Atomistry » Zinc » PDB 5kjc-5l0e » 5l03
Atomistry »
  Zinc »
    PDB 5kjc-5l0e »
      5l03 »

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: Thu Aug 21 04:28:23 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy