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Calcium in PDB 3njh: D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis.

Protein crystallography data

The structure of D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis., PDB code: 3njh was solved by J.Osipiuk, R.Mulligan, M.Bargassa, F.Collart, A.Joachimiak, Midwest Centerfor Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.30 / 1.94
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 97.986, 97.986, 65.844, 90.00, 90.00, 120.00
R / Rfree (%) 12.7 / 15.2

Other elements in 3njh:

The structure of D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis. also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis. (pdb code 3njh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis., PDB code: 3njh:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3njh

Go back to Calcium Binding Sites List in 3njh
Calcium binding site 1 out of 4 in the D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:37.1
occ:1.00
 OD1 A:ASP89 2.0 18.5 1.0
OD1 A:ASP91 2.0 26.1 1.0
O A:HOH180 2.4 23.8 1.0
O A:GLY71 2.4 19.5 1.0
O A:ILE72 2.6 21.0 1.0
OD2 A:ASP74 2.7 19.6 1.0
CG A:ASP89 3.0 18.8 1.0
OD1 A:ASP74 3.0 13.6 1.0
CG A:ASP74 3.2 17.0 1.0
CG A:ASP91 3.3 25.6 1.0
C A:ILE72 3.5 19.1 1.0
OD2 A:ASP89 3.5 26.4 1.0
C A:GLY71 3.6 19.2 1.0
CA A:ILE72 3.8 18.5 1.0
N A:ASP91 3.8 21.7 1.0
OD2 A:ASP91 4.0 29.4 1.0
O A:HOH165 4.0 29.9 1.0
CB A:ASP89 4.1 17.9 1.0
N A:ILE72 4.2 18.7 1.0
O A:ASP91 4.2 19.4 1.0
CA A:ASP89 4.2 17.5 1.0
N A:LEU90 4.3 18.6 1.0
C A:ASP91 4.3 21.8 1.0
CA A:ASP91 4.3 22.1 1.0
CB A:THR93 4.3 24.2 1.0
CB A:ASP91 4.3 22.6 1.0
N A:THR93 4.5 23.7 1.0
N A:ILE73 4.6 18.4 1.0
CB A:ASP74 4.6 15.8 1.0
C A:ASP89 4.6 17.6 1.0
N A:ASP74 4.7 16.9 1.0
O A:THR93 4.7 21.8 1.0
CA A:GLY71 4.7 19.6 1.0
C A:LEU90 4.8 20.2 1.0
C A:ILE73 4.9 17.6 1.0
CA A:THR93 4.9 23.6 1.0
CA A:ILE73 4.9 18.0 1.0
OG1 A:THR93 5.0 23.5 1.0

Calcium binding site 2 out of 4 in 3njh

Go back to Calcium Binding Sites List in 3njh
Calcium binding site 2 out of 4 in the D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:32.3
occ:1.00
 OD1 B:ASP89 2.3 13.1 1.0
O B:HOH131 2.4 18.7 1.0
OD1 B:ASP91 2.4 21.7 1.0
O B:ILE72 2.4 19.1 1.0
OD2 B:ASP74 2.5 14.2 1.0
O B:GLY71 2.5 18.8 1.0
OD1 B:ASP74 3.0 13.4 1.0
CG B:ASP74 3.0 15.8 1.0
CG B:ASP89 3.1 15.9 1.0
C B:ILE72 3.3 18.4 1.0
C B:GLY71 3.6 18.7 1.0
CG B:ASP91 3.6 21.9 1.0
OD2 B:ASP89 3.7 21.4 1.0
CA B:ILE72 3.7 18.5 1.0
N B:ASP91 4.0 18.0 1.0
N B:ILE72 4.1 18.4 1.0
CB B:ASP89 4.1 14.4 1.0
N B:LEU90 4.1 15.3 1.0
CA B:ASP89 4.2 14.0 1.0
O B:ASP91 4.3 18.2 1.0
OD2 B:ASP91 4.4 26.4 1.0
C B:ASP91 4.4 18.8 1.0
CB B:THR93 4.4 17.1 1.0
CB B:ASP74 4.4 15.2 1.0
N B:ILE73 4.5 17.8 1.0
CA B:ASP91 4.5 19.1 1.0
C B:ASP89 4.5 13.9 1.0
N B:ASP74 4.5 15.4 1.0
CB B:ASP91 4.5 19.3 1.0
N B:THR93 4.7 17.4 1.0
C B:ILE73 4.7 16.0 1.0
OG1 B:THR93 4.8 18.3 1.0
CA B:GLY71 4.8 19.5 1.0
O B:THR93 4.8 16.4 1.0
CA B:ILE73 4.8 16.7 1.0
C B:LEU90 4.9 17.7 1.0

Calcium binding site 3 out of 4 in 3njh

Go back to Calcium Binding Sites List in 3njh
Calcium binding site 3 out of 4 in the D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:35.8
occ:1.00
 O C:HOH235 2.2 34.3 1.0
OD1 C:ASP91 2.4 21.2 1.0
OD2 C:ASP74 2.4 16.6 1.0
O C:GLY71 2.4 17.1 1.0
OD1 C:ASP89 2.5 30.4 1.0
OD1 C:ASP74 2.6 17.9 1.0
O C:ILE72 2.7 18.3 1.0
CG C:ASP74 2.8 17.0 1.0
CG C:ASP91 3.3 26.6 1.0
C C:GLY71 3.3 17.3 1.0
O C:HOH216 3.5 21.3 1.0
C C:ILE72 3.6 17.8 1.0
OD2 C:ASP91 3.6 27.4 1.0
CG C:ASP89 3.7 26.2 1.0
CA C:ILE72 3.9 17.1 1.0
N C:ILE72 4.0 17.2 1.0
OG1 C:THR93 4.2 27.9 1.0
OD2 C:ASP89 4.2 27.7 1.0
CB C:THR93 4.2 27.1 1.0
CB C:ASP74 4.3 16.4 1.0
CA C:GLY71 4.3 18.0 1.0
N C:ASP91 4.3 26.8 1.0
N C:THR93 4.5 26.6 1.0
CB C:ASP91 4.6 26.4 1.0
C C:ASP91 4.6 26.7 1.0
N C:ILE73 4.7 16.7 1.0
N C:LEU90 4.7 26.2 1.0
O C:ASP91 4.7 26.2 1.0
N C:ASP74 4.7 16.9 1.0
CA C:ASP91 4.7 26.8 1.0
C C:ILE73 4.8 17.5 1.0
O C:THR93 4.8 25.4 1.0
CB C:ASP89 4.8 25.6 1.0
CA C:ASP89 4.9 24.8 1.0
CA C:THR93 4.9 26.7 1.0
CA C:ASP74 4.9 17.5 1.0

Calcium binding site 4 out of 4 in 3njh

Go back to Calcium Binding Sites List in 3njh
Calcium binding site 4 out of 4 in the D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of D37A Mutant of SO1698 Protein, An Aspartic Peptidase From Shewanella Oneidensis. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca504

b:31.9
occ:1.00
 OD1 D:ASP91 2.2 17.8 1.0
OD1 D:ASP89 2.3 22.4 1.0
O D:GLY71 2.3 16.9 1.0
OD2 D:ASP74 2.4 20.3 1.0
O D:HOH128 2.5 27.1 1.0
O D:ILE72 2.5 13.5 1.0
OD1 D:ASP74 2.7 22.9 1.0
CG D:ASP74 2.9 21.7 1.0
CG D:ASP91 3.2 20.1 1.0
C D:GLY71 3.4 17.0 1.0
CG D:ASP89 3.4 23.1 1.0
C D:ILE72 3.5 15.8 1.0
OD2 D:ASP91 3.6 19.9 1.0
CA D:ILE72 3.8 15.0 1.0
OD2 D:ASP89 3.9 20.3 1.0
N D:ILE72 4.0 16.3 1.0
N D:ASP91 4.2 22.8 1.0
CB D:ASP74 4.3 18.8 1.0
CB D:THR93 4.4 22.8 1.0
CA D:GLY71 4.4 18.2 1.0
N D:LEU90 4.5 22.1 1.0
CB D:ASP91 4.5 21.4 1.0
N D:THR93 4.5 22.6 1.0
OG1 D:THR93 4.6 21.6 1.0
C D:ASP91 4.6 22.1 1.0
CB D:ASP89 4.6 21.8 1.0
CA D:ASP89 4.6 21.6 1.0
CA D:ASP91 4.6 21.8 1.0
N D:ILE73 4.7 16.3 1.0
N D:ASP74 4.7 17.3 1.0
O D:ASP91 4.8 22.0 1.0
C D:ILE73 4.8 17.2 1.0
O D:THR93 4.8 23.0 1.0
O D:HOH300 4.9 27.2 1.0
N D:LYS92 4.9 22.6 1.0
CA D:THR93 5.0 22.5 1.0
C D:ASP89 5.0 21.6 1.0
CA D:ASP74 5.0 19.1 1.0
CA D:ILE73 5.0 16.6 1.0

Reference:

J.Osipiuk, R.Mulligan, M.Bargassa, J.E.Hamilton, M.A.Cunningham, A.Joachimiak. Characterization of Member of DUF1888 Protein Family, Self-Cleaving and Self-Assembling Endopeptidase. J.Biol.Chem. V. 287 19452 2012.
ISSN: ISSN 0021-9258
PubMed: 22493430
DOI: 10.1074/JBC.M112.358069
Page generated: Sat Jul 13 14:59:59 2024

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