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Zinc in PDB 7ca1: Crystal Structure of Dihydroorotase in Complex with Plumbagin From Saccharomyces Cerevisiae

Enzymatic activity of Crystal Structure of Dihydroorotase in Complex with Plumbagin From Saccharomyces Cerevisiae

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

Protein crystallography data

The structure of Crystal Structure of Dihydroorotase in Complex with Plumbagin From Saccharomyces Cerevisiae, PDB code: 7ca1 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) 45.90 / 3.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.24, 88.36, 103.42, 90, 95.16, 90
R / Rfree (%) 26.1 / 30.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Dihydroorotase in Complex with Plumbagin From Saccharomyces Cerevisiae (pdb code 7ca1). 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 Plumbagin From Saccharomyces Cerevisiae, PDB code: 7ca1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7ca1

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

b:84.8
occ:1.00
 OD1 A:ASP258 1.9 83.5 1.0
NE2 A:HIS16 2.0 85.4 1.0
NE2 A:HIS14 2.1 84.7 1.0
OQ1 A:KCX98 2.3 85.4 1.0
CE1 A:HIS16 2.9 85.7 1.0
CD2 A:HIS16 3.0 85.1 1.0
CD2 A:HIS14 3.0 84.6 1.0
CE1 A:HIS14 3.1 84.7 1.0
CG A:ASP258 3.2 82.7 1.0
CX A:KCX98 3.3 85.3 1.0
O4B A:LMR401 3.4 82.8 1.0
OQ2 A:KCX98 3.7 84.7 1.0
O2 A:LMR401 3.7 83.7 1.0
ZN A:ZN403 3.7 84.8 1.0
ND1 A:HIS16 4.0 85.6 1.0
OD2 A:ASP258 4.0 82.0 1.0
CG A:HIS16 4.0 85.4 1.0
CB A:ASP258 4.1 82.5 1.0
C4 A:LMR401 4.1 82.0 1.0
CG A:HIS14 4.1 84.5 1.0
ND1 A:HIS14 4.2 84.6 1.0
NZ A:KCX98 4.3 86.3 1.0
O4A A:LMR401 4.3 80.9 1.0
CA A:ASP258 4.4 83.2 1.0
CE A:KCX98 4.6 87.7 1.0
CD2 A:HIS180 4.6 83.6 1.0
CG A:MET41 4.7 87.1 1.0
OH A:TYR100 4.8 88.2 1.0
C2 A:LMR401 4.9 82.9 1.0
NE2 A:HIS180 5.0 84.1 1.0

Zinc binding site 2 out of 8 in 7ca1

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

b:84.8
occ:1.00
 OQ2 A:KCX98 2.2 84.7 1.0
ND1 A:HIS137 2.3 84.3 1.0
O4B A:LMR401 2.5 82.8 1.0
CE1 A:HIS137 2.6 83.6 1.0
CX A:KCX98 2.9 85.3 1.0
OQ1 A:KCX98 2.9 85.4 1.0
NE2 A:HIS180 3.3 84.1 1.0
CG A:HIS137 3.5 85.3 1.0
O A:LYS230 3.5 80.4 1.0
C4 A:LMR401 3.5 82.0 1.0
ZN A:ZN402 3.7 84.8 1.0
O4A A:LMR401 3.8 80.9 1.0
CD2 A:HIS180 3.8 83.6 1.0
NE2 A:HIS137 3.9 84.0 1.0
NZ A:KCX98 4.1 86.3 1.0
CG2 A:THR105 4.2 84.7 1.0
CB A:HIS137 4.2 86.2 1.0
CE1 A:HIS180 4.3 83.9 1.0
CD2 A:HIS137 4.3 85.2 1.0
OD1 A:ASP258 4.3 83.5 1.0
OG1 A:THR105 4.4 82.6 1.0
CB A:THR105 4.5 83.8 1.0
C A:LYS230 4.5 79.7 1.0
CE1 A:TYR100 4.6 88.1 1.0
C3 A:LMR401 4.9 81.8 1.0
NE2 A:HIS14 5.0 84.7 1.0
O2 A:LMR401 5.0 83.7 1.0
CD A:PRO231 5.0 81.0 1.0
CG A:ASP258 5.0 82.7 1.0
CG A:HIS180 5.0 83.4 1.0

Zinc binding site 3 out of 8 in 7ca1

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

b:69.2
occ:1.00
 OQ1 C:KCX98 2.2 69.7 1.0
ND1 C:HIS137 2.7 70.5 1.0
C6 C:90R401 3.0 69.9 1.0
CX C:KCX98 3.1 70.1 1.0
CE1 C:HIS137 3.1 70.7 1.0
C9 C:90R401 3.1 69.7 1.0
ZN C:ZN403 3.2 70.0 1.0
C2 C:90R401 3.3 70.2 1.0
NE2 C:HIS180 3.4 68.9 1.0
O1 C:90R401 3.5 69.8 1.0
C10 C:90R401 3.5 69.5 1.0
OQ2 C:KCX98 3.5 70.5 1.0
C1 C:90R401 3.6 70.2 1.0
C8 C:90R401 3.7 69.8 1.0
O C:LYS230 3.8 70.2 1.0
CG C:HIS137 4.0 70.7 1.0
NZ C:KCX98 4.0 69.8 1.0
CD2 C:HIS180 4.0 68.7 1.0
C5 C:90R401 4.1 70.6 1.0
CG2 C:THR105 4.1 76.1 1.0
CE1 C:TYR100 4.2 73.5 1.0
OG1 C:THR105 4.4 75.0 1.0
NE2 C:HIS137 4.4 70.8 1.0
CE1 C:HIS180 4.4 69.0 1.0
O3 C:90R401 4.4 70.8 1.0
CB C:THR105 4.4 75.7 1.0
NE2 C:HIS14 4.5 68.8 1.0
CB C:HIS137 4.6 70.5 1.0
C4 C:90R401 4.7 70.2 1.0
CD1 C:TYR100 4.7 74.7 1.0
CD2 C:HIS137 4.8 71.0 1.0
CE1 C:HIS14 4.9 68.6 1.0
C C:LYS230 5.0 70.1 1.0

Zinc binding site 4 out of 8 in 7ca1

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

b:70.0
occ:1.00
 NE2 C:HIS14 2.1 68.8 1.0
C10 C:90R401 2.2 69.5 1.0
OQ1 C:KCX98 2.3 69.7 1.0
C8 C:90R401 2.4 69.8 1.0
NE2 C:HIS16 2.5 69.9 1.0
CD2 C:HIS14 2.8 68.8 1.0
CX C:KCX98 3.0 70.1 1.0
OQ2 C:KCX98 3.0 70.5 1.0
C9 C:90R401 3.1 69.7 1.0
CE1 C:HIS16 3.1 70.2 1.0
CE1 C:HIS14 3.2 68.6 1.0
ZN C:ZN402 3.2 69.2 1.0
C1 C:90R401 3.4 70.2 1.0
CD2 C:HIS16 3.6 69.4 1.0
C6 C:90R401 3.9 69.9 1.0
CG C:HIS14 4.0 68.3 1.0
C2 C:90R401 4.1 70.2 1.0
ND1 C:HIS14 4.1 68.2 1.0
NZ C:KCX98 4.1 69.8 1.0
CG C:MET41 4.2 69.5 1.0
ND1 C:HIS16 4.3 69.8 1.0
OH C:TYR100 4.3 72.1 1.0
C4 C:90R401 4.4 70.2 1.0
O2 C:90R401 4.5 70.0 1.0
CD2 C:HIS180 4.5 68.7 1.0
CG C:HIS16 4.5 69.2 1.0
CB C:MET41 4.5 69.9 1.0
NE2 C:HIS180 4.5 68.9 1.0
CE1 C:TYR100 5.0 73.5 1.0

Zinc binding site 5 out of 8 in 7ca1

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Zinc binding site 5 out of 8 in the Crystal Structure of Dihydroorotase in Complex with Plumbagin 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 Plumbagin From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:72.3
occ:1.00
 OQ2 B:KCX98 2.0 72.6 1.0
NE2 B:HIS14 2.0 72.0 1.0
OD1 B:ASP258 2.1 71.8 1.0
NE2 B:HIS16 2.2 72.9 1.0
CE1 B:HIS14 2.9 72.0 1.0
CX B:KCX98 3.0 73.1 1.0
CE1 B:HIS16 3.1 73.2 1.0
CD2 B:HIS14 3.1 72.0 1.0
CD2 B:HIS16 3.2 72.7 1.0
C2 B:LMR501 3.3 72.8 1.0
C1 B:LMR501 3.3 72.5 1.0
CG B:ASP258 3.3 71.7 1.0
O1A B:LMR501 3.5 72.7 1.0
C3 B:LMR501 3.5 72.5 1.0
NZ B:KCX98 3.7 73.8 1.0
ZN B:ZN503 3.7 71.6 1.0
OQ1 B:KCX98 3.9 73.3 1.0
O1B B:LMR501 3.9 71.6 1.0
ND1 B:HIS14 4.0 71.9 1.0
OD2 B:ASP258 4.1 71.7 1.0
CG B:HIS14 4.1 72.0 1.0
OH B:TYR100 4.2 73.9 1.0
ND1 B:HIS16 4.2 73.4 1.0
CG B:HIS16 4.3 72.9 1.0
CB B:ASP258 4.3 71.3 1.0
CG B:MET41 4.5 73.5 1.0
CA B:ASP258 4.5 71.5 1.0
O2 B:LMR501 4.7 73.0 1.0
CD2 B:HIS180 4.7 71.5 1.0

Zinc binding site 6 out of 8 in 7ca1

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Zinc binding site 6 out of 8 in the Crystal Structure of Dihydroorotase in Complex with Plumbagin 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 Plumbagin From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:71.6
occ:1.00
 O1A B:LMR501 2.0 72.7 1.0
OQ1 B:KCX98 2.1 73.3 1.0
NE2 B:HIS180 2.2 71.8 1.0
ND1 B:HIS137 2.3 73.0 1.0
CE1 B:HIS137 2.7 72.4 1.0
OQ2 B:KCX98 2.8 72.6 1.0
CX B:KCX98 2.8 73.1 1.0
CD2 B:HIS180 2.8 71.5 1.0
C1 B:LMR501 3.2 72.5 1.0
CE1 B:HIS180 3.4 71.5 1.0
CG B:HIS137 3.5 73.1 1.0
ZN B:ZN502 3.7 72.3 1.0
O1B B:LMR501 3.9 71.6 1.0
NE2 B:HIS137 3.9 72.5 1.0
O B:LYS230 4.0 69.7 1.0
NZ B:KCX98 4.1 73.8 1.0
CG B:HIS180 4.1 71.1 1.0
C2 B:LMR501 4.1 72.8 1.0
CE1 B:HIS14 4.2 72.0 1.0
OD1 B:ASP258 4.2 71.8 1.0
CB B:HIS137 4.2 73.5 1.0
ND1 B:HIS180 4.3 71.0 1.0
CD2 B:HIS137 4.3 72.7 1.0
CE1 B:TYR100 4.6 74.3 1.0
NE2 B:HIS14 4.6 72.0 1.0
CE B:KCX98 4.7 75.3 1.0
CA B:HIS137 4.8 73.2 1.0
O2 B:LMR501 4.9 73.0 1.0
C B:LYS230 4.9 69.0 1.0
CG2 B:THR105 4.9 74.8 1.0
CG B:ASP258 5.0 71.7 1.0
CD B:PRO231 5.0 69.3 1.0

Zinc binding site 7 out of 8 in 7ca1

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

b:85.4
occ:1.00
 ND1 D:HIS137 2.1 84.5 1.0
C10 D:90R401 2.2 84.6 1.0
OQ1 D:KCX98 2.3 85.6 1.0
OQ2 D:KCX98 2.5 86.4 1.0
C8 D:90R401 2.6 85.9 1.0
NE2 D:HIS180 2.7 83.8 1.0
CX D:KCX98 2.7 86.4 1.0
CE1 D:HIS137 2.7 83.5 1.0
C9 D:90R401 3.2 84.3 1.0
CG D:HIS137 3.3 84.4 1.0
CD2 D:HIS180 3.4 83.9 1.0
CE1 D:HIS180 3.6 83.3 1.0
C1 D:90R401 3.7 86.6 1.0
ZN D:ZN403 3.9 86.3 1.0
NZ D:KCX98 3.9 87.5 1.0
NE2 D:HIS137 3.9 83.6 1.0
CB D:HIS137 3.9 85.2 1.0
C6 D:90R401 4.1 84.8 1.0
CD2 D:HIS137 4.2 83.9 1.0
O D:LYS230 4.3 79.8 1.0
C2 D:90R401 4.3 85.9 1.0
CG D:HIS180 4.6 83.2 1.0
CE1 D:TYR100 4.6 89.0 1.0
ND1 D:HIS180 4.6 82.9 1.0
CG2 D:THR105 4.7 88.5 1.0
C4 D:90R401 4.7 87.3 1.0
CE D:KCX98 4.8 87.9 1.0
CA D:HIS137 4.8 85.0 1.0
OD1 D:ASP258 4.8 85.9 1.0
O2 D:90R401 4.8 87.9 1.0
CE1 D:HIS14 4.9 86.3 1.0
C D:LYS230 4.9 78.7 1.0
NE2 D:HIS14 5.0 86.8 1.0

Zinc binding site 8 out of 8 in 7ca1

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

b:86.3
occ:1.00
 OQ2 D:KCX98 1.9 86.4 1.0
OD1 D:ASP258 2.0 85.9 1.0
NE2 D:HIS16 2.0 87.2 1.0
NE2 D:HIS14 2.1 86.8 1.0
CE1 D:HIS16 2.7 88.0 1.0
CX D:KCX98 2.8 86.4 1.0
CE1 D:HIS14 3.0 86.3 1.0
CD2 D:HIS14 3.1 87.3 1.0
CG D:ASP258 3.2 85.3 1.0
CD2 D:HIS16 3.2 87.4 1.0
NZ D:KCX98 3.5 87.5 1.0
C6 D:90R401 3.6 84.8 1.0
OQ1 D:KCX98 3.6 85.6 1.0
C2 D:90R401 3.7 85.9 1.0
C9 D:90R401 3.8 84.3 1.0
OD2 D:ASP258 3.9 84.6 1.0
ZN D:ZN402 3.9 85.4 1.0
ND1 D:HIS16 3.9 88.5 1.0
O1 D:90R401 4.0 84.2 1.0
C1 D:90R401 4.1 86.6 1.0
ND1 D:HIS14 4.1 86.6 1.0
CG D:HIS14 4.2 87.5 1.0
C10 D:90R401 4.2 84.6 1.0
CG D:HIS16 4.2 88.0 1.0
CB D:ASP258 4.3 85.7 1.0
C8 D:90R401 4.3 85.9 1.0
CD2 D:HIS180 4.3 83.9 1.0
C5 D:90R401 4.3 86.0 1.0
CG D:MET41 4.6 89.2 1.0
CA D:ASP258 4.6 86.3 1.0
OH D:TYR100 4.6 89.8 1.0
O3 D:90R401 4.6 85.3 1.0
NE2 D:HIS180 4.7 83.8 1.0
CE D:KCX98 4.8 87.9 1.0
C4 D:90R401 5.0 87.3 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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