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Calcium in PDB 6nbk: Crystal Structure of Arginase From Bacillus Cereus

Enzymatic activity of Crystal Structure of Arginase From Bacillus Cereus

All present enzymatic activity of Crystal Structure of Arginase From Bacillus Cereus:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Arginase From Bacillus Cereus, PDB code: 6nbk was solved by C.Chang, E.Evdokimova, M.Mcchesney, A.Joachimiak, A.Savchenko, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.44 / 1.91
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 148.022, 153.803, 83.137, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.3

Other elements in 6nbk:

The structure of Crystal Structure of Arginase From Bacillus Cereus also contains other interesting chemical elements:

Manganese (Mn) 14 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Arginase From Bacillus Cereus (pdb code 6nbk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Arginase From Bacillus Cereus, PDB code: 6nbk:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6nbk

Go back to Calcium Binding Sites List in 6nbk
Calcium binding site 1 out of 3 in the Crystal Structure of Arginase From Bacillus Cereus


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 Arginase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:26.2
occ:1.00
 O D:ASP275 2.4 9.0 1.0
O A:HOH448 2.5 8.8 1.0
O A:ASP275 2.5 8.0 1.0
O D:HOH503 2.5 8.5 1.0
O A:HOH523 2.5 9.3 1.0
O A:HOH648 2.5 11.8 1.0
C D:ASP275 3.6 12.1 1.0
C A:ASP275 3.7 10.6 1.0
O D:HOH476 4.0 10.2 1.0
O A:HOH516 4.0 10.0 1.0
CA A:GLU276 4.2 9.1 1.0
CA D:GLU276 4.2 11.2 1.0
O A:HOH656 4.3 25.4 1.0
N D:GLU276 4.3 11.7 1.0
O D:ILE273 4.3 9.2 1.0
N A:GLU276 4.4 9.2 1.0
O D:HOH490 4.4 29.4 1.0
O A:ILE273 4.4 8.3 1.0
N A:ARG277 4.6 10.1 1.0
O D:THR272 4.6 9.1 1.0
N D:ARG277 4.6 7.5 1.0
N D:ASP275 4.6 3.6 1.0
O A:THR272 4.6 8.5 1.0
N A:ASP275 4.7 4.9 1.0
CA D:ASP275 4.7 6.8 1.0
CA A:ASP275 4.8 9.8 1.0
C D:LEU274 4.9 11.4 1.0
C A:GLU276 5.0 12.6 1.0
C D:GLU276 5.0 7.8 1.0
O A:HOH670 5.0 31.1 1.0
C A:LEU274 5.0 8.4 1.0

Calcium binding site 2 out of 3 in 6nbk

Go back to Calcium Binding Sites List in 6nbk
Calcium binding site 2 out of 3 in the Crystal Structure of Arginase From Bacillus Cereus


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 Arginase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:28.2
occ:1.00
 O B:ASP275 2.4 11.4 1.0
O F:ASP275 2.5 10.0 1.0
O F:HOH636 2.5 13.8 1.0
O B:HOH493 2.5 10.6 1.0
O B:HOH435 2.5 9.0 1.0
O F:HOH487 2.5 9.5 1.0
C B:ASP275 3.6 15.2 1.0
C F:ASP275 3.7 14.8 1.0
O F:HOH527 3.9 10.4 1.0
O F:HOH658 4.0 24.4 1.0
O B:HOH501 4.1 11.0 1.0
CA B:GLU276 4.2 14.1 1.0
CA F:GLU276 4.2 10.2 1.0
O F:ILE273 4.3 10.3 1.0
N B:GLU276 4.4 9.9 1.0
N F:GLU276 4.4 9.3 1.0
O B:ILE273 4.4 6.5 1.0
O F:HOH558 4.4 28.5 1.0
N B:ARG277 4.5 9.3 1.0
O B:THR272 4.6 9.6 1.0
O F:THR272 4.6 9.1 1.0
N F:ASP275 4.6 9.2 1.0
N B:ASP275 4.7 8.7 1.0
N F:ARG277 4.7 10.1 1.0
CA B:ASP275 4.7 10.3 1.0
CA F:ASP275 4.8 8.5 1.0
O B:HOH630 4.8 33.3 1.0
O F:HOH664 4.9 36.6 1.0
C B:GLU276 4.9 10.3 1.0
C F:LEU274 5.0 9.3 1.0
C B:LEU274 5.0 15.0 1.0

Calcium binding site 3 out of 3 in 6nbk

Go back to Calcium Binding Sites List in 6nbk
Calcium binding site 3 out of 3 in the Crystal Structure of Arginase From Bacillus Cereus


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 Arginase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:27.0
occ:1.00
 O E:ASP275 2.4 11.4 1.0
O C:ASP275 2.4 8.7 1.0
O E:HOH437 2.4 11.7 1.0
O C:HOH447 2.5 12.0 1.0
O E:HOH599 2.5 12.2 1.0
O E:HOH469 2.5 12.9 1.0
C E:ASP275 3.6 14.0 1.0
C C:ASP275 3.6 12.4 1.0
O C:HOH492 4.0 9.9 1.0
O E:HOH501 4.0 9.7 1.0
O C:HOH594 4.1 26.6 1.0
CA E:GLU276 4.1 13.2 1.0
CA C:GLU276 4.2 10.8 1.0
O C:ILE273 4.3 9.0 1.0
N E:GLU276 4.3 12.9 1.0
N C:GLU276 4.3 12.5 1.0
O E:ILE273 4.4 9.7 1.0
O E:HOH620 4.4 27.0 1.0
N E:ARG277 4.5 6.8 1.0
O E:THR272 4.6 9.4 1.0
O C:THR272 4.6 9.9 1.0
N C:ASP275 4.6 7.7 1.0
N C:ARG277 4.6 7.6 1.0
N E:ASP275 4.7 7.5 1.0
CA E:ASP275 4.7 8.8 1.0
CA C:ASP275 4.7 9.0 1.0
C E:GLU276 4.9 12.0 1.0
C C:LEU274 5.0 12.1 1.0
C E:LEU274 5.0 13.6 1.0
C C:GLU276 5.0 9.3 1.0

Reference:

C.Chang, E.Evdokimova, M.Mcchesney, A.Joachimiak. Crystal Structure of Arginase From Bacillus Cereus To Be Published.
Page generated: Wed Jul 9 16:19:30 2025

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