos, E.D.Chrysina, N.G.Oikonomakos, D.D.Leonidas. Halogen-Substituted (C-Beta-D-Glucopyranosyl)-Hydroquinone Regioisomers: Synthesis, Enzymatic Evaluation and Their Binding to Glycogen Phosphorylase. Bioorg.Med.Chem. V. 19 5125 2011.
ISSN: ISSN 0968-0896
PubMed: 21821421
DOI: 10.1016/J.BMC.2011.07.024
Page generated: Sun Jul 21 01:07:03 2024

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