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Zinc in PDB 6v3m: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Compomplex with Ligand Hgn-0961 (BSI110840)

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Compomplex with Ligand Hgn-0961 (BSI110840)

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Compomplex with Ligand Hgn-0961 (BSI110840):
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 Hgn-0961 (BSI110840), PDB code: 6v3m 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) 44.39 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.310, 67.550, 60.570, 90.00, 96.32, 90.00
R / Rfree (%) 14.5 / 16.9

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 Hgn-0961 (BSI110840) (pdb code 6v3m). 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 Hgn-0961 (BSI110840), PDB code: 6v3m:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6v3m

Go back to Zinc Binding Sites List in 6v3m
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 Hgn-0961 (BSI110840)


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 Hgn-0961 (BSI110840) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:13.3
occ:0.79
 OD2 A:ASP10 2.0 13.5 1.0
O01 A:QOG202 2.0 17.5 0.8
NE2 A:HIS12 2.0 15.6 1.0
ND1 A:HIS44 2.1 14.1 1.0
CG A:ASP10 2.9 15.1 1.0
CE1 A:HIS44 3.0 14.6 1.0
S02 A:QOG202 3.0 16.9 0.8
CE1 A:HIS12 3.0 19.5 1.0
CD2 A:HIS12 3.0 12.9 1.0
O16 A:QOG202 3.1 13.4 0.8
CG A:HIS44 3.1 12.5 1.0
OD1 A:ASP10 3.1 15.7 1.0
CB A:HIS44 3.5 11.2 1.0
NE2 A:HIS44 4.1 12.6 1.0
ND1 A:HIS12 4.1 18.6 1.0
CG A:HIS12 4.2 15.3 1.0
C03 A:QOG202 4.2 15.2 0.8
S14 A:QOG202 4.2 18.2 0.8
CB A:ASP10 4.2 12.0 1.0
CD2 A:HIS44 4.2 12.4 1.0
O A:HOH355 4.2 22.5 0.6
N15 A:QOG202 4.3 17.5 0.8
O B:HOH338 4.4 30.7 1.0
CA A:VAL41 4.7 9.6 1.0
O A:VAL11 4.8 16.2 1.0

Zinc binding site 2 out of 3 in 6v3m

Go back to Zinc Binding Sites List in 6v3m
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 Hgn-0961 (BSI110840)


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 Hgn-0961 (BSI110840) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:21.4
occ:0.72
 OD2 B:ASP10 1.9 18.4 1.0
NE2 B:HIS12 2.0 21.4 1.0
O01 B:QOG202 2.0 18.6 0.7
ND1 B:HIS44 2.0 24.0 1.0
CG B:ASP10 2.7 24.8 1.0
CE1 B:HIS12 2.9 27.9 1.0
CE1 B:HIS44 2.9 32.7 1.0
OD1 B:ASP10 2.9 25.8 1.0
S02 B:QOG202 3.0 21.8 0.7
CD2 B:HIS12 3.0 26.3 1.0
O16 B:QOG202 3.1 20.7 0.7
CG B:HIS44 3.1 22.7 1.0
CB B:HIS44 3.5 20.7 1.0
ND1 B:HIS12 4.0 27.6 1.0
NE2 B:HIS44 4.1 27.2 1.0
CG B:HIS12 4.1 22.8 1.0
CB B:ASP10 4.1 17.1 1.0
C03 B:QOG202 4.2 22.3 0.7
CD2 B:HIS44 4.2 23.9 1.0
N15 B:QOG202 4.3 19.8 0.7
S14 B:QOG202 4.3 25.2 0.7
CA B:VAL41 4.7 22.6 1.0
O B:VAL11 4.8 22.0 1.0
O B:ASP40 5.0 22.8 1.0

Zinc binding site 3 out of 3 in 6v3m

Go back to Zinc Binding Sites List in 6v3m
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 Hgn-0961 (BSI110840)


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 Hgn-0961 (BSI110840) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:13.6
occ:0.58
 O01 C:QOG202 1.9 25.3 0.6
OD2 C:ASP10 2.0 18.2 1.0
NE2 C:HIS12 2.0 18.6 1.0
ND1 C:HIS44 2.1 14.4 1.0
S02 C:QOG202 2.8 23.9 0.6
CG C:ASP10 2.9 13.6 1.0
O16 C:QOG202 2.9 17.0 0.6
CE1 C:HIS12 2.9 26.7 1.0
CE1 C:HIS44 3.0 19.5 1.0
CD2 C:HIS12 3.1 20.4 1.0
OD1 C:ASP10 3.2 16.1 1.0
CG C:HIS44 3.2 13.8 1.0
CB C:HIS44 3.6 11.7 1.0
C03 C:QOG202 4.0 26.3 0.6
ND1 C:HIS12 4.0 27.5 1.0
NE2 C:HIS44 4.1 16.7 1.0
N15 C:QOG202 4.1 21.2 0.6
CG C:HIS12 4.1 17.6 1.0
S14 C:QOG202 4.2 23.9 0.6
CB C:ASP10 4.2 12.7 1.0
CD2 C:HIS44 4.2 16.7 1.0
OE2 A:GLU137 4.9 32.0 1.0
O C:VAL11 4.9 16.0 1.0

Reference:

J.Abendroth, J.K.Yano, P.G.Pierce, J.R.Horn, T.J.Hagen, P.S.Horanyi, D.D.Lorimer, T.E.Edwards. Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (Ispf) Burkholderia Pseudomallei in Compomplex with Ligand Hgn-0961 (BSI110840) To Be Published.
Page generated: Tue Oct 29 08:52:14 2024

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