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Zinc in PDB 7ca0: Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae

Enzymatic activity of Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae

All present enzymatic activity of Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae:
3.5.2.3;

Protein crystallography data

The structure of Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae, PDB code: 7ca0 was solved by H.H.Guan, Y.H.Huang, C.Y.Huang, C.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.57 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.471, 88.587, 103.572, 90, 95.28, 90
R / Rfree (%) 21 / 26.7

Other elements in 7ca0:

The structure of Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae (pdb code 7ca0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae, PDB code: 7ca0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7ca0

Go back to Zinc Binding Sites List in 7ca0
Zinc binding site 1 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:63.2
occ:1.00
 OD1 A:ASP258 2.0 53.6 1.0
O41 A:FOT501 2.0 59.8 0.7
NE2 A:HIS16 2.1 53.2 1.0
NE2 A:HIS14 2.1 51.2 1.0
OQ1 A:KCX98 2.2 56.2 1.0
CD2 A:HIS14 2.8 47.0 1.0
C41 A:FOT501 3.0 56.8 0.7
CD2 A:HIS16 3.0 53.3 1.0
CE1 A:HIS16 3.1 52.6 1.0
CG A:ASP258 3.1 57.3 1.0
CX A:KCX98 3.1 52.9 1.0
CE1 A:HIS14 3.2 48.0 1.0
C4 A:FOT501 3.3 54.6 0.7
OQ2 A:KCX98 3.4 53.0 1.0
OD2 A:ASP258 3.7 54.6 1.0
N3 A:FOT501 3.8 59.5 0.7
ZN A:ZN503 3.8 63.1 1.0
CG A:HIS14 4.0 50.6 1.0
C5 A:FOT501 4.0 59.1 0.7
ND1 A:HIS16 4.1 52.5 1.0
CB A:ASP258 4.1 50.5 1.0
CG A:HIS16 4.2 52.1 1.0
ND1 A:HIS14 4.2 46.5 1.0
O42 A:FOT501 4.2 63.1 0.7
NZ A:KCX98 4.2 52.8 1.0
F5 A:FOT501 4.4 68.5 0.7
CA A:ASP258 4.4 51.5 1.0
CD2 A:HIS180 4.4 52.5 1.0
CG A:MET41 4.5 52.3 1.0
OH A:TYR100 4.6 52.4 1.0
NE2 A:HIS180 4.6 58.2 1.0
C2 A:FOT501 4.8 53.3 0.7
O A:ASP258 4.9 54.4 1.0
C6 A:FOT501 5.0 57.8 0.7
C A:ASP258 5.0 56.1 1.0

Zinc binding site 2 out of 8 in 7ca0

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Zinc binding site 2 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:63.1
occ:1.00
 OQ2 A:KCX98 2.0 53.0 1.0
O41 A:FOT501 2.0 59.8 0.7
ND1 A:HIS137 2.1 59.3 1.0
NE2 A:HIS180 2.1 58.2 1.0
O42 A:FOT501 2.2 63.1 0.7
C41 A:FOT501 2.4 56.8 0.7
CE1 A:HIS137 2.7 52.2 1.0
CD2 A:HIS180 3.0 52.5 1.0
CX A:KCX98 3.0 52.9 1.0
CE1 A:HIS180 3.1 51.2 1.0
CG A:HIS137 3.3 54.3 1.0
OQ1 A:KCX98 3.4 56.2 1.0
ZN A:ZN502 3.8 63.2 1.0
CB A:HIS137 3.9 46.0 1.0
NE2 A:HIS137 3.9 53.1 1.0
C4 A:FOT501 3.9 54.6 0.7
O A:LYS230 4.1 53.0 1.0
ND1 A:HIS180 4.1 54.6 1.0
CG A:HIS180 4.1 51.9 1.0
CE1 A:HIS14 4.2 48.0 1.0
NZ A:KCX98 4.2 52.8 1.0
CD2 A:HIS137 4.2 54.9 1.0
NE2 A:HIS14 4.3 51.2 1.0
F5 A:FOT501 4.5 68.5 0.7
OD2 A:ASP258 4.5 54.6 1.0
CE A:KCX98 4.5 48.1 1.0
CE1 A:TYR100 4.6 51.7 1.0
CA A:HIS137 4.7 52.6 1.0
C5 A:FOT501 4.7 59.1 0.7
OD1 A:ASP258 4.7 53.6 1.0
CG2 A:THR105 4.8 53.8 1.0
CG A:ASP258 4.9 57.3 1.0
OG1 A:THR105 4.9 53.7 1.0
N3 A:FOT501 4.9 59.5 0.7
C A:LYS230 5.0 45.7 1.0

Zinc binding site 3 out of 8 in 7ca0

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Zinc binding site 3 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:61.5
occ:1.00
 OQ2 C:KCX98 2.0 53.4 1.0
NE2 C:HIS180 2.1 45.0 1.0
ND1 C:HIS137 2.1 53.9 1.0
O42 C:FOT401 2.3 46.6 0.8
O41 C:FOT401 2.4 49.7 0.8
CE1 C:HIS137 2.7 48.7 1.0
C41 C:FOT401 2.7 48.9 0.8
CD2 C:HIS180 3.0 42.3 1.0
CE1 C:HIS180 3.1 47.1 1.0
CX C:KCX98 3.1 56.1 1.0
CG C:HIS137 3.3 50.5 1.0
ZN C:ZN403 3.6 54.3 1.0
OQ1 C:KCX98 3.6 51.3 1.0
NE2 C:HIS137 3.9 52.0 1.0
CB C:HIS137 4.0 41.8 1.0
O C:LYS230 4.0 45.5 1.0
CE1 C:HIS14 4.1 47.1 1.0
C4 C:FOT401 4.1 47.3 0.8
CG C:HIS180 4.2 40.6 1.0
ND1 C:HIS180 4.2 47.4 1.0
NZ C:KCX98 4.2 55.8 1.0
NE2 C:HIS14 4.2 47.2 1.0
CD2 C:HIS137 4.2 42.6 1.0
OD2 C:ASP258 4.2 46.9 1.0
CE C:KCX98 4.5 44.9 1.0
CE1 C:TYR100 4.6 56.2 1.0
OD1 C:ASP258 4.6 48.2 1.0
CG C:ASP258 4.7 43.8 1.0
CG2 C:THR105 4.7 51.6 1.0
CA C:HIS137 4.7 44.8 1.0
N3 C:FOT401 4.8 55.9 0.8
OG1 C:THR105 4.9 60.4 1.0
C C:LYS230 4.9 43.6 1.0

Zinc binding site 4 out of 8 in 7ca0

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Zinc binding site 4 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:54.3
occ:1.00
 OD1 C:ASP258 2.0 48.2 1.0
NE2 C:HIS16 2.0 44.1 1.0
O42 C:FOT401 2.0 46.6 0.8
NE2 C:HIS14 2.0 47.2 1.0
OQ1 C:KCX98 2.1 51.3 1.0
CD2 C:HIS16 2.9 39.2 1.0
CD2 C:HIS14 2.9 43.8 1.0
CG C:ASP258 3.0 43.8 1.0
CX C:KCX98 3.0 56.1 1.0
C41 C:FOT401 3.0 48.9 0.8
CE1 C:HIS14 3.1 47.1 1.0
CE1 C:HIS16 3.1 46.6 1.0
OQ2 C:KCX98 3.3 53.4 1.0
N3 C:FOT401 3.5 55.9 0.8
C4 C:FOT401 3.5 47.3 0.8
OD2 C:ASP258 3.5 46.9 1.0
ZN C:ZN402 3.6 61.5 1.0
CB C:ASP258 4.0 41.0 1.0
CG C:HIS14 4.1 42.7 1.0
O41 C:FOT401 4.1 49.7 0.8
CG C:HIS16 4.1 43.2 1.0
ND1 C:HIS14 4.1 45.6 1.0
NZ C:KCX98 4.1 55.8 1.0
ND1 C:HIS16 4.2 39.8 1.0
CA C:ASP258 4.3 41.5 1.0
CD2 C:HIS180 4.4 42.3 1.0
CG C:MET41 4.4 43.6 1.0
NE2 C:HIS180 4.5 45.0 1.0
OH C:TYR100 4.6 43.6 1.0
C2 C:FOT401 4.7 48.3 0.8
C5 C:FOT401 4.7 46.1 0.8

Zinc binding site 5 out of 8 in 7ca0

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Zinc binding site 5 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:53.2
occ:1.00
 O41 B:FOT401 1.8 48.9 0.7
OD1 B:ASP258 2.0 41.2 1.0
NE2 B:HIS16 2.1 50.1 1.0
NE2 B:HIS14 2.1 40.2 1.0
OQ2 B:KCX98 2.2 54.5 1.0
C41 B:FOT401 2.8 45.1 0.7
CD2 B:HIS14 2.9 40.5 1.0
CE1 B:HIS16 3.0 43.4 1.0
CG B:ASP258 3.0 39.4 1.0
CX B:KCX98 3.1 52.6 1.0
CD2 B:HIS16 3.1 45.5 1.0
CE1 B:HIS14 3.2 42.9 1.0
C4 B:FOT401 3.3 47.3 0.7
N3 B:FOT401 3.3 54.2 0.7
OQ1 B:KCX98 3.4 50.1 1.0
ZN B:ZN403 3.6 58.6 1.0
OD2 B:ASP258 3.7 36.7 1.0
O42 B:FOT401 3.8 51.9 0.7
CG B:HIS14 4.1 37.4 1.0
CB B:ASP258 4.1 35.8 1.0
ND1 B:HIS16 4.1 49.1 1.0
NZ B:KCX98 4.2 49.6 1.0
ND1 B:HIS14 4.2 39.7 1.0
CG B:HIS16 4.2 46.1 1.0
CD2 B:HIS180 4.3 41.0 1.0
CA B:ASP258 4.4 37.3 1.0
OH B:TYR100 4.5 50.0 1.0
C5 B:FOT401 4.6 53.3 0.7
NE2 B:HIS180 4.6 46.9 1.0
C2 B:FOT401 4.6 46.9 0.7
CG B:MET41 4.6 45.5 1.0

Zinc binding site 6 out of 8 in 7ca0

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Zinc binding site 6 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:58.6
occ:1.00
 OQ1 B:KCX98 2.0 50.1 1.0
NE2 B:HIS180 2.0 46.9 1.0
ND1 B:HIS137 2.0 49.8 1.0
O42 B:FOT401 2.1 51.9 0.7
O41 B:FOT401 2.3 48.9 0.7
C41 B:FOT401 2.5 45.1 0.7
CE1 B:HIS137 2.8 46.6 1.0
CD2 B:HIS180 3.0 41.0 1.0
CX B:KCX98 3.0 52.6 1.0
CE1 B:HIS180 3.1 41.1 1.0
CG B:HIS137 3.2 47.9 1.0
OQ2 B:KCX98 3.3 54.5 1.0
ZN B:ZN402 3.6 53.2 1.0
CB B:HIS137 3.7 44.5 1.0
NE2 B:HIS137 4.0 52.2 1.0
C4 B:FOT401 4.0 47.3 0.7
CE1 B:HIS14 4.0 42.9 1.0
ND1 B:HIS180 4.1 42.7 1.0
CG B:HIS180 4.1 37.0 1.0
NE2 B:HIS14 4.1 40.2 1.0
CD2 B:HIS137 4.2 45.3 1.0
NZ B:KCX98 4.2 49.6 1.0
O B:LYS230 4.2 44.1 1.0
CE1 B:TYR100 4.5 45.7 1.0
OD2 B:ASP258 4.5 36.7 1.0
CA B:HIS137 4.5 46.7 1.0
OD1 B:ASP258 4.6 41.2 1.0
CE B:KCX98 4.6 41.9 1.0
CG2 B:THR105 4.7 55.7 1.0
CG B:ASP258 4.8 39.4 1.0
N3 B:FOT401 4.9 54.2 0.7
F5 B:FOT401 4.9 61.0 0.7
OG1 B:THR105 5.0 61.5 1.0
C5 B:FOT401 5.0 53.3 0.7
CD1 B:TYR100 5.0 44.8 1.0

Zinc binding site 7 out of 8 in 7ca0

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Zinc binding site 7 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:70.3
occ:1.00
 ND1 D:HIS137 2.1 55.5 1.0
NE2 D:HIS180 2.1 54.5 1.0
OQ1 D:KCX98 2.1 69.0 1.0
O41 D:FOT401 2.2 65.3 0.7
O42 D:FOT401 2.3 58.2 0.7
C41 D:FOT401 2.6 60.3 0.7
CE1 D:HIS137 2.7 57.8 1.0
CD2 D:HIS180 2.9 53.4 1.0
CE1 D:HIS180 3.2 51.9 1.0
CX D:KCX98 3.2 66.7 1.0
CG D:HIS137 3.3 58.6 1.0
OQ2 D:KCX98 3.5 61.5 1.0
ZN D:ZN403 3.8 71.4 1.0
NE2 D:HIS137 3.9 61.7 1.0
CB D:HIS137 3.9 57.6 1.0
O D:LYS230 4.0 54.3 1.0
C4 D:FOT401 4.1 59.6 0.7
CG D:HIS180 4.1 50.7 1.0
CE1 D:HIS14 4.1 54.5 1.0
OD2 D:ASP258 4.2 58.0 1.0
ND1 D:HIS180 4.2 47.9 1.0
CD2 D:HIS137 4.2 49.8 1.0
NE2 D:HIS14 4.3 58.3 1.0
NZ D:KCX98 4.3 65.8 1.0
CG2 D:THR105 4.6 67.3 1.0
CE1 D:TYR100 4.7 65.8 1.0
CA D:HIS137 4.7 60.4 1.0
CE D:KCX98 4.7 69.1 1.0
OD1 D:ASP258 4.7 54.2 1.0
CG D:ASP258 4.7 57.9 1.0
N3 D:FOT401 4.8 67.2 0.7
C D:LYS230 4.9 49.7 1.0
OG1 D:THR105 5.0 68.2 1.0

Zinc binding site 8 out of 8 in 7ca0

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Zinc binding site 8 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Dihydroorotase in Complex with 5-Fluoroorotic Acid From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn403

b:71.4
occ:1.00
 OQ2 D:KCX98 2.0 61.5 1.0
OD1 D:ASP258 2.0 54.2 1.0
NE2 D:HIS16 2.0 63.6 1.0
NE2 D:HIS14 2.1 58.3 1.0
O42 D:FOT401 2.1 58.2 0.7
CD2 D:HIS14 2.8 56.7 1.0
CX D:KCX98 3.0 66.7 1.0
CE1 D:HIS16 3.0 61.4 1.0
CG D:ASP258 3.0 57.9 1.0
C41 D:FOT401 3.0 60.3 0.7
CD2 D:HIS16 3.1 57.9 1.0
CE1 D:HIS14 3.2 54.5 1.0
N3 D:FOT401 3.3 67.2 0.7
C4 D:FOT401 3.4 59.6 0.7
OQ1 D:KCX98 3.4 69.0 1.0
OD2 D:ASP258 3.6 58.0 1.0
ZN D:ZN402 3.8 70.3 1.0
NZ D:KCX98 4.0 65.8 1.0
CG D:HIS14 4.0 57.4 1.0
CB D:ASP258 4.1 45.9 1.0
O41 D:FOT401 4.1 65.3 0.7
ND1 D:HIS16 4.1 61.8 1.0
ND1 D:HIS14 4.1 56.7 1.0
CG D:HIS16 4.2 60.9 1.0
CA D:ASP258 4.3 50.7 1.0
C2 D:FOT401 4.5 65.9 0.7
CG D:MET41 4.5 62.6 1.0
CD2 D:HIS180 4.6 53.4 1.0
C5 D:FOT401 4.6 62.9 0.7
OH D:TYR100 4.7 61.6 1.0
NE2 D:HIS180 4.9 54.5 1.0
C D:ASP258 4.9 52.9 1.0
O2 D:FOT401 4.9 67.8 0.7
O D:ASP258 4.9 52.8 1.0

Reference:

H.H.Guan, Y.H.Huang, C.Y.Huang, C.J.Chen. Crystal Structure of Dihydroorotase From Saccharomyces Cerevisiae To Be Published.
Page generated: Tue Oct 29 18:05:56 2024

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