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Zinc in PDB 2eg8: The Crystal Structure of E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid

Enzymatic activity of The Crystal Structure of E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid

All present enzymatic activity of The Crystal Structure of E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid:
3.5.2.3;

Protein crystallography data

The structure of The Crystal Structure of E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid, PDB code: 2eg8 was solved by M.Lee, M.J.Maher, J.M.Guss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.515, 79.708, 180.611, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 22.7

Other elements in 2eg8:

The structure of The Crystal Structure of E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid (pdb code 2eg8). 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 E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid, PDB code: 2eg8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2eg8

Go back to Zinc Binding Sites List in 2eg8
Zinc binding site 1 out of 4 in the The Crystal Structure of E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid


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 E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:49.6
occ:1.00
 OQ1 A:KCX102 2.0 39.8 1.0
NE2 A:HIS177 2.1 42.1 1.0
ND1 A:HIS139 2.1 48.9 1.0
O A:HOH559 2.2 35.3 1.0
O6 A:FOT410 2.6 62.0 1.0
CX A:KCX102 2.9 43.4 1.0
CE1 A:HIS139 3.0 47.1 1.0
CD2 A:HIS177 3.1 47.6 1.0
CE1 A:HIS177 3.1 45.4 1.0
CG A:HIS139 3.2 44.0 1.0
OQ2 A:KCX102 3.3 43.5 1.0
ZN A:ZN401 3.5 46.6 1.0
C6 A:FOT410 3.5 71.2 1.0
CB A:HIS139 3.6 46.8 1.0
NE2 A:HIS139 4.1 44.7 1.0
NZ A:KCX102 4.1 46.5 1.0
CE1 A:HIS16 4.1 40.0 1.0
N1 A:FOT410 4.2 63.0 1.0
CD2 A:HIS139 4.2 43.2 1.0
ND1 A:HIS177 4.2 45.2 1.0
CG A:HIS177 4.2 38.5 1.0
NE2 A:HIS16 4.2 39.2 1.0
CE2 A:TYR104 4.3 45.4 1.0
O A:LEU222 4.3 58.8 1.0
C5 A:FOT410 4.5 66.8 1.0
CA A:HIS139 4.5 44.0 1.0
OD2 A:ASP250 4.5 48.5 1.0
F5 A:FOT410 4.6 58.0 1.0
CE A:KCX102 4.6 40.5 1.0
OD1 A:ASP250 4.7 47.3 1.0
CD2 A:TYR104 4.8 46.7 1.0
CG A:ASP250 4.9 52.0 1.0

Zinc binding site 2 out of 4 in 2eg8

Go back to Zinc Binding Sites List in 2eg8
Zinc binding site 2 out of 4 in the The Crystal Structure of E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid


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 E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:46.6
occ:1.00
 O A:HOH559 2.0 35.3 1.0
NE2 A:HIS18 2.1 41.0 1.0
OD1 A:ASP250 2.1 47.3 1.0
NE2 A:HIS16 2.2 39.2 1.0
OQ2 A:KCX102 2.3 43.5 1.0
CE1 A:HIS18 3.0 50.9 1.0
CX A:KCX102 3.1 43.4 1.0
CD2 A:HIS16 3.1 47.0 1.0
CD2 A:HIS18 3.1 40.1 1.0
CG A:ASP250 3.1 52.0 1.0
CE1 A:HIS16 3.2 40.0 1.0
OQ1 A:KCX102 3.4 39.8 1.0
ZN A:ZN400 3.5 49.6 1.0
OD2 A:ASP250 3.6 48.5 1.0
NZ A:KCX102 4.1 46.5 1.0
ND1 A:HIS18 4.2 39.3 1.0
CG A:HIS18 4.2 41.4 1.0
O6 A:FOT410 4.2 62.0 1.0
C5 A:FOT410 4.2 66.8 1.0
C6 A:FOT410 4.2 71.2 1.0
CG A:HIS16 4.2 46.8 1.0
F5 A:FOT410 4.3 58.0 1.0
ND1 A:HIS16 4.3 40.9 1.0
CB A:ASP250 4.3 42.8 1.0
CD2 A:HIS177 4.3 47.6 1.0
CG A:MET42 4.4 34.4 1.0
NE2 A:HIS177 4.5 42.1 1.0
OH A:TYR104 4.6 45.6 1.0
CA A:ASP250 4.7 44.1 1.0
N1 A:FOT410 4.8 63.0 1.0
C4 A:FOT410 4.9 57.5 1.0
CB A:MET42 5.0 35.5 1.0

Zinc binding site 3 out of 4 in 2eg8

Go back to Zinc Binding Sites List in 2eg8
Zinc binding site 3 out of 4 in the The Crystal Structure of E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid


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 E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:50.7
occ:1.00
 OQ1 B:KCX102 1.9 42.4 1.0
O B:HOH539 2.0 46.4 1.0
NE2 B:HIS177 2.0 40.2 1.0
ND1 B:HIS139 2.2 40.2 1.0
O6 B:FOT410 2.5 69.9 0.8
CD2 B:HIS177 3.0 32.4 1.0
CX B:KCX102 3.0 40.6 1.0
CE1 B:HIS177 3.1 33.7 1.0
CE1 B:HIS139 3.1 55.6 1.0
CG B:HIS139 3.3 51.0 1.0
OQ2 B:KCX102 3.4 41.2 1.0
C6 B:FOT410 3.4 66.5 0.8
ZN B:ZN401 3.5 49.5 1.0
CB B:HIS139 3.7 46.7 1.0
CE1 B:HIS16 4.1 48.1 1.0
NZ B:KCX102 4.1 40.4 1.0
N1 B:FOT410 4.1 58.6 0.8
CG B:HIS177 4.1 39.1 1.0
ND1 B:HIS177 4.2 38.8 1.0
NE2 B:HIS16 4.2 47.8 1.0
NE2 B:HIS139 4.2 45.4 1.0
C5 B:FOT410 4.3 67.0 0.8
CD2 B:HIS139 4.3 34.4 1.0
F5 B:FOT410 4.4 55.8 0.8
CE2 B:TYR104 4.4 49.3 1.0
OD2 B:ASP250 4.5 44.7 1.0
CA B:HIS139 4.5 45.8 1.0
O B:LEU222 4.5 55.5 1.0
CE B:KCX102 4.6 32.6 1.0
O B:HOH541 4.8 54.3 1.0
OD1 B:ASP250 4.8 43.5 1.0
CD2 B:TYR104 4.9 49.9 1.0
CG B:ASP250 5.0 40.3 1.0
CD B:PRO223 5.0 55.4 1.0

Zinc binding site 4 out of 4 in 2eg8

Go back to Zinc Binding Sites List in 2eg8
Zinc binding site 4 out of 4 in the The Crystal Structure of E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid


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 E. Coli Dihydroorotase Complexed with 5- Fluoroorotic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:49.5
occ:1.00
 NE2 B:HIS18 2.0 42.5 1.0
O B:HOH539 2.0 46.4 1.0
OD1 B:ASP250 2.2 43.5 1.0
NE2 B:HIS16 2.2 47.8 1.0
OQ2 B:KCX102 2.2 41.2 1.0
CD2 B:HIS18 2.9 35.0 1.0
CE1 B:HIS18 3.1 38.8 1.0
CD2 B:HIS16 3.1 53.1 1.0
CX B:KCX102 3.1 40.6 1.0
CG B:ASP250 3.1 40.3 1.0
CE1 B:HIS16 3.2 48.1 1.0
OQ1 B:KCX102 3.4 42.4 1.0
ZN B:ZN400 3.5 50.7 1.0
OD2 B:ASP250 3.6 44.7 1.0
CG B:HIS18 4.1 42.3 1.0
F5 B:FOT410 4.1 55.8 0.8
C5 B:FOT410 4.1 67.0 0.8
ND1 B:HIS18 4.1 47.9 1.0
NZ B:KCX102 4.2 40.4 1.0
C6 B:FOT410 4.2 66.5 0.8
O6 B:FOT410 4.2 69.9 0.8
CG B:HIS16 4.3 48.5 1.0
CD2 B:HIS177 4.3 32.4 1.0
ND1 B:HIS16 4.3 44.3 1.0
CB B:ASP250 4.3 34.9 1.0
CG B:MET42 4.4 34.9 1.0
NE2 B:HIS177 4.5 40.2 1.0
OH B:TYR104 4.6 41.9 1.0
CA B:ASP250 4.7 36.1 1.0
C4 B:FOT410 4.8 52.7 0.8
N1 B:FOT410 4.8 58.6 0.8

Reference:

M.Lee, C.W.Chan, S.C.Graham, R.I.Christopherson, J.M.Guss, M.J.Maher. Structures of Ligand-Free and Inhibitor Complexes of Dihydroorotase From Escherichia Coli: Implications For Loop Movement in Inhibitor Design J.Mol.Biol. V. 370 812 2007.
ISSN: ISSN 0022-2836
PubMed: 17550785
DOI: 10.1016/J.JMB.2007.05.019
Page generated: Wed Oct 16 23:07:25 2024

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