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Calcium 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:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of A Dihydroorotase From Burkholderia Cenocepacia J2315, PDB code: 4lfy:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4lfy

Go back to Calcium Binding Sites List in 4lfy
Calcium 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 Calcium with other atoms in the Ca 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:Ca404

b:25.0
occ:1.00
 NH1 B:ARG225 3.2 13.3 1.0
O B:HOH527 3.2 9.2 1.0
O A:HOH737 3.3 38.3 1.0
NH2 A:ARG245 3.4 16.2 1.0
O B:HOH610 3.4 22.4 1.0
NE B:ARG245 3.5 16.0 1.0
NH2 A:ARG225 3.5 14.7 1.0
NH2 B:ARG225 3.6 13.8 1.0
CZ B:ARG225 3.7 13.2 1.0
CA B:CA404 3.8 26.9 1.0
CD B:ARG245 3.9 15.4 1.0
CG B:ARG245 4.0 15.5 1.0
CB B:PHE165 4.1 12.2 1.0
CZ A:ARG245 4.2 16.0 1.0
NE A:ARG245 4.2 15.5 1.0
NH1 A:ARG225 4.4 14.6 1.0
CZ A:ARG225 4.4 14.1 1.0
CZ B:ARG245 4.5 16.4 1.0
CG B:PHE165 4.6 12.2 1.0
NH2 B:ARG245 4.7 17.4 1.0
O B:HOH514 4.9 14.7 1.0
NE B:ARG225 4.9 12.7 1.0
O B:HOH567 5.0 24.4 1.0

Calcium binding site 2 out of 4 in 4lfy

Go back to Calcium Binding Sites List in 4lfy
Calcium 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 Calcium with other atoms in the Ca 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:Ca405

b:30.5
occ:1.00
 O B:HOH689 3.0 36.7 1.0
O A:HOH738 3.2 40.5 1.0
NH1 A:ARG245 3.4 15.8 1.0
CB A:ARG245 3.6 14.1 1.0
N A:GLU246 3.8 15.9 1.0
O B:HOH633 3.8 22.1 1.0
CG A:ARG245 3.8 15.0 1.0
CD A:ARG245 3.9 15.9 1.0
CG2 A:THR247 3.9 24.0 1.0
N A:THR247 4.0 17.4 1.0
CB A:GLU246 4.0 17.0 1.0
CB B:ASP163 4.2 14.9 1.0
CA A:GLU246 4.3 16.2 1.0
CA A:ARG245 4.4 13.8 1.0
C A:ARG245 4.4 14.6 1.0
OG1 A:THR247 4.4 22.4 1.0
CZ A:ARG245 4.5 16.0 1.0
OD1 B:ASP163 4.6 14.5 1.0
C A:GLU246 4.6 16.0 1.0
CB A:THR247 4.6 21.1 1.0
NE A:ARG245 4.7 15.5 1.0
O B:HOH615 4.7 22.2 1.0
CG B:ASP163 4.7 15.3 1.0
O B:HOH608 4.8 21.2 1.0
CA A:THR247 4.9 18.4 1.0
OD2 B:ASP166 5.0 14.4 1.0

Calcium binding site 3 out of 4 in 4lfy

Go back to Calcium Binding Sites List in 4lfy
Calcium 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 Calcium with other atoms in the Ca 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:Ca404

b:26.9
occ:1.00
 NH1 A:ARG225 3.1 14.6 1.0
O A:HOH501 3.2 10.8 1.0
O A:HOH737 3.2 38.3 1.0
NH2 B:ARG245 3.3 17.4 1.0
O A:HOH588 3.4 25.3 1.0
NH2 B:ARG225 3.5 13.8 1.0
NE A:ARG245 3.5 15.5 1.0
NH2 A:ARG225 3.7 14.7 1.0
CZ A:ARG225 3.7 14.1 1.0
CA A:CA404 3.8 25.0 1.0
CD A:ARG245 3.9 15.9 1.0
CB A:PHE165 4.0 10.9 1.0
CG A:ARG245 4.2 15.0 1.0
CZ B:ARG245 4.2 16.4 1.0
NE B:ARG245 4.3 16.0 1.0
CZ B:ARG225 4.4 13.2 1.0
NH1 B:ARG225 4.4 13.3 1.0
CG A:PHE165 4.5 11.1 1.0
CZ A:ARG245 4.6 16.0 1.0
O A:HOH605 4.8 16.0 1.0
NH2 A:ARG245 4.8 16.2 1.0
NE A:ARG225 4.9 13.7 1.0
CD2 A:PHE165 5.0 11.2 1.0

Calcium binding site 4 out of 4 in 4lfy

Go back to Calcium Binding Sites List in 4lfy
Calcium 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 Calcium with other atoms in the Ca 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:Ca405

b:24.4
occ:1.00
 O B:HOH687 2.9 33.0 1.0
O A:HOH573 2.9 28.4 1.0
O A:HOH591 3.3 26.7 1.0
NH1 B:ARG245 3.4 16.2 1.0
CG2 B:THR247 3.6 17.9 1.0
CB B:ARG245 3.6 14.7 1.0
N B:THR247 3.7 14.6 1.0
N B:GLU246 3.8 14.7 1.0
CD B:ARG245 3.9 15.4 1.0
CB B:GLU246 4.0 15.2 1.0
CG B:ARG245 4.0 15.5 1.0
OG1 B:THR247 4.1 17.9 1.0
O B:HOH686 4.3 30.9 1.0
CA B:GLU246 4.3 14.2 1.0
CB A:ASP163 4.3 14.0 1.0
O A:HOH541 4.3 16.3 1.0
CB B:THR247 4.4 16.8 1.0
C B:ARG245 4.5 13.8 1.0
CZ B:ARG245 4.5 16.4 1.0
CA B:ARG245 4.5 13.9 1.0
C B:GLU246 4.5 14.9 1.0
NE B:ARG245 4.6 16.0 1.0
CA B:THR247 4.7 15.2 1.0
O A:HOH561 4.7 22.3 1.0
O A:HOH592 4.8 18.4 1.0
OD1 A:ASP163 4.8 13.1 1.0
CG A:ASP163 4.9 13.7 1.0
CG B:GLU246 5.0 15.8 1.0
OD2 A:ASP166 5.0 13.0 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: Sat Dec 12 04:56:31 2020

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