Zinc in PDB 6mwj: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0863

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0863

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0863:
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- 0863, PDB code: 6mwj 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) 40.64 / 2.05
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.050, 67.400, 60.210, 90.00, 96.40, 90.00
R / Rfree (%) 14.9 / 19.7

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- 0863 (pdb code 6mwj). 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- 0863, PDB code: 6mwj:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6mwj

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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- 0863


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- 0863 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn200

b:18.4
occ:0.78
 NE2 A:HIS12 1.9 22.8 1.0
OD2 A:ASP10 2.0 22.8 1.0
O1 A:AZM201 2.0 24.3 0.9
ND1 A:HIS44 2.1 19.4 1.0
CG A:ASP10 2.9 25.9 1.0
CE1 A:HIS12 2.9 24.8 1.0
CD2 A:HIS12 2.9 21.1 1.0
CE1 A:HIS44 3.0 18.9 1.0
OD1 A:ASP10 3.1 25.5 1.0
S1 A:AZM201 3.1 25.5 0.9
CG A:HIS44 3.1 18.7 1.0
O2 A:AZM201 3.4 24.0 0.9
CB A:HIS44 3.5 13.8 1.0
ND1 A:HIS12 4.0 25.3 1.0
CG A:HIS12 4.0 20.3 1.0
S2 A:AZM201 4.1 24.2 0.9
NE2 A:HIS44 4.2 16.0 1.0
C1 A:AZM201 4.2 28.8 0.9
CD2 A:HIS44 4.2 16.8 1.0
CB A:ASP10 4.3 17.6 1.0
N1 A:AZM201 4.4 21.5 0.9
CA A:VAL41 4.7 14.7 1.0
O A:VAL11 4.7 27.5 1.0
O A:HOH367 4.8 25.2 1.0
O A:ASP40 4.9 13.2 1.0
O A:HOH304 4.9 56.8 1.0
CA A:HIS44 5.0 15.5 1.0

Zinc binding site 2 out of 3 in 6mwj

Go back to Zinc Binding Sites List in 6mwj
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- 0863


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- 0863 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:29.3
occ:0.51
 ND1 B:HIS44 2.0 45.4 1.0
NE2 B:HIS12 2.0 47.4 1.0
OD2 B:ASP10 2.2 46.0 1.0
O B:HOH347 2.7 38.5 1.0
CG B:ASP10 2.8 40.0 1.0
OD1 B:ASP10 2.8 32.8 1.0
CE1 B:HIS44 2.8 51.8 1.0
CE1 B:HIS12 2.9 48.5 1.0
CD2 B:HIS12 3.0 46.2 1.0
CG B:HIS44 3.1 40.2 1.0
CB B:HIS44 3.6 36.4 1.0
NE2 B:HIS44 4.0 46.8 1.0
ND1 B:HIS12 4.0 47.0 1.0
CD2 B:HIS44 4.1 45.3 1.0
CG B:HIS12 4.1 46.3 1.0
CB B:ASP10 4.2 30.4 1.0
O B:HOH348 4.3 43.3 1.0
CA B:VAL41 4.8 37.1 1.0
O B:VAL11 4.8 41.9 1.0

Zinc binding site 3 out of 3 in 6mwj

Go back to Zinc Binding Sites List in 6mwj
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- 0863


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- 0863 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:22.9
occ:0.61
 OD2 C:ASP10 1.9 23.1 1.0
NE2 C:HIS12 2.0 33.0 1.0
O C:HOH309 2.1 28.0 1.0
ND1 C:HIS44 2.2 21.7 1.0
O C:HOH359 2.4 29.0 1.0
CE1 C:HIS12 2.7 38.1 1.0
CG C:ASP10 2.9 22.2 1.0
CE1 C:HIS44 3.1 25.2 1.0
O C:HOH362 3.2 51.5 1.0
CD2 C:HIS12 3.2 34.8 1.0
CG C:HIS44 3.2 20.6 1.0
OD1 C:ASP10 3.2 22.7 1.0
CB C:HIS44 3.6 16.4 1.0
O C:HOH361 3.8 47.3 1.0
ND1 C:HIS12 3.9 41.2 1.0
CG C:HIS12 4.1 34.3 1.0
NE2 C:HIS44 4.2 24.4 1.0
CB C:ASP10 4.3 15.4 1.0
CD2 C:HIS44 4.3 20.5 1.0
NZ A:LYS134 4.7 26.8 0.6
O C:VAL11 4.9 16.8 1.0
OE2 A:GLU137 5.0 42.7 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: Wed Dec 16 12:20:43 2020

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