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Zinc in PDB 4yiw: Dihydroorotase From Bacillus Anthracis with Substrate Bound

Enzymatic activity of Dihydroorotase From Bacillus Anthracis with Substrate Bound

All present enzymatic activity of Dihydroorotase From Bacillus Anthracis with Substrate Bound:
3.5.2.3;

Protein crystallography data

The structure of Dihydroorotase From Bacillus Anthracis with Substrate Bound, PDB code: 4yiw was solved by H.Lei, B.D.Santarsiero, A.J.Rice, H.Lee, M.E.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.72 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.183, 81.676, 104.529, 90.00, 100.29, 90.00
R / Rfree (%) 20.6 / 26.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Dihydroorotase From Bacillus Anthracis with Substrate Bound (pdb code 4yiw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Dihydroorotase From Bacillus Anthracis with Substrate Bound, PDB code: 4yiw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4yiw

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Zinc binding site 1 out of 4 in the Dihydroorotase From Bacillus Anthracis with Substrate Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dihydroorotase From Bacillus Anthracis with Substrate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:43.6
occ:1.00
OD1 A:ASP304 2.3 26.5 1.0
NE2 A:HIS59 2.5 30.7 1.0
OD2 A:ASP151 2.5 40.3 1.0
NE2 A:HIS61 2.6 29.6 1.0
CG A:ASP304 3.2 25.1 1.0
ZN A:ZN502 3.3 48.2 1.0
CD2 A:HIS59 3.3 30.3 1.0
CG A:ASP151 3.4 39.6 1.0
CE1 A:HIS59 3.4 30.6 1.0
CE1 A:HIS61 3.4 28.9 1.0
OD2 A:ASP304 3.5 25.3 1.0
OD1 A:ASP151 3.5 38.1 1.0
CD2 A:HIS61 3.7 29.2 1.0
O5 A:NCD503 3.7 67.2 1.0
C5 A:NCD503 3.7 66.6 1.0
N3 A:NCD503 3.9 64.2 1.0
C6 A:NCD503 4.0 65.7 1.0
C4 A:NCD503 4.1 67.7 1.0
NE2 A:HIS231 4.3 28.0 1.0
ND1 A:HIS59 4.4 30.6 1.0
CG A:HIS59 4.5 30.2 1.0
CD2 A:HIS231 4.5 27.6 1.0
CB A:ASP304 4.5 24.4 1.0
ND1 A:HIS61 4.6 28.5 1.0
CG A:HIS61 4.7 28.4 1.0
CB A:ASP151 4.8 40.0 1.0
C2 A:NCD503 4.9 64.7 1.0
N1 A:NCD503 4.9 65.5 1.0
CG A:MET91 4.9 35.0 1.0
O62 A:NCD503 4.9 62.6 1.0
C61 A:NCD503 5.0 64.2 1.0

Zinc binding site 2 out of 4 in 4yiw

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Zinc binding site 2 out of 4 in the Dihydroorotase From Bacillus Anthracis with Substrate Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dihydroorotase From Bacillus Anthracis with Substrate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:48.2
occ:1.00
OD1 A:ASP151 2.5 38.1 1.0
ND1 A:HIS178 2.5 33.4 1.0
NE2 A:HIS231 2.6 28.0 1.0
O5 A:NCD503 2.7 67.2 1.0
CE1 A:HIS178 3.2 34.3 1.0
ZN A:ZN501 3.3 43.6 1.0
C4 A:NCD503 3.4 67.7 1.0
CG A:HIS178 3.4 32.8 1.0
CE1 A:HIS231 3.4 27.4 1.0
CG A:ASP151 3.5 39.6 1.0
CD2 A:HIS231 3.7 27.6 1.0
OD2 A:ASP151 3.8 40.3 1.0
CB A:HIS178 3.8 31.0 1.0
O4 A:NCD503 4.0 66.8 1.0
N A:GLY152 4.1 43.7 1.0
C5 A:NCD503 4.1 66.6 1.0
NE2 A:HIS178 4.2 34.0 1.0
O A:ASN277 4.3 29.6 1.0
CD2 A:HIS178 4.3 33.8 1.0
CE1 A:HIS59 4.4 30.6 1.0
NE2 A:HIS59 4.5 30.7 1.0
ND1 A:HIS231 4.6 27.8 1.0
N3 A:NCD503 4.6 64.2 1.0
CA A:GLY152 4.7 44.6 1.0
CA A:HIS178 4.8 29.7 1.0
CG A:HIS231 4.8 27.7 1.0
CB A:ASP151 4.8 40.0 1.0
OD2 A:ASP304 4.9 25.3 1.0
C A:ASP151 4.9 40.9 1.0

Zinc binding site 3 out of 4 in 4yiw

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Zinc binding site 3 out of 4 in the Dihydroorotase From Bacillus Anthracis with Substrate Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dihydroorotase From Bacillus Anthracis with Substrate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:41.7
occ:1.00
OD2 B:ASP151 2.4 52.0 1.0
OD1 B:ASP304 2.5 35.6 1.0
NE2 B:HIS61 2.5 40.7 1.0
NE2 B:HIS59 2.6 35.1 1.0
ZN B:ZN502 3.0 51.2 1.0
CG B:ASP304 3.2 34.3 1.0
CG B:ASP151 3.2 51.1 1.0
CE1 B:HIS61 3.3 40.6 1.0
OD1 B:ASP151 3.3 50.4 1.0
OD2 B:ASP304 3.3 33.9 1.0
CD2 B:HIS59 3.5 35.2 1.0
CE1 B:HIS59 3.6 35.5 1.0
O4 B:NCD503 3.6 72.9 1.0
CD2 B:HIS61 3.6 40.3 1.0
C6 B:NCD503 3.9 71.2 1.0
N3 B:NCD503 4.1 73.0 1.0
NE2 B:HIS231 4.2 31.3 1.0
C5 B:NCD503 4.2 70.7 1.0
C4 B:NCD503 4.2 71.0 1.0
ND1 B:HIS61 4.4 40.1 1.0
CB B:ASP304 4.4 33.6 1.0
CD2 B:HIS231 4.4 30.7 1.0
O62 B:NCD503 4.6 66.0 1.0
CG B:HIS61 4.6 39.7 1.0
CB B:ASP151 4.6 50.5 1.0
CG B:HIS59 4.7 35.6 1.0
ND1 B:HIS59 4.7 35.2 1.0
N1 B:NCD503 4.8 73.0 1.0
C61 B:NCD503 4.8 69.9 1.0
C2 B:NCD503 4.8 73.3 1.0
CG B:MET91 4.9 50.1 1.0

Zinc binding site 4 out of 4 in 4yiw

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Zinc binding site 4 out of 4 in the Dihydroorotase From Bacillus Anthracis with Substrate Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dihydroorotase From Bacillus Anthracis with Substrate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:51.2
occ:1.00
OD1 B:ASP151 2.4 50.4 1.0
O4 B:NCD503 2.5 72.9 1.0
ND1 B:HIS178 2.6 32.7 1.0
NE2 B:HIS231 2.6 31.3 1.0
ZN B:ZN501 3.0 41.7 1.0
C4 B:NCD503 3.2 71.0 1.0
CE1 B:HIS178 3.2 33.6 1.0
CE1 B:HIS231 3.3 30.4 1.0
CG B:ASP151 3.4 51.1 1.0
CG B:HIS178 3.6 33.0 1.0
OD2 B:ASP151 3.6 52.0 1.0
O5 B:NCD503 3.7 71.2 1.0
CD2 B:HIS231 3.8 30.7 1.0
N B:GLY152 4.0 51.5 1.0
CB B:HIS178 4.1 32.4 1.0
C5 B:NCD503 4.2 70.7 1.0
NE2 B:HIS59 4.3 35.1 1.0
NE2 B:HIS178 4.3 33.2 1.0
CE1 B:HIS59 4.4 35.5 1.0
OD2 B:ASP304 4.5 33.9 1.0
O B:ASN277 4.5 34.2 1.0
CD2 B:HIS178 4.5 33.2 1.0
ND1 B:HIS231 4.6 30.6 1.0
CB B:ASP151 4.7 50.5 1.0
C6 B:NCD503 4.7 71.2 1.0
CA B:GLY152 4.7 51.8 1.0
CG B:HIS231 4.8 30.4 1.0
C B:ASP151 4.8 50.4 1.0
CA B:ASP151 4.9 50.1 1.0
OD1 B:ASP304 5.0 35.6 1.0
CA B:HIS178 5.0 32.1 1.0

Reference:

A.J.Rice, H.Lei, B.D.Santarsiero, H.Lee, M.E.Johnson. Ca-Asp Bound X-Ray Structure and Inhibition of Bacillus Anthracis Dihydroorotase (Dhoase). Bioorg.Med.Chem. V. 24 4536 2016.
ISSN: ESSN 1464-3391
PubMed: 27499369
DOI: 10.1016/J.BMC.2016.07.055
Page generated: Wed Dec 16 05:57:25 2020

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