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Calcium in PDB 3gri: The Crystal Structure of A Dihydroorotase From Staphylococcus Aureus

Enzymatic activity of The Crystal Structure of A Dihydroorotase From Staphylococcus Aureus

All present enzymatic activity of The Crystal Structure of A Dihydroorotase From Staphylococcus Aureus:
3.5.2.3;

Protein crystallography data

The structure of The Crystal Structure of A Dihydroorotase From Staphylococcus Aureus, PDB code: 3gri was solved by J.S.Brunzelle, Z.Wawrzak, T.Skarina, O.Onopriyenko, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.217, 55.229, 85.647, 88.33, 76.56, 76.97
R / Rfree (%) 18.9 / 23.7

Other elements in 3gri:

The structure of The Crystal Structure of A Dihydroorotase From Staphylococcus Aureus also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Zinc (Zn) 2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 3gri

Go back to Calcium Binding Sites List in 3gri
Calcium binding site 1 out of 4 in the The Crystal Structure of A Dihydroorotase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of A Dihydroorotase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca700

b:34.0
occ:1.00
 O A:HOH490 2.1 29.0 1.0
O A:PHE391 2.2 31.4 1.0
O A:HOH527 2.3 25.5 1.0
O A:SER393 2.5 27.3 1.0
O A:HOH628 2.7 39.1 1.0
O A:HOH610 3.0 34.6 1.0
C A:PHE391 3.2 31.9 1.0
C A:SER393 3.6 28.6 1.0
CB A:PHE391 4.0 32.8 1.0
C A:LEU392 4.0 30.6 1.0
N A:LEU392 4.1 31.7 1.0
CA A:PHE391 4.1 32.4 1.0
CA A:LEU392 4.2 31.2 1.0
N A:SER393 4.2 29.8 1.0
O A:GLY388 4.3 34.5 1.0
O A:LEU392 4.3 30.9 1.0
O A:HOH574 4.4 44.0 1.0
CA A:LYS394 4.5 28.4 1.0
N A:LYS394 4.5 28.1 1.0
N A:PHE391 4.5 33.0 1.0
CA A:SER393 4.6 29.0 1.0
C A:LYS394 4.6 28.5 1.0
O A:LYS394 4.8 27.9 1.0

Calcium binding site 2 out of 4 in 3gri

Go back to Calcium Binding Sites List in 3gri
Calcium binding site 2 out of 4 in the The Crystal Structure of A Dihydroorotase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of A Dihydroorotase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:26.7
occ:1.00
 O A:GLY199 2.3 20.0 1.0
C A:GLY199 3.4 19.9 1.0
CA A:GLY199 4.1 20.1 1.0
O A:HOH631 4.4 44.8 1.0
OE2 A:GLU317 4.5 35.0 1.0
N A:ILE200 4.5 18.9 1.0
O A:HOH587 4.7 35.1 1.0
CA A:ILE200 4.8 18.5 1.0
CD A:PRO201 4.9 19.0 1.0

Calcium binding site 3 out of 4 in 3gri

Go back to Calcium Binding Sites List in 3gri
Calcium binding site 3 out of 4 in the The Crystal Structure of A Dihydroorotase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of A Dihydroorotase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca700

b:45.8
occ:1.00
 O B:PHE391 2.4 32.3 1.0
O B:SER393 2.5 31.1 1.0
O B:HOH540 2.5 27.2 1.0
O B:HOH665 2.7 41.3 1.0
C B:PHE391 3.5 32.9 1.0
C B:SER393 3.6 31.6 1.0
C B:LEU392 4.2 32.2 1.0
CB B:PHE391 4.2 33.6 1.0
N B:SER393 4.3 31.9 1.0
N B:LEU392 4.3 32.5 1.0
CA B:PHE391 4.3 33.3 1.0
CA B:LYS394 4.3 31.9 1.0
O B:LYS394 4.4 32.1 1.0
CA B:LEU392 4.4 32.1 1.0
N B:LYS394 4.4 31.4 1.0
O B:GLY388 4.5 35.0 1.0
C B:LYS394 4.5 32.1 1.0
O B:LEU392 4.5 32.0 1.0
CA B:SER393 4.6 31.7 1.0
N B:PHE391 4.8 33.8 1.0
O B:ALA395 4.9 32.4 1.0

Calcium binding site 4 out of 4 in 3gri

Go back to Calcium Binding Sites List in 3gri
Calcium binding site 4 out of 4 in the The Crystal Structure of A Dihydroorotase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of A Dihydroorotase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:28.9
occ:1.00
 O B:HOH479 2.3 24.8 1.0
O B:HOH493 2.3 38.2 1.0
OE2 B:GLU104 2.5 28.2 1.0
OE1 B:GLU142 2.6 23.2 1.0
OE2 B:GLU142 2.6 23.3 1.0
CD B:GLU142 3.0 23.0 1.0
CD B:GLU104 3.5 27.0 1.0
CG B:GLU104 3.9 26.5 1.0
CG B:GLU142 4.5 22.5 1.0
O B:HOH457 4.5 38.5 1.0
O B:HOH586 4.6 31.3 1.0
OE1 B:GLU104 4.7 27.4 1.0
OE1 B:GLN107 4.7 34.2 1.0
NE2 B:GLN107 4.8 30.2 1.0

Reference:

J.S.Brunzelle, Z.Wawrzak, T.Skarina, O.Onopriyenko, A.Savchenko, W.F.Anderson. The Crystal Structure of A Dihydroorotase From Staphylococcus Aureus To Be Published.
Page generated: Sat Jul 13 10:46:32 2024

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