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Zinc in PDB 2z2a: THR109GLY Dihydroorotase From E. Coli

Enzymatic activity of THR109GLY Dihydroorotase From E. Coli

All present enzymatic activity of THR109GLY Dihydroorotase From E. Coli:
3.5.2.3;

Protein crystallography data

The structure of THR109GLY Dihydroorotase From E. Coli, PDB code: 2z2a 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 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.435, 78.193, 179.961, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 19.6

Zinc Binding Sites:

The binding sites of Zinc atom in the THR109GLY Dihydroorotase From E. Coli (pdb code 2z2a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the THR109GLY Dihydroorotase From E. Coli, PDB code: 2z2a:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2z2a

Go back to Zinc Binding Sites List in 2z2a
Zinc binding site 1 out of 4 in the THR109GLY Dihydroorotase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of THR109GLY Dihydroorotase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:22.5
occ:1.00
OD1 A:ASP250 2.0 30.0 1.0
O A:HOH1411 2.1 22.0 1.0
NE2 A:HIS18 2.1 32.9 1.0
NE2 A:HIS16 2.1 29.6 1.0
OQ1 A:KCX102 2.1 31.3 1.0
CX A:KCX102 3.0 31.8 1.0
CG A:ASP250 3.0 31.2 1.0
CD2 A:HIS18 3.1 30.0 1.0
CD2 A:HIS16 3.1 28.8 1.0
CE1 A:HIS16 3.1 32.8 1.0
CE1 A:HIS18 3.1 33.5 1.0
OQ2 A:KCX102 3.4 31.6 1.0
OD2 A:ASP250 3.5 32.6 1.0
ZN A:ZN401 3.5 24.5 1.0
NZ A:KCX102 4.1 29.1 1.0
ND1 A:HIS18 4.2 28.4 1.0
ND1 A:HIS16 4.2 29.2 1.0
CG A:HIS18 4.2 28.6 1.0
CG A:HIS16 4.2 31.3 1.0
CB A:ASP250 4.3 32.0 1.0
CD2 A:HIS177 4.3 31.6 1.0
C6 A:DOR1410 4.3 21.1 1.0
C4 A:DOR1410 4.3 52.6 1.0
C5 A:DOR1410 4.4 22.6 1.0
CG A:MET42 4.4 28.5 1.0
NE2 A:HIS177 4.4 31.3 1.0
O4 A:DOR1410 4.5 33.1 1.0
CA A:ASP250 4.7 29.4 1.0
OH A:TYR104 4.7 31.5 1.0
N3 A:DOR1410 4.7 30.9 1.0

Zinc binding site 2 out of 4 in 2z2a

Go back to Zinc Binding Sites List in 2z2a
Zinc binding site 2 out of 4 in the THR109GLY Dihydroorotase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of THR109GLY Dihydroorotase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:24.5
occ:1.00
NE2 A:HIS177 2.1 31.3 1.0
OQ2 A:KCX102 2.1 31.6 1.0
O A:HOH1411 2.2 22.0 1.0
ND1 A:HIS139 2.2 29.3 1.0
O4 A:DOR1410 2.8 33.1 1.0
CE1 A:HIS139 3.0 32.0 1.0
CX A:KCX102 3.0 31.8 1.0
CE1 A:HIS177 3.0 28.2 1.0
CD2 A:HIS177 3.0 31.6 1.0
CG A:HIS139 3.2 31.7 1.0
OQ1 A:KCX102 3.3 31.3 1.0
ZN A:ZN400 3.5 22.5 1.0
C4 A:DOR1410 3.6 52.6 1.0
CB A:HIS139 3.6 32.7 1.0
CE1 A:HIS16 4.1 32.8 1.0
ND1 A:HIS177 4.1 29.6 1.0
NE2 A:HIS139 4.2 30.7 1.0
NZ A:KCX102 4.2 29.1 1.0
CG A:HIS177 4.2 32.7 1.0
N3 A:DOR1410 4.2 30.9 1.0
NE2 A:HIS16 4.3 29.6 1.0
CD2 A:HIS139 4.3 31.3 1.0
CE2 A:TYR104 4.4 29.5 1.0
OD2 A:ASP250 4.4 32.6 1.0
O A:LEU222 4.5 33.7 1.0
C5 A:DOR1410 4.6 22.6 1.0
CA A:HIS139 4.6 28.2 1.0
CE A:KCX102 4.6 33.6 1.0
O A:HOH1680 4.6 45.8 1.0
OD1 A:ASP250 4.7 30.0 1.0
CD2 A:TYR104 4.9 34.5 1.0
CG A:ASP250 4.9 31.2 1.0

Zinc binding site 3 out of 4 in 2z2a

Go back to Zinc Binding Sites List in 2z2a
Zinc binding site 3 out of 4 in the THR109GLY Dihydroorotase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of THR109GLY Dihydroorotase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn400

b:26.1
occ:1.00
NE2 B:HIS18 2.0 28.4 1.0
O B:HOH2411 2.1 14.4 0.5
NE2 B:HIS16 2.1 35.3 1.0
OD1 B:ASP250 2.1 33.3 1.0
OQ1 B:KCX102 2.1 29.6 1.0
O4 B:NCD2410 2.1 38.0 0.5
CD2 B:HIS18 3.0 28.6 1.0
CG B:ASP250 3.0 32.7 1.0
CE1 B:HIS18 3.0 34.4 1.0
CX B:KCX102 3.1 33.9 1.0
CD2 B:HIS16 3.1 31.5 1.0
CE1 B:HIS16 3.1 30.7 1.0
C4 B:NCD2410 3.2 39.0 0.5
OD2 B:ASP250 3.4 34.8 1.0
OQ2 B:KCX102 3.5 31.2 1.0
ZN B:ZN401 3.6 27.7 1.0
C5 B:NCD2410 3.9 32.8 0.5
NZ B:KCX102 4.1 30.9 1.0
O5 B:NCD2410 4.1 24.6 0.5
ND1 B:HIS18 4.1 32.8 1.0
CG B:HIS18 4.1 27.1 1.0
ND1 B:HIS16 4.2 30.4 1.0
CD2 B:HIS177 4.2 32.7 1.0
CG B:HIS16 4.2 28.6 1.0
CB B:ASP250 4.2 29.1 1.0
C6 B:DOR1411 4.3 24.0 0.5
C6 B:NCD2410 4.3 30.3 0.5
C5 B:DOR1411 4.3 23.7 0.5
CG B:MET42 4.4 29.6 1.0
NE2 B:HIS177 4.4 28.0 1.0
C4 B:DOR1411 4.5 23.2 0.5
N3 B:NCD2410 4.6 32.3 0.5
OH B:TYR104 4.7 33.5 1.0
CA B:ASP250 4.7 29.6 1.0
N3 B:DOR1411 4.7 22.9 0.5

Zinc binding site 4 out of 4 in 2z2a

Go back to Zinc Binding Sites List in 2z2a
Zinc binding site 4 out of 4 in the THR109GLY Dihydroorotase From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of THR109GLY Dihydroorotase From E. Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:27.7
occ:1.00
OQ2 B:KCX102 2.0 31.2 1.0
NE2 B:HIS177 2.0 28.0 1.0
ND1 B:HIS139 2.1 31.4 1.0
O B:HOH2411 2.3 14.4 0.5
O5 B:NCD2410 2.4 24.6 0.5
O4 B:NCD2410 2.5 38.0 0.5
C4 B:NCD2410 2.8 39.0 0.5
CX B:KCX102 3.0 33.9 1.0
CE1 B:HIS139 3.0 29.9 1.0
CE1 B:HIS177 3.0 30.5 1.0
CD2 B:HIS177 3.0 32.7 1.0
CG B:HIS139 3.2 29.9 1.0
OQ1 B:KCX102 3.3 29.6 1.0
O4 B:DOR1411 3.4 42.9 0.5
ZN B:ZN400 3.6 26.1 1.0
CB B:HIS139 3.6 30.9 1.0
C4 B:DOR1411 3.8 23.2 0.5
NE2 B:HIS139 4.1 29.9 1.0
NZ B:KCX102 4.1 30.9 1.0
ND1 B:HIS177 4.1 30.6 1.0
CG B:HIS177 4.2 30.4 1.0
CE1 B:HIS16 4.2 30.7 1.0
N3 B:DOR1411 4.2 22.9 0.5
CD2 B:HIS139 4.2 34.1 1.0
C5 B:NCD2410 4.3 32.8 0.5
NE2 B:HIS16 4.4 35.3 1.0
CE2 B:TYR104 4.4 33.1 1.0
OD2 B:ASP250 4.4 34.8 1.0
C5 B:DOR1411 4.5 23.7 0.5
CA B:HIS139 4.5 28.4 1.0
CE B:KCX102 4.6 31.9 1.0
O B:LEU222 4.6 34.8 1.0
N3 B:NCD2410 4.8 32.3 0.5
CD2 B:TYR104 4.9 27.4 1.0
OD1 B:ASP250 5.0 33.3 1.0
CG B:ASP250 5.0 32.7 1.0

Reference:

M.Lee, M.J.Maher, R.I.Christopherson, J.M.Guss. Kinetic and Structural Analysis of Mutant Escherichia Coli Dihydroorotases: A Flexible Loop Stabilizes the Transition State Biochemistry V. 46 10538 2007.
ISSN: ISSN 0006-2960
PubMed: 17711307
DOI: 10.1021/BI701098E
Page generated: Wed Dec 16 04:04:04 2020

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