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Zinc in PDB 4lfy: Crystal Structure of A Dihydroorotase From Burkholderia Cenocepacia J2315

Enzymatic activity of Crystal Structure of A Dihydroorotase From Burkholderia Cenocepacia J2315

All present enzymatic activity of Crystal Structure of A Dihydroorotase From Burkholderia Cenocepacia J2315:
3.5.2.3;

Protein crystallography data

The structure of Crystal Structure of A Dihydroorotase From Burkholderia Cenocepacia J2315, PDB code: 4lfy was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.480, 89.870, 153.390, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.7

Other elements in 4lfy:

The structure of Crystal Structure of A Dihydroorotase From Burkholderia Cenocepacia J2315 also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Dihydroorotase From Burkholderia Cenocepacia J2315 (pdb code 4lfy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Dihydroorotase From Burkholderia Cenocepacia J2315, PDB code: 4lfy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4lfy

Go back to Zinc Binding Sites List in 4lfy
Zinc binding site 1 out of 4 in the Crystal Structure of A Dihydroorotase From Burkholderia Cenocepacia J2315


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 A Dihydroorotase From Burkholderia Cenocepacia J2315 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:10.7
occ:0.75
 O A:HOH656 2.0 17.5 1.0
OQ1 A:KCX117 2.1 15.0 1.0
NE2 A:HIS33 2.1 11.0 1.0
OD1 A:ASP268 2.1 10.7 1.0
NE2 A:HIS31 2.2 10.2 1.0
CX A:KCX117 3.0 16.8 1.0
CE1 A:HIS33 3.1 11.1 1.0
CD2 A:HIS33 3.1 10.3 1.0
CG A:ASP268 3.1 11.7 1.0
CE1 A:HIS31 3.1 10.6 1.0
CD2 A:HIS31 3.1 9.7 1.0
ZN A:ZN402 3.4 14.4 0.8
OQ2 A:KCX117 3.5 14.6 1.0
OD2 A:ASP268 3.6 11.8 1.0
NZ A:KCX117 4.1 16.1 1.0
ND1 A:HIS33 4.2 10.0 1.0
ND1 A:HIS31 4.2 10.3 1.0
CD2 A:HIS192 4.2 11.2 1.0
CG A:HIS33 4.3 9.6 1.0
CG A:HIS31 4.3 9.5 1.0
NE2 A:HIS192 4.3 12.2 1.0
CB A:ASP268 4.3 10.1 1.0
CG A:MET57 4.5 11.8 1.0
O A:HOH736 4.7 33.1 1.0
OH A:TYR119 4.7 21.9 1.0
CA A:ASP268 4.8 10.0 1.0
O A:HOH590 5.0 26.0 1.0

Zinc binding site 2 out of 4 in 4lfy

Go back to Zinc Binding Sites List in 4lfy
Zinc binding site 2 out of 4 in the Crystal Structure of A Dihydroorotase From Burkholderia Cenocepacia J2315


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 A Dihydroorotase From Burkholderia Cenocepacia J2315 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:14.4
occ:0.75
 OQ2 A:KCX117 1.8 14.6 1.0
NE2 A:HIS192 2.1 12.2 1.0
O A:HOH656 2.1 17.5 1.0
ND1 A:HIS154 2.2 13.6 1.0
CX A:KCX117 2.9 16.8 1.0
CE1 A:HIS154 3.0 14.0 1.0
CE1 A:HIS192 3.0 11.8 1.0
CD2 A:HIS192 3.1 11.2 1.0
OQ1 A:KCX117 3.2 15.0 1.0
CG A:HIS154 3.3 13.6 1.0
ZN A:ZN401 3.4 10.7 0.8
CB A:HIS154 3.7 12.8 1.0
O A:HOH736 3.9 33.1 1.0
CE1 A:HIS31 3.9 10.6 1.0
NZ A:KCX117 4.1 16.1 1.0
ND1 A:HIS192 4.1 10.9 1.0
NE2 A:HIS154 4.1 15.1 1.0
NE2 A:HIS31 4.1 10.2 1.0
CG A:HIS192 4.2 10.8 1.0
CD2 A:HIS154 4.3 15.8 1.0
O A:LEU240 4.4 19.9 1.0
CE1 A:TYR119 4.5 27.0 1.0
OD2 A:ASP268 4.5 11.8 1.0
CE A:KCX117 4.5 15.7 1.0
CA A:HIS154 4.6 11.0 1.0
OD1 A:ASP268 4.7 10.7 1.0
CG A:ASP268 4.9 11.7 1.0
CD1 A:TYR119 4.9 23.8 1.0

Zinc binding site 3 out of 4 in 4lfy

Go back to Zinc Binding Sites List in 4lfy
Zinc binding site 3 out of 4 in the Crystal Structure of A Dihydroorotase From Burkholderia Cenocepacia J2315


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 A Dihydroorotase From Burkholderia Cenocepacia J2315 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:11.8
occ:0.75
 OQ2 B:KCX117 2.0 15.9 1.0
O B:HOH636 2.0 20.4 1.0
OD1 B:ASP268 2.1 13.3 1.0
NE2 B:HIS33 2.1 12.2 1.0
NE2 B:HIS31 2.2 12.7 1.0
CX B:KCX117 3.0 17.0 1.0
CE1 B:HIS33 3.1 12.5 1.0
CD2 B:HIS33 3.1 12.0 1.0
CG B:ASP268 3.1 13.2 1.0
CE1 B:HIS31 3.2 12.6 1.0
CD2 B:HIS31 3.2 11.8 1.0
ZN B:ZN402 3.4 15.0 0.8
OQ1 B:KCX117 3.4 15.4 1.0
OD2 B:ASP268 3.6 13.8 1.0
NZ B:KCX117 4.1 16.9 1.0
ND1 B:HIS33 4.2 12.4 1.0
CD2 B:HIS192 4.2 12.5 1.0
CG B:HIS33 4.2 12.4 1.0
NE2 B:HIS192 4.3 12.9 1.0
ND1 B:HIS31 4.3 12.1 1.0
CB B:ASP268 4.3 12.0 1.0
CG B:HIS31 4.3 11.5 1.0
OH B:TYR119 4.6 21.9 1.0
CG B:MET57 4.7 13.9 1.0
O B:HOH652 4.7 34.3 1.0
CA B:ASP268 4.7 11.2 1.0
O B:HOH588 4.9 25.3 1.0
CE1 B:TYR119 5.0 25.5 1.0

Zinc binding site 4 out of 4 in 4lfy

Go back to Zinc Binding Sites List in 4lfy
Zinc binding site 4 out of 4 in the Crystal Structure of A Dihydroorotase From Burkholderia Cenocepacia J2315


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 A Dihydroorotase From Burkholderia Cenocepacia J2315 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:15.0
occ:0.75
 OQ1 B:KCX117 1.9 15.4 1.0
O B:HOH636 1.9 20.4 1.0
NE2 B:HIS192 2.1 12.9 1.0
ND1 B:HIS154 2.1 14.3 1.0
CX B:KCX117 2.8 17.0 1.0
CE1 B:HIS192 3.0 12.3 1.0
CE1 B:HIS154 3.0 15.9 1.0
OQ2 B:KCX117 3.1 15.9 1.0
CD2 B:HIS192 3.1 12.5 1.0
CG B:HIS154 3.2 14.2 1.0
ZN B:ZN401 3.4 11.8 0.8
CB B:HIS154 3.6 13.1 1.0
NZ B:KCX117 4.0 16.9 1.0
CE1 B:HIS31 4.0 12.6 1.0
NE2 B:HIS154 4.1 16.3 1.0
ND1 B:HIS192 4.1 12.2 1.0
NE2 B:HIS31 4.2 12.7 1.0
CG B:HIS192 4.2 11.1 1.0
CD2 B:HIS154 4.3 16.2 1.0
CE1 B:TYR119 4.3 25.5 1.0
CE B:KCX117 4.5 16.5 1.0
OD2 B:ASP268 4.5 13.8 1.0
O B:LEU240 4.5 25.5 1.0
CA B:HIS154 4.5 12.2 1.0
OD1 B:ASP268 4.6 13.3 1.0
CD1 B:TYR119 4.8 24.0 1.0
CG B:ASP268 4.9 13.2 1.0

Reference:

C.M.Lukacs, J.W.Fairman, T.E.Edwards, D.Lorimer. Crystal Structure of A Dihydroorotase From Burkholderia Cenocepacia J2315 To Be Published.
Page generated: Wed Aug 20 20:02:06 2025

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