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Zinc in PDB 2vun: The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily

Enzymatic activity of The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily

All present enzymatic activity of The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily:
3.5.2.18;

Protein crystallography data

The structure of The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily, PDB code: 2vun was solved by D.Kress, A.Alhapel, A.J.Pierik, L.-O.Essen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 107.83 / 1.89
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 146.352, 159.824, 161.683, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 19.8

Other elements in 2vun:

The structure of The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily (pdb code 2vun). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily, PDB code: 2vun:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2vun

Go back to Zinc Binding Sites List in 2vun
Zinc binding site 1 out of 4 in the The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:26.9
occ:1.00
 OE2 A:GLU164 2.0 21.4 1.0
NE2 A:HIS69 2.1 20.0 1.0
NE2 A:HIS67 2.1 16.7 1.0
O A:HOH2362 2.1 31.3 1.0
OD1 A:ASP276 2.5 19.0 1.0
CE1 A:HIS69 2.9 19.4 1.0
CE1 A:HIS67 3.0 15.6 1.0
CD A:GLU164 3.0 19.5 1.0
CD2 A:HIS67 3.1 14.4 1.0
CL A:CL501 3.2 51.0 1.0
CD2 A:HIS69 3.2 18.3 1.0
CG A:ASP276 3.3 18.6 1.0
OE1 A:GLU164 3.5 21.8 1.0
FE A:FE402 3.6 25.3 1.0
OD2 A:ASP276 3.7 18.8 1.0
O A:HOH2205 3.9 30.1 1.0
ND1 A:HIS69 4.1 18.2 1.0
ND1 A:HIS67 4.1 14.4 1.0
CG A:HIS67 4.2 15.1 1.0
CG A:HIS69 4.3 16.4 1.0
CD2 A:HIS220 4.3 17.1 1.0
CG A:GLU164 4.3 19.0 1.0
CB A:ASP276 4.3 16.3 1.0
NE2 A:HIS220 4.5 18.8 1.0
CB A:ALA99 4.6 14.6 1.0
O A:HOH2222 4.7 28.3 1.0
CA A:ASP276 4.7 16.4 1.0
O A:HOH2275 4.8 48.3 1.0

Zinc binding site 2 out of 4 in 2vun

Go back to Zinc Binding Sites List in 2vun
Zinc binding site 2 out of 4 in the The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:31.4
occ:1.00
 OE2 B:GLU164 2.0 28.2 1.0
O B:HOH2314 2.0 34.0 1.0
OD1 B:ASP276 2.0 24.5 1.0
NE2 B:HIS67 2.1 21.9 1.0
NE2 B:HIS69 2.1 24.2 1.0
CE1 B:HIS69 2.9 22.3 1.0
CE1 B:HIS67 3.0 19.8 1.0
CD B:GLU164 3.0 26.1 1.0
CG B:ASP276 3.1 21.6 1.0
CD2 B:HIS67 3.1 19.7 1.0
CD2 B:HIS69 3.2 22.7 1.0
CL B:CL501 3.3 49.9 1.0
OE1 B:GLU164 3.5 29.1 1.0
OD2 B:ASP276 3.6 24.6 1.0
FE B:FE402 3.7 31.4 1.0
O B:HOH2173 3.9 36.8 1.0
O B:HOH2227 4.1 51.7 1.0
ND1 B:HIS69 4.1 22.0 1.0
ND1 B:HIS67 4.1 19.7 1.0
CD2 B:HIS220 4.2 21.4 1.0
CG B:HIS67 4.2 18.2 1.0
CB B:ASP276 4.2 19.5 1.0
CG B:HIS69 4.3 20.7 1.0
CG B:GLU164 4.3 26.6 1.0
NE2 B:HIS220 4.5 24.2 1.0
CB B:ALA99 4.6 18.9 1.0
O B:HOH2188 4.6 39.3 1.0
CA B:ASP276 4.7 19.2 1.0

Zinc binding site 3 out of 4 in 2vun

Go back to Zinc Binding Sites List in 2vun
Zinc binding site 3 out of 4 in the The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:33.7
occ:1.00
 OE2 C:GLU164 2.0 30.7 1.0
OD1 C:ASP276 2.0 26.2 1.0
NE2 C:HIS67 2.1 21.8 1.0
O C:HOH2312 2.1 34.0 1.0
NE2 C:HIS69 2.1 25.3 1.0
CE1 C:HIS69 3.0 23.2 1.0
CE1 C:HIS67 3.0 20.2 1.0
CG C:ASP276 3.0 23.2 1.0
CD C:GLU164 3.1 27.9 1.0
CD2 C:HIS67 3.1 19.4 1.0
CD2 C:HIS69 3.2 22.5 1.0
CL C:CL501 3.4 56.4 1.0
OE1 C:GLU164 3.6 30.7 1.0
OD2 C:ASP276 3.6 25.6 1.0
FE C:FE402 3.7 32.5 1.0
O C:HOH2177 3.9 37.7 1.0
O C:HOH2215 4.1 50.9 1.0
ND1 C:HIS67 4.1 19.2 1.0
ND1 C:HIS69 4.1 22.6 1.0
CB C:ASP276 4.2 21.2 1.0
CD2 C:HIS220 4.2 25.2 1.0
CG C:HIS67 4.2 17.6 1.0
CG C:HIS69 4.3 21.1 1.0
CG C:GLU164 4.3 27.7 1.0
NE2 C:HIS220 4.5 26.6 1.0
CA C:ASP276 4.6 20.9 1.0
CB C:ALA99 4.6 18.8 1.0
O C:HOH2186 4.7 41.9 1.0

Zinc binding site 4 out of 4 in 2vun

Go back to Zinc Binding Sites List in 2vun
Zinc binding site 4 out of 4 in the The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Enamidase at 1.9 A Resolution - A New Member of the Amidohydrolase Superfamily within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:33.2
occ:1.00
 OE2 D:GLU164 2.0 29.2 1.0
OD1 D:ASP276 2.0 25.3 1.0
O D:HOH2246 2.1 30.8 1.0
NE2 D:HIS67 2.1 22.2 1.0
NE2 D:HIS69 2.1 25.8 1.0
CE1 D:HIS69 2.9 24.6 1.0
CE1 D:HIS67 3.0 20.3 1.0
CG D:ASP276 3.0 22.4 1.0
CD D:GLU164 3.1 28.1 1.0
CD2 D:HIS67 3.1 19.7 1.0
CD2 D:HIS69 3.2 24.5 1.0
CL D:CL501 3.2 61.6 1.0
OE1 D:GLU164 3.5 31.5 1.0
OD2 D:ASP276 3.6 23.7 1.0
FE D:FE402 3.6 33.6 1.0
O D:HOH2139 3.7 37.0 1.0
ND1 D:HIS69 4.1 23.2 1.0
ND1 D:HIS67 4.1 19.7 1.0
CB D:ASP276 4.2 21.1 1.0
CG D:HIS67 4.2 19.2 1.0
CG D:HIS69 4.2 22.1 1.0
CD2 D:HIS220 4.3 22.9 1.0
CG D:GLU164 4.3 28.0 1.0
O D:HOH2149 4.6 38.8 1.0
CA D:ASP276 4.6 20.7 1.0
NE2 D:HIS220 4.6 25.1 1.0
CB D:ALA99 4.6 19.4 1.0
O D:HOH2150 4.6 47.7 1.0

Reference:

D.Kress, A.Alhapel, A.J.Pierik, L.-O.Essen. The Crystal Structure of Enamidase: A Bifunctional Enzyme of the Nicotinate Catabolism. J.Mol.Biol. V. 384 837 2008.
ISSN: ISSN 0022-2836
PubMed: 18805424
DOI: 10.1016/J.JMB.2008.09.002
Page generated: Thu Oct 17 04:34:12 2024

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