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Zinc in PDB 2h39: Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose

Enzymatic activity of Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose

All present enzymatic activity of Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose:
2.7.7.12;

Protein crystallography data

The structure of Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose, PDB code: 2h39 was solved by J.G.Mccoy, G.E.Wesenberg, G.N.Phillips Jr., E.Bitto, C.A.Bingman, Centerfor Eukaryotic Structural Genomics (Cesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.73 / 2.23
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.318, 95.454, 110.504, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 24.3

Other elements in 2h39:

The structure of Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose (pdb code 2h39). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose, PDB code: 2h39:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2h39

Go back to Zinc Binding Sites List in 2h39
Zinc binding site 1 out of 4 in the Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn352

b:37.6
occ:1.00
 ND1 A:HIS133 1.9 16.5 1.0
ND1 A:HIS184 2.2 29.0 1.0
SG A:CYS63 2.4 29.4 1.0
SG A:CYS66 2.5 31.8 1.0
CE1 A:HIS133 2.9 16.9 1.0
CG A:HIS133 2.9 24.0 1.0
CE1 A:HIS184 3.1 29.8 1.0
CG A:HIS184 3.1 25.7 1.0
CB A:CYS63 3.3 29.2 1.0
CB A:HIS133 3.3 27.4 1.0
CB A:HIS184 3.5 23.7 1.0
N A:CYS63 3.6 28.1 1.0
N A:CYS66 3.8 29.0 1.0
CA A:HIS133 3.8 30.7 1.0
CB A:CYS66 3.9 28.7 1.0
CA A:CYS63 3.9 26.7 1.0
NE2 A:HIS133 4.0 19.1 1.0
CD2 A:HIS133 4.0 18.2 1.0
NE2 A:HIS184 4.1 28.0 1.0
CD2 A:HIS184 4.2 30.0 1.0
O A:CYS63 4.2 28.1 1.0
CA A:CYS66 4.2 29.5 1.0
C A:SER62 4.2 30.1 1.0
C A:CYS63 4.3 25.5 1.0
C A:PHE65 4.4 28.8 1.0
CA A:HIS184 4.5 23.3 1.0
N A:HIS133 4.5 32.0 1.0
N A:PHE65 4.5 25.9 1.0
CB A:PHE65 4.5 23.5 1.0
O B:HOH551 4.6 29.3 1.0
CA A:SER62 4.7 30.1 1.0
CA A:PHE65 4.7 26.9 1.0
C A:HIS133 4.9 30.7 1.0
O A:SER62 5.0 29.2 1.0
O A:HIS133 5.0 31.3 1.0

Zinc binding site 2 out of 4 in 2h39

Go back to Zinc Binding Sites List in 2h39
Zinc binding site 2 out of 4 in the Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn353

b:16.2
occ:1.00
 ND1 A:HIS255 2.1 17.2 1.0
ND1 A:HIS310 2.1 13.2 1.0
SG A:CYS216 2.3 11.5 1.0
SG A:CYS219 2.4 14.1 1.0
CE1 A:HIS255 2.9 18.2 1.0
CE1 A:HIS310 3.0 12.4 1.0
CG A:HIS255 3.1 18.5 1.0
CG A:HIS310 3.1 10.5 1.0
CB A:CYS216 3.2 13.2 1.0
CB A:CYS219 3.4 14.6 1.0
N A:CYS219 3.5 14.1 1.0
CB A:HIS310 3.5 9.8 1.0
CB A:HIS255 3.6 19.7 1.0
CA A:CYS219 3.8 14.8 1.0
CA A:HIS255 3.9 19.7 1.0
NE2 A:HIS255 4.1 15.2 1.0
NE2 A:HIS310 4.1 10.1 1.0
CD2 A:HIS255 4.2 18.5 1.0
CD2 A:HIS310 4.2 11.3 1.0
O A:HOH594 4.2 14.1 1.0
C A:LEU218 4.4 13.2 1.0
CA A:CYS216 4.5 13.4 1.0
O A:CYS216 4.6 12.8 1.0
C A:CYS216 4.7 12.6 1.0
CA A:HIS310 4.8 9.8 1.0
CB A:LEU218 4.8 10.0 1.0
N A:LEU218 4.9 10.3 1.0
C A:HIS255 4.9 21.2 1.0
N A:HIS255 4.9 20.9 1.0
CA A:LEU218 4.9 11.8 1.0
O A:PRO307 5.0 12.9 1.0

Zinc binding site 3 out of 4 in 2h39

Go back to Zinc Binding Sites List in 2h39
Zinc binding site 3 out of 4 in the Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn352

b:26.8
occ:1.00
 ND1 B:HIS133 2.1 18.4 1.0
ND1 B:HIS184 2.1 15.7 1.0
SG B:CYS63 2.4 26.4 1.0
SG B:CYS66 2.5 25.1 1.0
CE1 B:HIS133 3.0 21.0 1.0
CG B:HIS133 3.1 20.6 1.0
CE1 B:HIS184 3.1 13.7 1.0
CG B:HIS184 3.1 15.6 1.0
CB B:CYS63 3.4 25.8 1.0
CB B:HIS133 3.4 18.5 1.0
CB B:HIS184 3.5 12.7 1.0
N B:CYS63 3.5 28.1 1.0
N B:CYS66 3.6 19.9 1.0
CB B:CYS66 3.7 21.1 1.0
CA B:HIS133 3.7 19.4 1.0
CA B:CYS63 3.9 26.4 1.0
CA B:CYS66 4.0 20.6 1.0
C B:SER62 4.1 31.3 1.0
NE2 B:HIS133 4.2 22.5 1.0
CD2 B:HIS133 4.2 17.3 1.0
NE2 B:HIS184 4.2 18.6 1.0
O B:CYS63 4.2 24.6 1.0
CD2 B:HIS184 4.3 12.7 1.0
C B:PHE65 4.3 20.1 1.0
C B:CYS63 4.3 23.6 1.0
CB B:PHE65 4.3 19.1 1.0
CA B:HIS184 4.4 14.2 1.0
N B:HIS133 4.5 20.1 1.0
O A:HOH582 4.5 13.1 1.0
CA B:SER62 4.5 33.7 1.0
N B:PHE65 4.6 19.4 1.0
CA B:PHE65 4.6 19.7 1.0
O B:SER62 4.7 31.4 1.0
C B:HIS133 4.9 19.6 1.0

Zinc binding site 4 out of 4 in 2h39

Go back to Zinc Binding Sites List in 2h39
Zinc binding site 4 out of 4 in the Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn353

b:16.1
occ:1.00
 ND1 B:HIS255 2.1 12.9 1.0
ND1 B:HIS310 2.1 13.2 1.0
SG B:CYS216 2.2 12.4 1.0
SG B:CYS219 2.3 15.6 1.0
CE1 B:HIS255 2.9 15.3 1.0
CE1 B:HIS310 3.1 13.7 1.0
CG B:HIS310 3.1 12.7 1.0
CB B:CYS216 3.2 12.9 1.0
CG B:HIS255 3.2 15.8 1.0
CB B:HIS310 3.4 8.4 1.0
CB B:CYS219 3.5 13.3 1.0
N B:CYS219 3.5 15.0 1.0
CB B:HIS255 3.7 14.2 1.0
CA B:CYS219 3.9 15.1 1.0
CA B:HIS255 4.0 17.7 1.0
NE2 B:HIS255 4.1 14.5 1.0
NE2 B:HIS310 4.2 12.1 1.0
CD2 B:HIS310 4.2 11.2 1.0
CD2 B:HIS255 4.3 13.0 1.0
C B:LEU218 4.3 14.1 1.0
O B:HOH597 4.4 19.7 1.0
CA B:CYS216 4.5 14.8 1.0
CB B:LEU218 4.7 9.5 1.0
CA B:HIS310 4.7 10.2 1.0
O B:CYS216 4.8 14.0 1.0
O B:PRO307 4.8 16.5 1.0
C B:CYS216 4.8 14.8 1.0
CA B:LEU218 4.9 11.9 1.0
N B:HIS255 4.9 18.8 1.0
N B:LEU218 4.9 12.3 1.0
O B:HOH590 4.9 11.7 1.0
C B:HIS255 5.0 19.4 1.0
N B:SER256 5.0 18.0 1.0

Reference:

J.G.Mccoy, G.E.Wesenberg, G.N.Phillips Jr., E.Bitto, C.A.Bingman. Crystal Structure of An Adp-Glucose Phosphorylase From Arabidopsis Thaliana with Bound Adp-Glucose To Be Published.
Page generated: Wed Dec 16 03:29:51 2020

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