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Zinc in PDB 6mwi: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0456

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0456

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Complex with Ligand Hgn- 0456:
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- 0456, PDB code: 6mwi 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) 40.81 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.000, 67.350, 60.790, 90.00, 96.45, 90.00
R / Rfree (%) 13.7 / 17

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- 0456 (pdb code 6mwi). 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- 0456, PDB code: 6mwi:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6mwi

Go back to Zinc Binding Sites List in 6mwi
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- 0456


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- 0456 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:12.8
occ:0.86
 O A:HOH444 2.0 15.7 1.0
OD2 A:ASP10 2.0 11.0 1.0
ND1 A:HIS44 2.0 8.8 1.0
NE2 A:HIS12 2.0 10.7 1.0
O A:HOH436 2.6 22.8 1.0
O B:HOH387 2.8 21.1 1.0
CG A:ASP10 2.9 12.1 1.0
CE1 A:HIS44 2.9 10.4 1.0
CD2 A:HIS12 3.0 10.0 1.0
CE1 A:HIS12 3.0 11.8 1.0
CG A:HIS44 3.0 9.2 1.0
OD1 A:ASP10 3.1 12.4 1.0
CB A:HIS44 3.4 9.3 1.0
O A:HOH327 3.6 24.2 1.0
NE2 A:HIS44 4.1 8.6 1.0
ND1 A:HIS12 4.1 11.0 1.0
CG A:HIS12 4.1 9.3 1.0
CD2 A:HIS44 4.1 8.3 1.0
CB A:ASP10 4.2 7.2 1.0
O A:HOH383 4.5 16.6 1.0
CA A:VAL41 4.7 5.9 1.0
O A:ASP40 4.9 8.8 1.0
O A:VAL11 4.9 10.3 1.0
CA A:HIS44 4.9 5.5 1.0

Zinc binding site 2 out of 3 in 6mwi

Go back to Zinc Binding Sites List in 6mwi
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- 0456


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- 0456 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:16.4
occ:0.80
 NE2 B:HIS12 2.0 16.9 1.0
O2 B:EZL202 2.0 13.7 0.7
OD2 B:ASP10 2.0 12.5 1.0
ND1 B:HIS44 2.1 13.9 1.0
CG B:ASP10 2.8 14.4 1.0
CE1 B:HIS12 2.9 21.6 1.0
S1 B:EZL202 2.9 17.1 0.7
OD1 B:ASP10 2.9 14.8 1.0
CD2 B:HIS12 3.0 19.8 1.0
CE1 B:HIS44 3.0 18.2 1.0
O1 B:EZL202 3.1 13.6 0.7
CG B:HIS44 3.1 11.9 1.0
CB B:HIS44 3.5 11.1 1.0
O B:HOH312 3.5 30.4 1.0
ND1 B:HIS12 4.0 20.3 1.0
C1 B:EZL202 4.0 22.1 0.7
CG B:HIS12 4.1 17.4 1.0
S2 B:EZL202 4.1 25.7 0.7
NE2 B:HIS44 4.2 16.0 1.0
CB B:ASP10 4.2 10.2 1.0
CD2 B:HIS44 4.2 12.2 1.0
N1 B:EZL202 4.3 14.6 0.7
CA B:VAL41 4.6 10.7 1.0
O B:VAL11 4.7 14.8 1.0
NZ C:LYS134 4.7 24.7 0.5
O B:ASP40 5.0 13.3 1.0

Zinc binding site 3 out of 3 in 6mwi

Go back to Zinc Binding Sites List in 6mwi
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- 0456


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- 0456 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:13.9
occ:0.75
 OD2 C:ASP10 2.0 13.2 1.0
NE2 C:HIS12 2.0 16.4 1.0
ND1 C:HIS44 2.0 10.1 1.0
O C:HOH316 2.3 28.0 1.0
O C:HOH401 2.5 34.4 1.0
O A:HOH428 2.5 19.8 1.0
CE1 C:HIS12 2.9 24.9 1.0
CG C:ASP10 2.9 10.8 1.0
CE1 C:HIS44 2.9 14.6 1.0
CD2 C:HIS12 3.1 20.5 1.0
CG C:HIS44 3.1 10.7 1.0
OD1 C:ASP10 3.2 13.9 1.0
CB C:HIS44 3.5 10.8 1.0
O C:HOH407 3.9 22.3 1.0
ND1 C:HIS12 4.0 25.9 1.0
NE2 C:HIS44 4.1 12.7 1.0
CG C:HIS12 4.1 17.8 1.0
CD2 C:HIS44 4.2 10.7 1.0
CB C:ASP10 4.3 7.4 1.0
NZ A:LYS134 4.6 20.2 0.4
O C:VAL11 4.9 10.6 1.0
OE2 A:GLU137 4.9 33.0 1.0
O C:HOH395 5.0 15.4 0.6

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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