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Iron 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:

Chlorine (Cl) 4 atoms
Zinc (Zn) 4 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 4 binding sites of Iron 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 Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2vun

Go back to Iron Binding Sites List in 2vun
Iron 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 Iron with other atoms in the Fe 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:Fe402

b:25.3
occ:1.00
 ND1 A:HIS193 1.9 23.7 1.0
NE2 A:HIS220 1.9 18.8 1.0
OE1 A:GLU164 2.1 21.8 1.0
O A:HOH2205 2.2 30.1 1.0
O A:HOH2362 2.2 31.3 1.0
O A:HOH2222 2.4 28.3 1.0
CE1 A:HIS193 2.6 24.0 1.0
CD2 A:HIS220 2.8 17.1 1.0
CE1 A:HIS220 3.0 18.2 1.0
CD A:GLU164 3.1 19.5 1.0
CG A:HIS193 3.1 22.4 1.0
OE2 A:GLU164 3.3 21.4 1.0
ZN A:ZN401 3.6 26.9 1.0
CB A:HIS193 3.8 20.6 1.0
NE2 A:HIS193 3.8 24.0 1.0
CL A:CL501 3.8 51.0 1.0
CG A:HIS220 4.0 17.1 1.0
ND1 A:HIS220 4.0 17.2 1.0
CD2 A:HIS193 4.1 23.2 1.0
CA A:HIS193 4.3 20.2 1.0
CG A:GLU164 4.4 19.0 1.0
CE1 A:HIS67 4.6 15.6 1.0
OD2 A:ASP276 4.7 18.8 1.0
NE2 A:HIS67 4.7 16.7 1.0
O A:GLY224 4.7 17.3 1.0
CA A:GLY224 4.9 16.7 1.0
CB A:GLU164 5.0 18.9 1.0

Iron binding site 2 out of 4 in 2vun

Go back to Iron Binding Sites List in 2vun
Iron 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 Iron with other atoms in the Fe 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:Fe402

b:31.4
occ:1.00
 ND1 B:HIS193 1.9 29.8 1.0
NE2 B:HIS220 1.9 24.2 1.0
O B:HOH2173 2.0 36.8 1.0
OE1 B:GLU164 2.1 29.1 1.0
O B:HOH2314 2.2 34.0 1.0
O B:HOH2188 2.5 39.3 1.0
CE1 B:HIS193 2.6 29.8 1.0
CD2 B:HIS220 2.8 21.4 1.0
CE1 B:HIS220 2.9 22.5 1.0
CD B:GLU164 3.0 26.1 1.0
CG B:HIS193 3.1 29.5 1.0
OE2 B:GLU164 3.3 28.2 1.0
ZN B:ZN401 3.7 31.4 1.0
CB B:HIS193 3.7 28.3 1.0
NE2 B:HIS193 3.8 30.4 1.0
CL B:CL501 3.8 49.9 1.0
CG B:HIS220 4.0 20.8 1.0
ND1 B:HIS220 4.0 21.6 1.0
CD2 B:HIS193 4.1 30.9 1.0
CA B:HIS193 4.3 28.2 1.0
CG B:GLU164 4.4 26.6 1.0
CE1 B:HIS67 4.7 19.8 1.0
O B:GLY224 4.7 18.6 1.0
OD2 B:ASP276 4.7 24.6 1.0
NE2 B:HIS67 4.8 21.9 1.0
OD1 B:ASP276 4.9 24.5 1.0
CB B:GLU164 4.9 26.2 1.0
CA B:GLY224 4.9 18.3 1.0

Iron binding site 3 out of 4 in 2vun

Go back to Iron Binding Sites List in 2vun
Iron 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 Iron with other atoms in the Fe 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:Fe402

b:32.5
occ:1.00
 NE2 C:HIS220 1.9 26.6 1.0
ND1 C:HIS193 1.9 32.5 1.0
OE1 C:GLU164 2.0 30.7 1.0
O C:HOH2177 2.1 37.7 1.0
O C:HOH2312 2.2 34.0 1.0
CE1 C:HIS193 2.6 32.1 1.0
O C:HOH2186 2.6 41.9 1.0
CD2 C:HIS220 2.8 25.2 1.0
CE1 C:HIS220 2.9 26.5 1.0
CD C:GLU164 3.0 27.9 1.0
CG C:HIS193 3.1 31.1 1.0
OE2 C:GLU164 3.3 30.7 1.0
ZN C:ZN401 3.7 33.7 1.0
CL C:CL501 3.7 56.4 1.0
NE2 C:HIS193 3.8 31.9 1.0
CB C:HIS193 3.8 30.3 1.0
ND1 C:HIS220 4.0 25.4 1.0
CG C:HIS220 4.0 24.1 1.0
CD2 C:HIS193 4.0 32.2 1.0
CA C:HIS193 4.3 30.1 1.0
CG C:GLU164 4.4 27.7 1.0
CE1 C:HIS67 4.6 20.2 1.0
OD2 C:ASP276 4.7 25.6 1.0
O C:GLY224 4.8 22.0 1.0
NE2 C:HIS67 4.8 21.8 1.0
CA C:GLY224 4.9 21.9 1.0
OD1 C:ASP276 4.9 26.2 1.0
CB C:GLU164 4.9 26.7 1.0

Iron binding site 4 out of 4 in 2vun

Go back to Iron Binding Sites List in 2vun
Iron 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 Iron with other atoms in the Fe 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:Fe402

b:33.6
occ:1.00
 NE2 D:HIS220 1.9 25.1 1.0
ND1 D:HIS193 1.9 33.3 1.0
O D:HOH2139 2.0 37.0 1.0
OE1 D:GLU164 2.1 31.5 1.0
O D:HOH2246 2.2 30.8 1.0
CE1 D:HIS193 2.5 33.4 1.0
O D:HOH2149 2.6 38.8 1.0
CD2 D:HIS220 2.8 22.9 1.0
CE1 D:HIS220 3.0 24.1 1.0
CD D:GLU164 3.0 28.1 1.0
CG D:HIS193 3.1 32.5 1.0
OE2 D:GLU164 3.3 29.2 1.0
ZN D:ZN401 3.6 33.2 1.0
NE2 D:HIS193 3.8 33.5 1.0
CB D:HIS193 3.8 31.6 1.0
CL D:CL501 3.9 61.6 1.0
CG D:HIS220 4.0 22.4 1.0
ND1 D:HIS220 4.0 22.8 1.0
CD2 D:HIS193 4.1 33.8 1.0
CA D:HIS193 4.3 31.4 1.0
CG D:GLU164 4.4 28.0 1.0
O D:HOH2062 4.6 47.2 1.0
CE1 D:HIS67 4.6 20.3 1.0
OD2 D:ASP276 4.6 23.7 1.0
O D:GLY224 4.7 19.5 1.0
NE2 D:HIS67 4.7 22.2 1.0
OD1 D:ASP276 4.8 25.3 1.0
O D:HOH2150 4.8 47.7 1.0
CA D:GLY224 4.9 19.3 1.0
CB D:GLU164 5.0 27.3 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: Sun Aug 4 03:06:27 2024

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