Atomistry » Zinc » PDB 3eju-3eyd » 3ern
Atomistry »
  Zinc »
    PDB 3eju-3eyd »
      3ern »

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

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

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

Protein crystallography data

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

Resolution Low / High (Å) 20.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.856, 54.236, 118.384, 90.00, 94.99, 90.00
R / Rfree (%) 21.8 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Aracmp (pdb code 3ern). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Aracmp, PDB code: 3ern:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3ern

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


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 Aracmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn800

b:91.0
occ:1.00
ND1 A:HIS42 2.3 27.3 0.5
NE2 A:HIS10 2.3 34.6 1.0
CD2 A:HIS42 2.6 21.0 0.5
OD2 A:ASP8 2.7 31.8 1.0
CG A:HIS42 3.0 22.2 0.5
NE2 A:HIS42 3.0 19.6 0.5
CE1 A:HIS10 3.1 35.2 1.0
CE1 A:HIS42 3.1 27.2 0.5
OD1 A:ASP8 3.2 32.5 1.0
CG A:HIS42 3.3 25.9 0.5
CG A:ASP8 3.3 30.4 1.0
CD2 A:HIS10 3.4 33.2 1.0
O A:HOH937 3.5 41.2 1.0
ND1 A:HIS42 3.6 20.5 0.5
CE1 A:HIS42 3.6 20.2 0.5
CB A:HIS42 3.6 24.9 0.5
CB A:HIS42 3.7 24.0 0.5
ND1 A:HIS10 4.2 35.1 1.0
NE2 A:HIS42 4.2 27.6 0.5
CD2 A:HIS42 4.3 26.2 0.5
CG A:HIS10 4.4 32.9 1.0
OG A:SER35 4.6 51.1 1.0
O A:HOH929 4.7 54.4 1.0
CB A:ASP8 4.8 28.6 1.0
O A:ASP38 5.0 33.6 1.0

Zinc binding site 2 out of 4 in 3ern

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


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 Aracmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn800

b:94.0
occ:1.00
OD2 B:ASP8 2.1 19.8 1.0
NE2 B:HIS10 2.3 25.5 1.0
O1 B:SO4801 3.0 53.8 1.0
CD2 B:HIS10 3.0 26.2 1.0
ND1 B:HIS42 3.0 25.5 1.0
CG B:HIS42 3.1 25.3 1.0
O B:HOH940 3.2 47.0 1.0
CG B:ASP8 3.2 19.7 1.0
CB B:HIS42 3.3 25.4 1.0
CE1 B:HIS10 3.4 28.0 1.0
OD1 B:ASP8 3.5 19.1 1.0
CE1 B:HIS42 3.7 23.3 1.0
O B:HOH917 3.7 38.1 1.0
CD2 B:HIS42 3.8 24.8 1.0
NE2 B:HIS42 4.1 24.1 1.0
CG B:HIS10 4.2 25.5 1.0
O B:ASP38 4.3 28.1 1.0
ND1 B:HIS10 4.4 26.1 1.0
S B:SO4801 4.4 53.4 1.0
CA B:VAL39 4.5 26.3 1.0
CB B:ASP8 4.5 21.5 1.0
C B:ASP38 4.5 28.0 1.0
C B:GLY37 4.5 30.9 1.0
N B:VAL39 4.6 27.0 1.0
CA B:GLY37 4.6 32.0 1.0
O2 B:SO4801 4.6 54.0 1.0
N B:ASP38 4.7 29.8 1.0
CG1 B:VAL39 4.7 26.3 1.0
O B:GLY37 4.9 30.7 1.0
CA B:HIS42 4.9 25.0 1.0
O B:HOH914 5.0 25.9 1.0

Zinc binding site 3 out of 4 in 3ern

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


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 Aracmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn800

b:84.9
occ:1.00
NE2 D:HIS10 2.3 30.0 1.0
OD2 D:ASP8 2.3 27.2 1.0
CD2 D:HIS42 2.8 23.9 1.0
OD1 D:ASP8 2.9 27.4 1.0
CG D:HIS42 2.9 22.7 1.0
CG D:ASP8 3.0 25.0 1.0
NE2 D:HIS42 3.0 23.1 1.0
CE1 D:HIS10 3.1 30.7 1.0
O D:HOH953 3.1 49.6 1.0
ND1 D:HIS42 3.2 25.5 1.0
CE1 D:HIS42 3.3 24.3 1.0
O D:HOH943 3.3 42.6 1.0
CD2 D:HIS10 3.3 30.1 1.0
CB D:HIS42 3.7 21.9 1.0
ND1 D:HIS10 4.2 31.1 1.0
CG D:HIS10 4.4 30.0 1.0
CB D:ASP8 4.4 24.2 1.0
OP3 E:CAR900 4.7 53.1 1.0

Zinc binding site 4 out of 4 in 3ern

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Clycodiphosphate Synthase Complexed with Aracmp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn800

b:96.1
occ:1.00
OD2 E:ASP8 2.4 31.1 1.0
NE2 E:HIS10 2.4 32.2 1.0
O2 E:SO4801 2.7 60.9 1.0
ND1 E:HIS42 2.9 28.5 1.0
O E:HOH943 3.1 45.7 1.0
CG E:HIS42 3.2 27.0 1.0
CD2 E:HIS10 3.2 31.4 1.0
CG E:ASP8 3.4 30.7 1.0
CB E:HIS42 3.4 26.9 1.0
CE1 E:HIS10 3.5 32.8 1.0
CE1 E:HIS42 3.6 26.6 1.0
OD1 E:ASP8 3.6 33.6 1.0
CD2 E:HIS42 4.0 26.8 1.0
S E:SO4801 4.0 60.6 1.0
O E:ASP38 4.2 31.6 1.0
OG E:SER35 4.2 39.9 1.0
NE2 E:HIS42 4.2 27.0 1.0
O1 E:SO4801 4.3 60.7 1.0
C E:ASP38 4.4 31.7 1.0
CG E:HIS10 4.4 31.1 1.0
CA E:GLY37 4.5 35.1 1.0
C E:GLY37 4.5 34.3 1.0
CA E:VAL39 4.5 29.9 1.0
ND1 E:HIS10 4.5 31.7 1.0
N E:VAL39 4.5 30.7 1.0
N E:ASP38 4.6 33.3 1.0
CB E:ASP8 4.7 29.1 1.0
O3 E:SO4801 4.8 61.2 1.0
O E:GLY37 4.9 34.1 1.0
O4 E:SO4801 4.9 61.3 1.0
CA E:HIS42 4.9 27.1 1.0
CG1 E:VAL39 5.0 30.4 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: Wed Dec 16 04:16:52 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy