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Zinc in PDB 6l0f: Crystal Structure of Dihydroorotase in Complex with 5-Aminouracil From Saccharomyces Cerevisiae

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

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

Protein crystallography data

The structure of Crystal Structure of Dihydroorotase in Complex with 5-Aminouracil From Saccharomyces Cerevisiae, PDB code: 6l0f 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) 34.30 / 3.26
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.649, 88.739, 103.395, 90.00, 95.67, 90.00
R / Rfree (%) 20 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Dihydroorotase in Complex with 5-Aminouracil From Saccharomyces Cerevisiae (pdb code 6l0f). 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-Aminouracil From Saccharomyces Cerevisiae, PDB code: 6l0f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6l0f

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Zinc binding site 1 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Aminouracil 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-Aminouracil From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:84.1
occ:1.00
 OD1 A:ASP258 2.0 58.0 1.0
NE2 A:HIS14 2.0 59.5 1.0
NE2 A:HIS16 2.0 59.7 1.0
CD2 A:HIS14 2.7 53.7 1.0
CE1 A:HIS16 3.0 52.9 1.0
CD2 A:HIS16 3.1 54.9 1.0
OQ1 A:KCX98 3.1 64.7 1.0
CE1 A:HIS14 3.2 57.3 1.0
CG A:ASP258 3.2 57.7 1.0
O2 A:WBU401 3.2 61.6 1.0
N3 A:WBU401 3.3 62.0 1.0
C2 A:WBU401 3.5 62.6 1.0
CX A:KCX98 3.7 65.2 1.0
OQ2 A:KCX98 3.8 66.4 1.0
CG A:HIS14 4.0 51.3 1.0
ZN A:ZN403 4.0 93.0 1.0
OD2 A:ASP258 4.1 64.1 1.0
ND1 A:HIS14 4.1 55.9 1.0
ND1 A:HIS16 4.1 49.5 1.0
CB A:ASP258 4.2 55.0 1.0
CG A:HIS16 4.2 50.4 1.0
CG A:MET41 4.2 51.4 1.0
C4 A:WBU401 4.3 57.1 1.0
CA A:ASP258 4.3 52.2 1.0
OH A:TYR100 4.3 52.0 1.0
N1 A:WBU401 4.5 62.7 1.0
O4 A:WBU401 4.7 54.0 1.0
CD2 A:HIS180 4.7 61.0 1.0
NZ A:KCX98 4.8 61.5 1.0
C A:ASP258 4.9 51.5 1.0
CB A:MET41 4.9 51.0 1.0
O A:ASP258 5.0 56.1 1.0

Zinc binding site 2 out of 8 in 6l0f

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Zinc binding site 2 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Aminouracil 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-Aminouracil From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:93.0
occ:1.00
 ND1 A:HIS137 2.0 62.3 1.0
NE2 A:HIS180 2.1 66.3 1.0
OQ2 A:KCX98 2.2 66.4 1.0
O2 A:WBU401 2.3 61.6 1.0
CE1 A:HIS137 2.4 58.4 1.0
CD2 A:HIS180 2.8 61.0 1.0
CE1 A:HIS180 3.1 61.0 1.0
CX A:KCX98 3.3 65.2 1.0
CG A:HIS137 3.4 57.6 1.0
C2 A:WBU401 3.4 62.6 1.0
O A:LYS230 3.6 58.0 1.0
NE2 A:HIS137 3.7 54.6 1.0
CG A:HIS180 4.0 56.3 1.0
OQ1 A:KCX98 4.0 64.7 1.0
ZN A:ZN402 4.0 84.1 1.0
OD1 A:ASP258 4.0 58.0 1.0
ND1 A:HIS180 4.0 58.7 1.0
NZ A:KCX98 4.1 61.5 1.0
CB A:HIS137 4.1 56.2 1.0
N1 A:WBU401 4.1 62.7 1.0
CD2 A:HIS137 4.2 56.6 1.0
CE1 A:HIS14 4.3 57.3 1.0
N3 A:WBU401 4.4 62.0 1.0
NE2 A:HIS14 4.4 59.5 1.0
OD2 A:ASP258 4.5 64.1 1.0
CG A:ASP258 4.5 57.7 1.0
C A:LYS230 4.6 54.4 1.0
CD A:PRO231 4.8 51.1 1.0
CG2 A:THR105 4.9 57.1 1.0
CE2 A:TYR100 4.9 53.6 1.0
CA A:HIS137 4.9 55.9 1.0
OG1 A:THR105 5.0 53.7 1.0

Zinc binding site 3 out of 8 in 6l0f

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Zinc binding site 3 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Aminouracil 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-Aminouracil From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:80.4
occ:1.00
 OQ1 B:KCX98 2.0 65.3 1.0
OD1 B:ASP258 2.0 53.0 1.0
NE2 B:HIS14 2.1 61.9 1.0
NE2 B:HIS16 2.1 55.5 1.0
O2 B:WBU401 2.6 67.5 1.0
CX B:KCX98 2.7 67.2 1.0
CE1 B:HIS16 2.8 56.6 1.0
OQ2 B:KCX98 3.0 69.0 1.0
CD2 B:HIS14 3.0 54.5 1.0
C2 B:WBU401 3.1 70.7 1.0
CE1 B:HIS14 3.1 56.7 1.0
CG B:ASP258 3.1 51.7 1.0
N3 B:WBU401 3.2 71.2 1.0
CD2 B:HIS16 3.3 51.6 1.0
OD2 B:ASP258 3.8 57.6 1.0
ZN B:ZN403 3.8 0.1 1.0
NZ B:KCX98 3.8 65.1 1.0
ND1 B:HIS16 4.0 49.7 1.0
CG B:HIS14 4.1 51.7 1.0
ND1 B:HIS14 4.1 53.7 1.0
N1 B:WBU401 4.2 70.0 1.0
OH B:TYR100 4.2 59.2 1.0
CB B:ASP258 4.3 46.9 1.0
CG B:HIS16 4.3 48.4 1.0
C4 B:WBU401 4.3 64.5 1.0
CG B:MET41 4.4 50.1 1.0
CD2 B:HIS180 4.5 53.8 1.0
NE2 B:HIS180 4.5 59.4 1.0
CA B:ASP258 4.6 43.6 1.0
O4 B:WBU401 4.9 58.2 1.0
CB B:MET41 5.0 50.1 1.0

Zinc binding site 4 out of 8 in 6l0f

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Zinc binding site 4 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Aminouracil 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-Aminouracil From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:0.1
occ:1.00
 ND1 B:HIS137 1.9 70.3 1.0
NE2 B:HIS180 2.1 59.4 1.0
CE1 B:HIS137 2.1 68.8 1.0
OQ2 B:KCX98 2.2 69.0 1.0
O2 B:WBU401 2.5 67.5 1.0
CE1 B:HIS180 2.8 58.9 1.0
CD2 B:HIS180 3.0 53.8 1.0
CG B:HIS137 3.2 61.0 1.0
CX B:KCX98 3.3 67.2 1.0
NE2 B:HIS137 3.3 59.5 1.0
C2 B:WBU401 3.6 70.7 1.0
OQ1 B:KCX98 3.7 65.3 1.0
O B:LYS230 3.8 60.9 1.0
ZN B:ZN402 3.8 80.4 1.0
ND1 B:HIS180 3.9 56.7 1.0
CD2 B:HIS137 3.9 55.6 1.0
CG B:HIS180 4.0 51.5 1.0
N1 B:WBU401 4.1 70.0 1.0
CB B:HIS137 4.2 57.5 1.0
CE1 B:HIS14 4.3 56.7 1.0
NZ B:KCX98 4.4 65.1 1.0
OD1 B:ASP258 4.5 53.0 1.0
CG2 B:THR105 4.5 71.7 1.0
NE2 B:HIS14 4.6 61.9 1.0
OD2 B:ASP258 4.6 57.6 1.0
C B:LYS230 4.7 56.8 1.0
N3 B:WBU401 4.7 71.2 1.0
CE B:KCX98 4.7 55.6 1.0
CD B:PRO231 4.7 51.5 1.0
CG B:ASP258 4.8 51.7 1.0
CA B:HIS137 4.9 51.8 1.0
OG1 B:THR105 4.9 67.7 1.0
CB B:THR105 4.9 71.3 1.0
CE1 B:TYR100 5.0 64.5 1.0

Zinc binding site 5 out of 8 in 6l0f

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Zinc binding site 5 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Aminouracil 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-Aminouracil From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:0.9
occ:1.00
 OD1 C:ASP258 2.0 68.2 1.0
OQ2 C:KCX98 2.0 86.5 1.0
NE2 C:HIS16 2.0 77.7 1.0
NE2 C:HIS14 2.1 78.1 1.0
CD2 C:HIS14 2.9 69.2 1.0
CE1 C:HIS16 3.0 74.3 1.0
CE1 C:HIS14 3.0 72.8 1.0
CD2 C:HIS16 3.0 70.7 1.0
O2 C:WBU401 3.1 75.5 1.0
CX C:KCX98 3.1 89.1 1.0
N3 C:WBU401 3.2 77.4 1.0
CG C:ASP258 3.2 68.1 1.0
C2 C:WBU401 3.4 77.2 1.0
ZN C:ZN403 3.9 0.4 1.0
OD2 C:ASP258 4.0 74.1 1.0
OQ1 C:KCX98 4.0 86.5 1.0
CG C:HIS14 4.0 66.0 1.0
ND1 C:HIS14 4.0 67.3 1.0
NZ C:KCX98 4.1 90.4 1.0
ND1 C:HIS16 4.1 70.3 1.0
CB C:ASP258 4.1 64.5 1.0
CG C:HIS16 4.2 67.0 1.0
C4 C:WBU401 4.2 74.5 1.0
OH C:TYR100 4.4 71.8 1.0
CA C:ASP258 4.5 61.0 1.0
CD2 C:HIS180 4.5 67.4 1.0
CG C:MET41 4.5 70.8 1.0
O4 C:WBU401 4.5 69.4 1.0
N1 C:WBU401 4.6 75.0 1.0
NE2 C:HIS180 4.8 71.4 1.0

Zinc binding site 6 out of 8 in 6l0f

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Zinc binding site 6 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Aminouracil 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-Aminouracil From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:0.4
occ:1.00
 ND1 C:HIS137 2.0 74.4 1.0
NE2 C:HIS180 2.0 71.4 1.0
O2 C:WBU401 2.5 75.5 1.0
OQ1 C:KCX98 2.5 86.5 1.0
CE1 C:HIS137 2.6 69.5 1.0
CD2 C:HIS180 2.8 67.4 1.0
CE1 C:HIS180 3.1 66.5 1.0
CX C:KCX98 3.2 89.1 1.0
OQ2 C:KCX98 3.2 86.5 1.0
CG C:HIS137 3.3 71.4 1.0
C2 C:WBU401 3.6 77.2 1.0
O C:LYS230 3.7 65.0 1.0
NE2 C:HIS137 3.9 69.5 1.0
ZN C:ZN402 3.9 0.9 1.0
CG C:HIS180 3.9 60.7 1.0
CB C:HIS137 4.0 69.5 1.0
ND1 C:HIS180 4.1 62.8 1.0
CD2 C:HIS137 4.2 71.2 1.0
N3 C:WBU401 4.4 77.4 1.0
NZ C:KCX98 4.5 90.4 1.0
OD1 C:ASP258 4.5 68.2 1.0
N1 C:WBU401 4.5 75.0 1.0
CE1 C:HIS14 4.5 72.8 1.0
C C:LYS230 4.6 60.1 1.0
CD C:PRO231 4.7 57.4 1.0
NE2 C:HIS14 4.7 78.1 1.0
CG2 C:THR105 4.7 77.9 1.0
CA C:HIS137 4.7 69.0 1.0
OG1 C:THR105 4.9 72.1 1.0
CE2 C:TYR100 5.0 78.1 1.0
OD2 C:ASP258 5.0 74.1 1.0
CG C:ASP258 5.0 68.1 1.0

Zinc binding site 7 out of 8 in 6l0f

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Zinc binding site 7 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Aminouracil 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-Aminouracil From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:94.9
occ:1.00
 ND1 D:HIS137 2.0 53.9 1.0
NE2 D:HIS180 2.0 54.0 1.0
OQ1 D:KCX98 2.1 61.9 1.0
CE1 D:HIS137 2.8 50.5 1.0
CE1 D:HIS180 2.9 53.1 1.0
CD2 D:HIS180 3.1 48.8 1.0
CX D:KCX98 3.1 59.6 1.0
CG D:HIS137 3.2 50.0 1.0
O2 D:WBU401 3.2 57.7 1.0
OQ2 D:KCX98 3.4 59.0 1.0
CB D:HIS137 3.8 50.4 1.0
ZN D:ZN403 3.8 83.4 1.0
NE2 D:HIS137 4.0 49.4 1.0
ND1 D:HIS180 4.0 48.0 1.0
CG D:HIS180 4.1 46.3 1.0
O D:LYS230 4.1 51.0 1.0
CD2 D:HIS137 4.2 49.4 1.0
C2 D:WBU401 4.3 60.0 1.0
CE1 D:HIS14 4.3 49.3 1.0
NZ D:KCX98 4.3 55.4 1.0
CA D:HIS137 4.5 49.7 1.0
OD1 D:ASP258 4.5 53.7 1.0
NE2 D:HIS14 4.5 56.2 1.0
N1 D:WBU401 4.7 62.0 1.0
CD D:PRO231 4.7 44.5 1.0
CE2 D:TYR100 4.7 50.9 1.0
CE D:KCX98 4.7 50.1 1.0
C D:LYS230 4.9 45.6 1.0
CG2 D:THR105 5.0 60.4 1.0

Zinc binding site 8 out of 8 in 6l0f

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Zinc binding site 8 out of 8 in the Crystal Structure of Dihydroorotase in Complex with 5-Aminouracil 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-Aminouracil From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn403

b:83.4
occ:1.00
 OD1 D:ASP258 2.0 53.7 1.0
NE2 D:HIS16 2.0 55.6 1.0
NE2 D:HIS14 2.1 56.2 1.0
OQ2 D:KCX98 2.2 59.0 1.0
O2 D:WBU401 2.3 57.7 1.0
CD2 D:HIS16 3.0 51.7 1.0
CD2 D:HIS14 3.0 50.2 1.0
CE1 D:HIS14 3.0 49.3 1.0
CE1 D:HIS16 3.1 53.1 1.0
C2 D:WBU401 3.2 60.0 1.0
CX D:KCX98 3.2 59.6 1.0
CG D:ASP258 3.2 52.4 1.0
N3 D:WBU401 3.5 59.2 1.0
OQ1 D:KCX98 3.6 61.9 1.0
ZN D:ZN402 3.8 94.9 1.0
OD2 D:ASP258 4.0 54.6 1.0
ND1 D:HIS14 4.1 47.6 1.0
CG D:HIS14 4.1 48.4 1.0
CB D:ASP258 4.1 48.3 1.0
CG D:HIS16 4.1 46.6 1.0
ND1 D:HIS16 4.1 49.2 1.0
NZ D:KCX98 4.2 55.4 1.0
N1 D:WBU401 4.3 62.0 1.0
CD2 D:HIS180 4.3 48.8 1.0
CA D:ASP258 4.4 45.2 1.0
OH D:TYR100 4.4 49.8 1.0
NE2 D:HIS180 4.5 54.0 1.0
CG D:MET41 4.5 45.4 1.0
C4 D:WBU401 4.8 56.0 1.0

Reference:

H.H.Guan, Y.H.Huang, C.Y.Huang, C.J.Chen. Crystal Structure of Dihydroorotase in Complex with 5-Aminouracil From Saccharomyces Cerevisiae To Be Published.
Page generated: Tue Oct 29 02:13:05 2024

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