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Zinc in PDB 6mwk: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0883

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0883

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0883:
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- 0883, PDB code: 6mwk 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) 40.94 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.330, 68.040, 60.670, 90.00, 96.46, 90.00
R / Rfree (%) 14.2 / 17.9

Other elements in 6mwk:

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0883 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

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- 0883 (pdb code 6mwk). 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- 0883, PDB code: 6mwk:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6mwk

Go back to Zinc Binding Sites List in 6mwk
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- 0883


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- 0883 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:13.6
occ:0.82
 N06 A:K4Y202 2.0 15.2 0.8
ND1 A:HIS44 2.0 12.2 1.0
OD2 A:ASP10 2.0 13.2 1.0
NE2 A:HIS12 2.0 10.6 1.0
N08 A:K4Y202 2.7 12.4 0.8
C07 A:K4Y202 2.8 19.1 0.8
CG A:ASP10 2.9 12.4 1.0
CE1 A:HIS44 2.9 12.7 1.0
O A:HOH304 2.9 40.1 1.0
C05 A:K4Y202 3.0 14.2 0.8
CE1 A:HIS12 3.0 12.2 1.0
CD2 A:HIS12 3.0 10.7 1.0
CG A:HIS44 3.0 11.2 1.0
OD1 A:ASP10 3.1 14.7 1.0
CB A:HIS44 3.4 8.2 1.0
NE2 A:HIS44 4.1 12.2 1.0
C19 A:K4Y202 4.1 18.7 0.8
ND1 A:HIS12 4.1 14.2 1.0
CD2 A:HIS44 4.1 12.3 1.0
CG A:HIS12 4.2 10.0 1.0
N04 A:K4Y202 4.2 22.1 0.8
CB A:ASP10 4.3 9.6 1.0
S09 A:K4Y202 4.3 21.3 0.8
O11 A:K4Y202 4.6 13.9 0.8
C03 A:K4Y202 4.7 17.2 0.8
CA A:VAL41 4.7 8.3 1.0
O B:HOH388 4.8 45.6 1.0
O A:ASP40 4.9 7.3 1.0
O A:HOH407 4.9 18.0 1.0
CA A:HIS44 5.0 7.7 1.0
O A:VAL11 5.0 12.8 1.0
C18 A:K4Y202 5.0 27.1 0.8

Zinc binding site 2 out of 3 in 6mwk

Go back to Zinc Binding Sites List in 6mwk
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- 0883


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- 0883 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:17.0
occ:0.67
 NE2 B:HIS12 2.0 20.2 1.0
OD2 B:ASP10 2.0 14.4 1.0
N06 B:K4Y202 2.0 13.2 0.8
ND1 B:HIS44 2.1 18.4 1.0
N08 B:K4Y202 2.7 19.8 0.8
CG B:ASP10 2.8 17.1 1.0
C07 B:K4Y202 2.8 20.7 0.8
CE1 B:HIS12 2.9 24.9 1.0
OD1 B:ASP10 2.9 13.4 1.0
CE1 B:HIS44 3.0 19.8 1.0
CD2 B:HIS12 3.0 20.8 1.0
C05 B:K4Y202 3.1 19.7 0.8
CG B:HIS44 3.1 13.4 1.0
CB B:HIS44 3.5 12.2 1.0
ND1 B:HIS12 4.0 20.9 1.0
CG B:HIS12 4.1 19.0 1.0
NE2 B:HIS44 4.1 20.6 1.0
C19 B:K4Y202 4.1 19.9 0.8
CB B:ASP10 4.2 9.7 1.0
CD2 B:HIS44 4.2 16.5 1.0
N04 B:K4Y202 4.3 21.2 0.8
S09 B:K4Y202 4.3 21.9 0.8
CA B:VAL41 4.6 12.5 1.0
C03 B:K4Y202 4.7 21.0 0.8
O11 B:K4Y202 4.7 23.9 0.8
O B:VAL11 4.8 15.5 1.0
O B:ASP40 4.9 13.2 1.0
N B:VAL41 5.0 13.2 1.0

Zinc binding site 3 out of 3 in 6mwk

Go back to Zinc Binding Sites List in 6mwk
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- 0883


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- 0883 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn200

b:14.2
occ:0.79
 OD2 C:ASP10 2.0 14.8 1.0
NE2 C:HIS12 2.0 15.4 1.0
N06 C:K4Y201 2.0 13.5 0.8
ND1 C:HIS44 2.0 10.7 1.0
N08 C:K4Y201 2.7 14.4 0.8
C07 C:K4Y201 2.8 20.8 0.8
CG C:ASP10 2.9 14.1 1.0
CE1 C:HIS12 2.9 23.0 1.0
CE1 C:HIS44 3.0 14.8 1.0
CG C:HIS44 3.0 9.8 1.0
C05 C:K4Y201 3.1 16.3 0.8
CD2 C:HIS12 3.1 16.6 1.0
OD1 C:ASP10 3.1 11.2 1.0
CB C:HIS44 3.4 11.1 1.0
ND1 C:HIS12 4.1 22.1 1.0
NE2 C:HIS44 4.1 16.2 1.0
C19 C:K4Y201 4.1 16.1 0.8
CD2 C:HIS44 4.2 10.4 1.0
CG C:HIS12 4.2 14.4 1.0
CB C:ASP10 4.2 8.9 1.0
S09 C:K4Y201 4.3 20.6 0.8
N04 C:K4Y201 4.3 19.2 0.8
O11 C:K4Y201 4.6 24.8 0.8
C03 C:K4Y201 4.7 19.4 0.8
CA C:VAL41 4.7 9.1 1.0
CA C:HIS44 4.9 8.4 1.0
O C:HOH343 4.9 24.9 1.0
O C:ASP40 5.0 11.7 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: Tue Oct 29 03:26:59 2024

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