Zinc in PDB 6nmo: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Compomplex with Ligand Sr-4.

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Compomplex with Ligand Sr-4.

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Compomplex with Ligand Sr-4.:
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 Compomplex with Ligand Sr-4., PDB code: 6nmo 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) 44.49 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.080, 67.600, 60.810, 90.00, 96.48, 90.00
R / Rfree (%) 12.6 / 15.9

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 Compomplex with Ligand Sr-4. (pdb code 6nmo). 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 Compomplex with Ligand Sr-4., PDB code: 6nmo:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6nmo

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


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 Compomplex with Ligand Sr-4. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:15.6
occ:0.79
 OD2 A:ASP10 2.0 13.3 1.0
NE2 A:HIS12 2.1 12.6 1.0
ND1 A:HIS44 2.1 11.5 1.0
O7 A:MLI203 2.2 16.2 0.7
O A:HOH315 2.2 19.1 1.0
O A:HOH304 2.4 25.5 1.0
CG A:ASP10 2.9 12.2 1.0
CE1 A:HIS12 3.0 14.4 1.0
CE1 A:HIS44 3.0 12.4 1.0
CD2 A:HIS12 3.1 13.2 1.0
C2 A:MLI203 3.1 18.4 0.7
OD1 A:ASP10 3.1 15.3 1.0
CG A:HIS44 3.2 10.0 1.0
O6 A:MLI203 3.4 18.7 0.7
CB A:HIS44 3.5 8.9 1.0
ND1 A:HIS12 4.1 14.0 1.0
O B:HOH303 4.2 28.2 1.0
NE2 A:HIS44 4.2 11.8 1.0
CG A:HIS12 4.2 12.1 1.0
CD2 A:HIS44 4.3 11.0 1.0
O A:HOH436 4.3 53.2 1.0
CB A:ASP10 4.3 10.3 1.0
C1 A:MLI203 4.5 19.7 0.7
O9 A:MLI203 4.6 18.2 0.7
C3 A:MLI203 4.7 18.9 0.7
O A:VAL11 4.9 12.6 1.0
O B:HOH301 4.9 30.2 1.0
CA A:VAL41 4.9 9.5 1.0

Zinc binding site 2 out of 3 in 6nmo

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


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 Compomplex with Ligand Sr-4. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:25.3
occ:0.46
 OD2 B:ASP10 1.9 17.6 1.0
ND1 B:HIS44 2.0 18.8 1.0
NE2 B:HIS12 2.1 27.4 1.0
O C:HOH425 2.1 31.6 1.0
CG B:ASP10 2.7 16.4 1.0
CE1 B:HIS44 2.9 20.6 1.0
OD1 B:ASP10 2.9 18.1 1.0
O C:HOH306 3.0 44.3 1.0
CE1 B:HIS12 3.0 28.2 1.0
O B:HOH308 3.0 28.3 1.0
CD2 B:HIS12 3.0 26.8 1.0
CG B:HIS44 3.2 17.5 1.0
CB B:HIS44 3.7 15.2 1.0
NE2 B:HIS44 4.0 21.9 1.0
ND1 B:HIS12 4.1 27.5 1.0
CB B:ASP10 4.2 13.5 1.0
CG B:HIS12 4.2 23.9 1.0
CD2 B:HIS44 4.2 20.1 1.0
NZ C:LYS134 4.2 19.0 0.5
O B:HOH313 4.3 48.7 1.0
CA B:VAL41 4.8 15.8 1.0
O B:VAL11 4.9 18.0 1.0
O B:ASP40 5.0 15.8 1.0

Zinc binding site 3 out of 3 in 6nmo

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


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 Compomplex with Ligand Sr-4. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:13.3
occ:0.71
 N2 C:QMS202 2.0 11.6 0.7
OD2 C:ASP10 2.1 13.3 1.0
NE2 C:HIS12 2.1 12.9 1.0
ND1 C:HIS44 2.2 10.7 1.0
O C:HOH325 2.2 16.5 1.0
N1 C:QMS202 2.2 11.1 0.7
C4 C:QMS202 2.9 12.7 0.7
C8 C:QMS202 3.0 12.1 0.7
C3 C:QMS202 3.0 12.8 0.7
CE1 C:HIS44 3.0 11.9 1.0
CG C:ASP10 3.0 11.5 1.0
CE1 C:HIS12 3.0 14.4 1.0
CD2 C:HIS12 3.1 12.7 1.0
CG C:HIS44 3.3 10.6 1.0
OD1 C:ASP10 3.3 12.8 1.0
S1 C:QMS202 3.4 11.6 0.7
O1 C:QMS202 3.4 12.0 0.7
CB C:HIS44 3.7 10.3 1.0
C7 C:QMS202 3.9 12.2 0.7
ND1 C:HIS12 4.2 14.7 1.0
NE2 C:HIS44 4.2 12.6 1.0
CG C:HIS12 4.2 12.8 1.0
C5 C:QMS202 4.3 13.8 0.7
C9 C:QMS202 4.3 12.7 0.7
C2 C:QMS202 4.3 13.7 0.7
CD2 C:HIS44 4.4 12.4 1.0
CB C:ASP10 4.4 9.3 1.0
O2 C:QMS202 4.6 13.0 0.7
C10 C:QMS202 4.8 13.8 0.7
OE2 A:GLU137 4.9 23.5 1.0

Reference:

J.Abendroth, D.M.Dranow, P.G.Pierce, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Compomplex with Ligand Sr-4. To Be Published.
Page generated: Wed Dec 16 12:24:15 2020

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