Atomistry » Zinc » PDB 5l03-5lbz » 5l12
Atomistry »
  Zinc »
    PDB 5l03-5lbz »
      5l12 »

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: Sun Oct 27 20:44:26 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