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Zinc in PDB 5l03: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to L-Tryptophan Hydroxamate

Enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to L-Tryptophan Hydroxamate

All present enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to L-Tryptophan Hydroxamate:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to L-Tryptophan Hydroxamate, PDB code: 5l03 was solved by J.M.Blain, D.Ghose, J.L.Gorman, G.M.Goshu, G.Ranieri, L.Zhao, B.Bode, R.Meganathan, R.L.Walter, T.J.Hagen, J.R.Horn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.71 / 1.47
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.515, 68.126, 60.659, 90.00, 96.93, 90.00
R / Rfree (%) 17.9 / 20

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to L-Tryptophan Hydroxamate (pdb code 5l03). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to L-Tryptophan Hydroxamate, PDB code: 5l03:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5l03

Go back to Zinc Binding Sites List in 5l03
Zinc binding site 1 out of 3 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to L-Tryptophan Hydroxamate


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 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to L-Tryptophan Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:14.9
occ:0.73
 N A:6ZB202 1.9 17.8 1.0
OD2 A:ASP10 2.0 18.1 1.0
ND1 A:HIS44 2.0 14.1 1.0
NE2 A:HIS12 2.0 18.5 1.0
N03 A:6ZB202 2.9 23.3 1.0
CG A:ASP10 2.9 16.7 1.0
CE1 A:HIS12 2.9 20.5 1.0
CE1 A:HIS44 2.9 14.3 1.0
CG A:HIS44 3.1 11.4 1.0
CA A:6ZB202 3.1 26.1 1.0
CD2 A:HIS12 3.1 15.4 1.0
OD1 A:ASP10 3.1 19.6 1.0
C A:6ZB202 3.4 26.3 1.0
CB A:HIS44 3.4 13.7 1.0
O A:HOH385 3.7 30.7 1.0
CB A:6ZB202 3.8 22.1 1.0
O04 A:6ZB202 4.0 18.7 1.0
ND1 A:HIS12 4.1 22.8 1.0
NE2 A:HIS44 4.1 13.7 1.0
CD2 A:HIS44 4.2 12.0 1.0
CG A:HIS12 4.2 18.3 1.0
CB A:ASP10 4.3 15.4 1.0
O A:6ZB202 4.6 27.4 1.0
CA A:VAL41 4.6 13.3 1.0
O A:ASP40 4.8 12.7 1.0
NZ B:LYS134 4.9 48.5 1.0
CA A:HIS44 5.0 11.0 1.0
CG A:6ZB202 5.0 25.6 1.0

Zinc binding site 2 out of 3 in 5l03

Go back to Zinc Binding Sites List in 5l03
Zinc binding site 2 out of 3 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to L-Tryptophan Hydroxamate


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 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to L-Tryptophan Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:32.4
occ:0.52
 OD1 B:ASP10 1.9 29.6 1.0
NE2 B:HIS12 2.0 33.4 1.0
O B:HOH337 2.0 37.3 1.0
ND1 B:HIS44 2.1 38.2 1.0
OD2 B:ASP10 2.5 35.9 1.0
CG B:ASP10 2.5 33.4 1.0
CE1 B:HIS12 2.9 44.9 1.0
CE1 B:HIS44 3.0 39.3 1.0
CD2 B:HIS12 3.1 34.9 1.0
CG B:HIS44 3.3 31.9 1.0
CB B:HIS44 3.7 29.8 1.0
CB B:ASP10 4.0 26.4 1.0
ND1 B:HIS12 4.1 40.3 1.0
CG B:HIS12 4.2 36.0 1.0
NE2 B:HIS44 4.2 41.0 1.0
CD2 B:HIS44 4.3 36.4 1.0
NZ C:LYS134 4.5 41.0 1.0
CA B:VAL41 4.6 31.8 1.0
O B:ASP40 4.8 30.2 1.0
O B:VAL11 4.9 32.0 1.0
C B:ASP40 5.0 30.7 1.0
C B:ALA39 5.0 37.5 1.0

Zinc binding site 3 out of 3 in 5l03

Go back to Zinc Binding Sites List in 5l03
Zinc binding site 3 out of 3 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to L-Tryptophan Hydroxamate


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 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to L-Tryptophan Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:21.6
occ:0.57
 OD2 C:ASP10 2.0 25.1 1.0
NE2 C:HIS12 2.0 27.8 1.0
ND1 C:HIS44 2.0 22.0 1.0
O C:HOH388 2.1 28.1 1.0
CG C:ASP10 2.8 23.4 1.0
CE1 C:HIS44 2.9 24.5 1.0
CE1 C:HIS12 3.0 32.9 1.0
CD2 C:HIS12 3.0 26.3 1.0
CG C:HIS44 3.0 21.7 1.0
OD1 C:ASP10 3.0 24.6 1.0
CB C:HIS44 3.4 21.4 1.0
O A:HOH382 4.0 54.3 1.0
NE2 C:HIS44 4.1 28.1 1.0
ND1 C:HIS12 4.1 34.6 1.0
CG C:HIS12 4.1 26.3 1.0
CD2 C:HIS44 4.1 25.9 1.0
CB C:ASP10 4.2 22.2 1.0
O C:HOH348 4.4 32.3 1.0
NZ A:LYS134 4.6 41.9 1.0
CA C:VAL41 4.7 21.9 1.0
O C:ASP40 4.9 22.8 1.0
CA C:HIS44 4.9 20.8 1.0

Reference:

J.M.Blain, D.Ghose, J.L.Gorman, G.M.Goshu, G.Ranieri, L.Zhao, B.Bode, R.Meganathan, R.L.Walter, T.J.Hagen, J.R.Horn. Synthesis and Characterization of the Burkholderia Pseudomallei Ispf Inhibitor L-Tryptophan Hydroxamate To Be Published.
Page generated: Sun Oct 27 20:44:26 2024

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