Atomistry » Zinc » PDB 6nkn-6o3p » 6nmo
Atomistry »
  Zinc »
    PDB 6nkn-6o3p »
      6nmo »

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: Tue Oct 29 03:57:16 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy