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Zinc in PDB 2uzh: Mycobacterium Smegmatis 2C-Methyl-D-Erythritol-2,4- Cyclodiphosphate Synthase (Ispf)

Enzymatic activity of Mycobacterium Smegmatis 2C-Methyl-D-Erythritol-2,4- Cyclodiphosphate Synthase (Ispf)

All present enzymatic activity of Mycobacterium Smegmatis 2C-Methyl-D-Erythritol-2,4- Cyclodiphosphate Synthase (Ispf):
4.6.1.12;

Protein crystallography data

The structure of Mycobacterium Smegmatis 2C-Methyl-D-Erythritol-2,4- Cyclodiphosphate Synthase (Ispf), PDB code: 2uzh was solved by L.Buetow, A.C.Brown, T.Parish, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.30 / 2.2
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 159.121, 159.121, 54.160, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 20.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Mycobacterium Smegmatis 2C-Methyl-D-Erythritol-2,4- Cyclodiphosphate Synthase (Ispf) (pdb code 2uzh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Mycobacterium Smegmatis 2C-Methyl-D-Erythritol-2,4- Cyclodiphosphate Synthase (Ispf), PDB code: 2uzh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 2uzh

Go back to Zinc Binding Sites List in 2uzh
Zinc binding site 1 out of 3 in the Mycobacterium Smegmatis 2C-Methyl-D-Erythritol-2,4- Cyclodiphosphate Synthase (Ispf)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mycobacterium Smegmatis 2C-Methyl-D-Erythritol-2,4- Cyclodiphosphate Synthase (Ispf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1157

b:41.7
occ:0.75
NE2 A:HIS13 2.1 45.5 1.0
ND1 A:HIS45 2.2 34.0 1.0
OD2 A:ASP11 2.2 27.9 1.0
CE1 A:HIS13 2.4 44.1 1.0
O3B C:CDP1158 2.9 31.7 0.5
CG A:ASP11 3.0 26.1 1.0
CE1 A:HIS45 3.1 32.1 1.0
OD1 A:ASP11 3.1 25.2 1.0
CG A:HIS45 3.2 29.9 1.0
CD2 A:HIS13 3.3 44.9 1.0
CB A:HIS45 3.6 22.7 1.0
ND1 A:HIS13 3.6 44.0 1.0
O1B C:CDP1158 3.7 47.3 0.5
O3B C:CDP1158 4.0 46.4 0.5
O2B C:CDP1158 4.0 44.8 0.5
PB C:CDP1158 4.1 30.8 0.5
CG A:HIS13 4.1 42.1 1.0
O2B C:CDP1158 4.1 28.4 0.5
PB C:CDP1158 4.1 46.8 0.5
NE2 A:HIS45 4.2 31.6 1.0
CD2 A:HIS45 4.3 30.2 1.0
CB A:ASP11 4.4 24.8 1.0
O2A C:CDP1158 4.7 34.5 0.5
O1B C:CDP1158 4.8 30.9 0.5
CD1 A:LEU60 4.9 28.0 1.0

Zinc binding site 2 out of 3 in 2uzh

Go back to Zinc Binding Sites List in 2uzh
Zinc binding site 2 out of 3 in the Mycobacterium Smegmatis 2C-Methyl-D-Erythritol-2,4- Cyclodiphosphate Synthase (Ispf)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mycobacterium Smegmatis 2C-Methyl-D-Erythritol-2,4- Cyclodiphosphate Synthase (Ispf) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1157

b:39.6
occ:0.50
OD2 C:ASP11 2.2 29.1 1.0
NE2 C:HIS13 2.3 39.9 1.0
ND1 C:HIS45 2.3 31.2 1.0
OD1 C:ASP11 2.6 29.2 1.0
CG C:ASP11 2.7 23.5 1.0
O1B B:CDP1158 2.8 20.6 0.5
CD2 C:HIS13 3.0 37.6 1.0
CE1 C:HIS45 3.2 28.8 1.0
CG C:HIS45 3.2 28.0 1.0
CE1 C:HIS13 3.4 36.7 1.0
CB C:HIS45 3.5 21.9 1.0
O1B B:CDP1158 3.5 23.4 0.5
O2B B:CDP1158 3.8 16.5 0.5
PB B:CDP1158 4.0 15.7 0.5
O3B B:CDP1158 4.0 6.6 0.5
PB B:CDP1158 4.2 18.8 0.5
CB C:ASP11 4.2 20.6 1.0
CG C:HIS13 4.2 35.5 1.0
O2B B:CDP1158 4.2 16.1 0.5
NE2 C:HIS45 4.3 30.7 1.0
CD2 C:HIS45 4.4 30.1 1.0
ND1 C:HIS13 4.4 37.6 1.0
O3B B:CDP1158 4.6 24.7 0.5
CD1 C:LEU60 4.6 23.5 1.0
O B:HOH2106 4.7 32.0 1.0

Zinc binding site 3 out of 3 in 2uzh

Go back to Zinc Binding Sites List in 2uzh
Zinc binding site 3 out of 3 in the Mycobacterium Smegmatis 2C-Methyl-D-Erythritol-2,4- Cyclodiphosphate Synthase (Ispf)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mycobacterium Smegmatis 2C-Methyl-D-Erythritol-2,4- Cyclodiphosphate Synthase (Ispf) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1157

b:26.8
occ:0.75
ND1 B:HIS45 2.0 25.3 1.0
NE2 B:HIS13 2.1 29.1 1.0
O1B A:CDP1158 2.2 30.1 0.5
OD1 B:ASP11 2.4 18.8 1.0
O2B A:CDP1158 2.4 20.3 0.5
OD2 B:ASP11 2.5 26.4 1.0
CG B:ASP11 2.8 19.4 1.0
CE1 B:HIS45 2.9 24.9 1.0
CD2 B:HIS13 3.0 23.9 1.0
CG B:HIS45 3.1 22.7 1.0
CE1 B:HIS13 3.2 27.4 1.0
CB B:HIS45 3.5 16.3 1.0
PB A:CDP1158 3.6 16.3 0.5
PB A:CDP1158 3.6 25.3 0.5
O3B A:CDP1158 3.9 14.5 0.5
O1B A:CDP1158 4.0 9.2 0.5
NE2 B:HIS45 4.1 22.0 1.0
O2B A:CDP1158 4.1 25.8 0.5
CD2 B:HIS45 4.2 22.9 1.0
CG B:HIS13 4.2 24.8 1.0
CB B:ASP11 4.2 17.2 1.0
O3A A:CDP1158 4.2 27.8 0.5
ND1 B:HIS13 4.2 27.4 1.0
O1A A:CDP1158 4.5 19.3 0.5
CD1 B:LEU60 4.6 28.1 1.0
O3B A:CDP1158 4.7 29.2 0.5
O A:HOH2077 4.9 27.8 1.0

Reference:

L.Buetow, A.C.Brown, T.Parish, W.N.Hunter. The Structure of Mycobacteria 2C-Methyl-D- Erythritol-2,4-Cyclodiphosphate Synthase, An Essential Enzyme, Provides A Platform For Drug Discovery. Bmc Struct.Biol. V. 7 68 2007.
ISSN: ISSN 1472-6807
PubMed: 17956607
DOI: 10.1186/1472-6807-7-68
Page generated: Sat Sep 26 03:58:51 2020
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