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Zinc in PDB 3elc: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand, PDB code: 3elc was solved by W.N.Hunter, N.L.Ramsden, V.Ulaganathan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.676, 54.833, 88.506, 90.00, 99.66, 90.00
R / Rfree (%) 20.8 / 29.1

Other elements in 3elc:

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand (pdb code 3elc). 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 Complexed with Ligand, PDB code: 3elc:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3elc

Go back to Zinc Binding Sites List in 3elc
Zinc binding site 1 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand


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 Complexed with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:52.8
occ:0.50
 ND1 A:HIS42 2.2 37.3 0.5
NE2 A:HIS10 2.2 46.2 1.0
OD2 A:ASP8 2.3 40.4 1.0
ND1 A:HIS42 2.3 37.0 0.5
CE1 A:HIS42 2.8 37.4 0.5
OD1 A:ASP8 3.0 36.8 1.0
CG A:ASP8 3.0 38.8 1.0
CD2 A:HIS10 3.0 47.0 1.0
CE1 A:HIS42 3.1 37.2 0.5
CE1 A:HIS10 3.1 46.2 1.0
O A:HOH919 3.1 58.3 1.0
CG A:HIS42 3.3 36.8 0.5
CG A:HIS42 3.4 36.4 0.5
O A:HOH917 3.8 37.5 1.0
CB A:HIS42 3.9 36.3 0.5
CB A:HIS42 3.9 36.3 0.5
NE2 A:HIS42 3.9 34.8 0.5
ND1 A:HIS10 4.1 46.7 1.0
CG A:HIS10 4.1 45.1 1.0
CD2 A:HIS42 4.2 36.3 0.5
NE2 A:HIS42 4.2 37.6 0.5
OG A:SER35 4.3 52.7 1.0
CD2 A:HIS42 4.4 36.4 0.5
CB A:ASP8 4.5 38.5 1.0
O A:VAL9 4.8 41.2 1.0
CG1 A:VAL39 4.8 43.7 1.0
CA A:VAL39 4.9 43.1 1.0
O A:ASP38 5.0 45.0 1.0

Zinc binding site 2 out of 3 in 3elc

Go back to Zinc Binding Sites List in 3elc
Zinc binding site 2 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand


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 Complexed with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:86.5
occ:0.50
 ND1 B:HIS42 2.2 47.5 0.5
NE2 B:HIS10 2.2 57.6 1.0
ND1 B:HIS42 2.4 46.1 0.5
OD2 B:ASP8 2.5 47.2 1.0
OD1 B:ASP8 2.7 49.8 1.0
CE1 B:HIS42 2.8 47.5 0.5
CG B:ASP8 3.0 48.0 1.0
CE1 B:HIS10 3.0 58.2 1.0
CD2 B:HIS10 3.1 56.7 1.0
CE1 B:HIS42 3.1 46.8 0.5
CG B:HIS42 3.4 46.0 0.5
CG B:HIS42 3.5 45.7 0.5
CB B:HIS42 3.9 44.7 0.5
CB B:HIS42 3.9 44.6 0.5
O B:HOH938 3.9 26.2 1.0
NE2 B:HIS42 4.0 47.2 0.5
ND1 B:HIS10 4.0 56.6 1.0
CG B:HIS10 4.1 56.2 1.0
CD2 B:HIS42 4.3 46.5 0.5
NE2 B:HIS42 4.3 47.2 0.5
CB B:ASP8 4.5 47.2 1.0
O B:VAL9 4.5 53.0 1.0
CD2 B:HIS42 4.5 46.1 0.5
OE1 C:GLU135 4.9 51.6 1.0

Zinc binding site 3 out of 3 in 3elc

Go back to Zinc Binding Sites List in 3elc
Zinc binding site 3 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase Complexed with Ligand


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 Complexed with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn803

b:70.2
occ:0.50
 NE2 C:HIS10 2.2 44.8 1.0
ND1 C:HIS42 2.2 37.7 0.5
ND1 C:HIS42 2.3 41.6 0.5
OD2 C:ASP8 2.4 35.0 1.0
CE1 C:HIS42 2.9 37.0 0.5
CE1 C:HIS42 3.0 41.5 0.5
CD2 C:HIS10 3.0 43.9 1.0
CG C:ASP8 3.1 35.4 1.0
OD1 C:ASP8 3.2 34.7 1.0
CE1 C:HIS10 3.2 45.1 1.0
CG C:HIS42 3.3 38.0 0.5
CG C:HIS42 3.4 39.9 0.5
O C:HOH905 3.7 37.9 1.0
O C:HOH927 3.8 37.2 1.0
CB C:HIS42 3.9 39.0 0.5
CB C:HIS42 3.9 39.5 0.5
NE2 C:HIS42 4.0 36.9 0.5
OG C:SER35 4.1 57.9 1.0
CG C:HIS10 4.2 43.6 1.0
CD2 C:HIS42 4.2 36.9 0.5
ND1 C:HIS10 4.2 44.7 1.0
NE2 C:HIS42 4.2 40.0 0.5
CD2 C:HIS42 4.5 38.9 0.5
CB C:ASP8 4.6 36.5 1.0
O C:VAL9 4.6 40.8 1.0

Reference:

N.L.Ramsden, L.Buetow, A.Dawson, L.A.Kemp, V.Ulaganathan, R.Brenk, G.Klebe, W.N.Hunter. A Structure-Based Approach to Ligand Discovery For 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase: A Target For Antimicrobial Therapy J.Med.Chem. V. 52 2531 2009.
ISSN: ISSN 0022-2623
PubMed: 19320487
DOI: 10.1021/JM801475N
Page generated: Thu Oct 24 12:51:14 2024

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