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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

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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: Thu Oct 24 12:54:51 2024

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