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Zinc in PDB 5l12: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase From Burkholderia Pseudomallei Double Mutant

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase From Burkholderia Pseudomallei Double Mutant

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase From Burkholderia Pseudomallei Double Mutant:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase From Burkholderia Pseudomallei Double Mutant, PDB code: 5l12 was solved by J.M.Blain, G.Raneiri, R.L.Walter, T.J.Hagen, J.R.Horn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.07 / 1.72
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.859, 68.140, 60.408, 90.00, 96.57, 90.00
R / Rfree (%) 16.5 / 20.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase From Burkholderia Pseudomallei Double Mutant (pdb code 5l12). 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-Clycodiphosphate Synthase From Burkholderia Pseudomallei Double Mutant, PDB code: 5l12:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5l12

Go back to Zinc Binding Sites List in 5l12
Zinc binding site 1 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase From Burkholderia Pseudomallei Double Mutant


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-Clycodiphosphate Synthase From Burkholderia Pseudomallei Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:23.1
occ:0.63
 OD2 A:ASP10 1.9 27.2 1.0
O A:HOH408 2.0 34.7 1.0
NE2 A:HIS12 2.0 33.3 1.0
ND1 A:HIS44 2.0 27.2 1.0
CG A:ASP10 2.8 28.2 1.0
CE1 A:HIS12 2.9 32.7 1.0
OD1 A:ASP10 2.9 30.6 1.0
CE1 A:HIS44 3.0 25.2 1.0
HE1 A:HIS12 3.0 39.3 1.0
CG A:HIS44 3.0 21.7 1.0
CD2 A:HIS12 3.1 28.0 1.0
HE1 A:HIS44 3.2 30.2 1.0
HB2 A:HIS44 3.2 23.2 1.0
HB3 A:HIS44 3.2 23.2 1.0
HD2 A:HIS12 3.3 33.6 1.0
CB A:HIS44 3.4 19.3 1.0
HZ1 B:LYS134 3.6 72.2 1.0
HA A:VAL41 3.7 25.8 1.0
ND1 A:HIS12 4.0 32.9 1.0
NE2 A:HIS44 4.1 24.0 1.0
CG A:HIS12 4.1 34.0 1.0
CD2 A:HIS44 4.2 23.4 1.0
CB A:ASP10 4.2 28.3 1.0
HZ3 B:LYS134 4.3 72.2 1.0
HA A:ALA39 4.3 34.0 1.0
NZ B:LYS134 4.3 60.1 1.0
HB3 A:ASP10 4.4 34.0 1.0
O A:HOH398 4.4 22.4 1.0
HB2 A:ASP10 4.4 34.0 1.0
HG23 A:VAL41 4.5 30.5 1.0
HZ2 B:LYS134 4.5 72.2 1.0
CA A:VAL41 4.6 21.5 1.0
H A:VAL11 4.7 34.6 1.0
O A:ASP40 4.8 21.1 1.0
HD1 A:HIS12 4.8 39.5 1.0
O A:VAL11 4.9 29.6 1.0
HE2 A:HIS44 4.9 28.8 1.0
CA A:HIS44 4.9 22.4 1.0
HD13 A:ILE59 5.0 49.5 1.0

Zinc binding site 2 out of 3 in 5l12

Go back to Zinc Binding Sites List in 5l12
Zinc binding site 2 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase From Burkholderia Pseudomallei Double Mutant


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-Clycodiphosphate Synthase From Burkholderia Pseudomallei Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:41.9
occ:0.41
 OD2 B:ASP10 1.9 43.4 1.0
NE2 B:HIS12 2.0 47.2 1.0
ND1 B:HIS44 2.1 47.5 1.0
O B:HOH353 2.1 49.2 1.0
OD1 B:ASP10 2.5 45.0 1.0
CG B:ASP10 2.6 42.5 1.0
CE1 B:HIS44 2.8 58.2 1.0
HE1 B:HIS44 2.9 69.8 1.0
CE1 B:HIS12 3.0 59.9 1.0
CD2 B:HIS12 3.1 51.3 1.0
HE1 B:HIS12 3.1 71.8 1.0
CG B:HIS44 3.2 46.5 1.0
HD2 B:HIS12 3.3 61.5 1.0
HB2 B:HIS44 3.5 49.4 1.0
HB3 B:HIS44 3.6 49.4 1.0
HA B:VAL41 3.6 48.8 1.0
HZ1 C:LYS134 3.7 68.8 1.0
CB B:HIS44 3.7 41.2 1.0
NE2 B:HIS44 4.0 52.4 1.0
CB B:ASP10 4.0 35.0 1.0
ND1 B:HIS12 4.1 54.0 1.0
HA B:ALA39 4.1 58.6 1.0
CG B:HIS12 4.2 52.9 1.0
CD2 B:HIS44 4.2 53.3 1.0
HZ3 C:LYS134 4.3 68.8 1.0
HB2 B:ASP10 4.3 42.0 1.0
HB3 B:ASP10 4.3 42.0 1.0
NZ C:LYS134 4.4 57.4 1.0
HG23 B:VAL41 4.5 61.9 1.0
H B:VAL11 4.5 47.6 1.0
CA B:VAL41 4.6 40.7 1.0
HZ2 C:LYS134 4.6 68.8 1.0
O B:VAL11 4.7 44.8 1.0
HE2 B:HIS44 4.8 62.8 1.0
O B:ASP40 4.8 41.1 1.0
HD1 B:HIS12 4.9 64.8 1.0
C B:ALA39 4.9 51.3 1.0
CA B:ALA39 4.9 48.8 1.0
N B:VAL41 4.9 40.4 1.0
C B:ASP40 5.0 41.7 1.0

Zinc binding site 3 out of 3 in 5l12

Go back to Zinc Binding Sites List in 5l12
Zinc binding site 3 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase From Burkholderia Pseudomallei Double Mutant


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-Clycodiphosphate Synthase From Burkholderia Pseudomallei Double Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:32.2
occ:0.63
 OD2 C:ASP10 1.9 34.7 1.0
ND1 C:HIS44 2.0 30.6 1.0
NE2 C:HIS12 2.0 39.5 1.0
O C:HOH383 2.1 41.1 1.0
CG C:ASP10 2.7 32.3 1.0
CE1 C:HIS44 2.9 32.2 1.0
CE1 C:HIS12 2.9 39.5 1.0
OD1 C:ASP10 3.0 33.3 1.0
CG C:HIS44 3.0 32.9 1.0
CD2 C:HIS12 3.1 36.3 1.0
HE1 C:HIS12 3.1 47.5 1.0
HE1 C:HIS44 3.1 38.7 1.0
HB3 C:HIS44 3.2 33.5 1.0
HB2 C:HIS44 3.2 33.5 1.0
HD2 C:HIS12 3.3 43.5 1.0
CB C:HIS44 3.4 27.9 1.0
HA C:VAL41 3.7 34.5 1.0
HZ1 A:LYS134 3.9 49.7 1.0
NE2 C:HIS44 4.1 37.0 1.0
ND1 C:HIS12 4.1 48.7 1.0
CD2 C:HIS44 4.1 33.0 1.0
CB C:ASP10 4.1 29.4 1.0
CG C:HIS12 4.2 40.9 1.0
O A:HOH311 4.2 71.2 1.0
HA C:ALA39 4.3 50.0 1.0
HB2 C:ASP10 4.4 35.3 1.0
HB3 C:ASP10 4.4 35.3 1.0
O C:HOH388 4.4 40.3 1.0
HZ3 A:LYS134 4.5 49.7 1.0
NZ A:LYS134 4.5 41.4 1.0
HG23 C:VAL41 4.5 46.8 1.0
CA C:VAL41 4.7 28.7 1.0
HZ2 A:LYS134 4.7 49.7 1.0
H C:VAL11 4.7 37.2 1.0
HD13 C:ILE59 4.8 69.6 1.0
HE2 C:HIS44 4.8 44.4 1.0
O C:ASP40 4.8 32.5 1.0
HD1 C:HIS12 4.8 58.4 1.0
O C:VAL11 4.9 32.9 1.0
CA C:HIS44 4.9 24.4 1.0
HD2 C:HIS44 5.0 39.6 1.0

Reference:

J.M.Blain, G.Raneiri, R.L.Walter, T.J.Hagen, J.R.Horn. Enzyme Engineering For the Development of A High-Throughput Temperature Screen of Burkholderia Pseudomallei Ispf Inhibitors To Be Published.
Page generated: Wed Dec 16 06:28:11 2020

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