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Zinc in PDB 6mwf: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0459

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0459

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0459:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0459, PDB code: 6mwf was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.66 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.030, 67.930, 60.760, 90.00, 96.58, 90.00
R / Rfree (%) 14.9 / 18.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0459 (pdb code 6mwf). 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 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0459, PDB code: 6mwf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6mwf

Go back to Zinc Binding Sites List in 6mwf
Zinc binding site 1 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0459


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 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0459 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:12.8
occ:0.85
 OD2 A:ASP10 2.0 13.9 1.0
ND1 A:HIS44 2.0 10.2 1.0
NE2 A:HIS12 2.0 14.1 1.0
NAL A:SFY202 2.1 14.6 0.8
NAM A:SFY202 2.7 12.6 0.8
CAO A:SFY202 2.9 9.9 0.8
CG A:ASP10 2.9 12.5 1.0
CE1 A:HIS44 3.0 13.8 1.0
CE1 A:HIS12 3.0 12.5 1.0
CG A:HIS44 3.0 10.0 1.0
CD2 A:HIS12 3.0 11.6 1.0
CAF A:SFY202 3.2 25.7 0.8
OD1 A:ASP10 3.2 14.0 1.0
CB A:HIS44 3.4 11.3 1.0
O A:HOH350 3.7 10.1 1.0
NE2 A:HIS44 4.1 11.3 1.0
ND1 A:HIS12 4.1 14.4 1.0
CD2 A:HIS44 4.1 9.4 1.0
CG A:HIS12 4.2 13.0 1.0
CAG A:SFY202 4.2 19.5 0.8
CB A:ASP10 4.3 7.8 1.0
SAQ A:SFY202 4.3 26.3 0.8
CAD A:SFY202 4.4 29.3 0.8
CA A:VAL41 4.6 8.4 1.0
OAB A:SFY202 4.7 23.9 0.8
O A:ASP40 4.8 11.0 1.0
CAE A:SFY202 4.9 25.7 0.8
CA A:HIS44 4.9 7.7 1.0
O A:VAL11 4.9 13.2 1.0
CAJ A:SFY202 4.9 25.5 0.8

Zinc binding site 2 out of 3 in 6mwf

Go back to Zinc Binding Sites List in 6mwf
Zinc binding site 2 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0459


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 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0459 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:18.5
occ:0.62
 O C:HOH385 1.9 31.4 1.0
NE2 B:HIS12 2.0 19.9 1.0
OD2 B:ASP10 2.0 17.1 1.0
ND1 B:HIS44 2.0 21.5 1.0
O B:HOH414 2.7 29.3 1.0
CG B:ASP10 2.8 19.1 1.0
CE1 B:HIS44 2.9 25.4 1.0
CE1 B:HIS12 3.0 24.7 1.0
CD2 B:HIS12 3.0 23.0 1.0
OD1 B:ASP10 3.0 17.6 1.0
CG B:HIS44 3.1 16.8 1.0
O B:HOH326 3.4 11.6 1.0
CB B:HIS44 3.5 17.7 1.0
NE2 B:HIS44 4.1 22.5 1.0
ND1 B:HIS12 4.1 21.2 1.0
CG B:HIS12 4.1 20.8 1.0
O B:HOH420 4.1 33.4 1.0
CD2 B:HIS44 4.2 21.2 1.0
CB B:ASP10 4.2 11.7 1.0
NZ C:LYS134 4.4 41.6 1.0
CA B:VAL41 4.7 14.6 1.0
O B:VAL11 4.8 20.3 1.0
O B:ASP40 4.9 20.7 1.0

Zinc binding site 3 out of 3 in 6mwf

Go back to Zinc Binding Sites List in 6mwf
Zinc binding site 3 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0459


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 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0459 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn200

b:14.5
occ:0.69
 OD2 C:ASP10 2.0 16.5 1.0
NE2 C:HIS12 2.0 18.5 1.0
NAL C:SFY201 2.0 17.4 0.8
ND1 C:HIS44 2.0 14.1 1.0
NAM C:SFY201 2.5 20.2 0.8
CAO C:SFY201 2.7 25.6 0.8
CE1 C:HIS12 2.9 26.3 1.0
CG C:ASP10 2.9 14.7 1.0
O C:HOH304 2.9 34.9 1.0
CE1 C:HIS44 3.0 17.9 1.0
CD2 C:HIS12 3.1 20.2 1.0
CG C:HIS44 3.1 13.1 1.0
CAF C:SFY201 3.1 26.6 0.8
OD1 C:ASP10 3.1 15.8 1.0
CB C:HIS44 3.4 12.1 1.0
ND1 C:HIS12 4.0 26.6 1.0
CAG C:SFY201 4.0 28.8 0.8
NE2 C:HIS44 4.1 17.1 1.0
SAQ C:SFY201 4.1 33.7 0.8
CG C:HIS12 4.1 17.1 1.0
CD2 C:HIS44 4.2 13.9 1.0
CB C:ASP10 4.3 10.3 1.0
CAD C:SFY201 4.3 31.8 0.8
OAB C:SFY201 4.6 37.1 0.8
CAE C:SFY201 4.7 32.2 0.8
CA C:VAL41 4.8 11.9 1.0
CA C:HIS44 5.0 11.0 1.0

Reference:

J.Abendroth, D.M.Dranow, P.G.Pierce, J.R.Horn, T.J.Hagen, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn-0456. To Be Published.
Page generated: Tue Oct 29 03:25:59 2024

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