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Calcium in PDB 7y6m: Intracellular Subtilisin From Bacillus Sp.

Protein crystallography data

The structure of Intracellular Subtilisin From Bacillus Sp., PDB code: 7y6m was solved by N.Hussin, H.Jamaluddin, M.A.Jonet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.05 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.057, 78.778, 113.19, 90, 90, 90
R / Rfree (%) 18.9 / 26.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Intracellular Subtilisin From Bacillus Sp. (pdb code 7y6m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Intracellular Subtilisin From Bacillus Sp., PDB code: 7y6m:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7y6m

Go back to Calcium Binding Sites List in 7y6m
Calcium binding site 1 out of 4 in the Intracellular Subtilisin From Bacillus Sp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Intracellular Subtilisin From Bacillus Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:52.0
occ:1.00
 OE1 C:GLU205 2.8 39.2 1.0
OD2 C:ASP198 2.9 42.0 1.0
OE2 C:GLU205 3.2 46.6 1.0
O C:ASP200 3.2 41.9 1.0
N C:ASP198 3.2 36.9 1.0
O C:THR203 3.3 44.4 1.0
CD C:GLU205 3.4 36.1 1.0
CG C:ASP198 3.6 41.0 1.0
N C:GLY199 3.7 39.1 1.0
CA C:GLY197 3.8 32.3 1.0
CB C:ALA233 3.9 27.4 1.0
OG1 C:THR203 4.0 44.2 1.0
C C:GLY197 4.0 41.6 1.0
N C:ALA233 4.1 33.3 1.0
CA C:ASP198 4.1 37.7 1.0
C C:ASP200 4.1 46.4 1.0
N C:ASP200 4.2 39.7 1.0
O C:SER231 4.2 24.8 1.0
CB C:ASP198 4.3 35.9 1.0
OD1 C:ASP198 4.4 44.9 1.0
C C:ASP198 4.4 47.6 1.0
C C:THR203 4.5 45.4 1.0
CA C:ALA233 4.6 29.9 1.0
C C:GLY199 4.6 41.3 1.0
CA C:GLY199 4.7 31.0 1.0
CA C:ASP200 4.7 44.9 1.0
CD2 C:LEU309 4.8 25.8 1.0
CG C:GLU205 4.8 30.4 1.0
O C:HOH529 4.9 29.6 1.0
C C:ASN232 4.9 34.2 1.0

Calcium binding site 2 out of 4 in 7y6m

Go back to Calcium Binding Sites List in 7y6m
Calcium binding site 2 out of 4 in the Intracellular Subtilisin From Bacillus Sp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Intracellular Subtilisin From Bacillus Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:20.3
occ:1.00
 O4 C:PEG401 2.2 27.0 1.0
O2 C:PEG401 2.3 21.1 1.0
O C:VAL215 2.4 21.6 1.0
O C:ASN213 2.5 18.0 1.0
OD1 C:ASP238 2.5 13.5 1.0
C4 C:PEG401 2.7 23.8 1.0
C3 C:PEG401 2.7 22.1 1.0
OD2 C:ASP238 2.7 18.6 1.0
CG C:ASP238 3.0 17.6 1.0
C C:ASN213 3.6 16.4 1.0
C2 C:PEG401 3.6 23.8 1.0
C C:VAL215 3.6 18.2 1.0
O C:GLU236 4.0 17.9 1.0
CA C:ASN213 4.2 16.9 1.0
O C:TYR212 4.2 19.0 1.0
N C:VAL215 4.3 16.2 1.0
C C:GLU214 4.3 17.8 1.0
OE1 C:GLU236 4.4 20.9 1.0
O C:GLU214 4.5 22.9 1.0
CB C:ASP238 4.5 18.9 1.0
N C:ALA217 4.5 17.6 1.0
N C:ILE216 4.5 15.3 1.0
CA C:ILE216 4.5 18.8 1.0
CA C:VAL215 4.6 17.2 1.0
N C:GLU214 4.6 16.0 1.0
CG C:ASN213 4.8 15.6 1.0
C1 C:PEG401 4.8 29.6 1.0
CA C:GLU214 4.8 20.6 1.0
OH C:TYR293 4.8 19.8 1.0
O D:HOH519 4.8 17.3 1.0
ND2 C:ASN213 4.8 17.7 1.0
OD1 C:ASN213 4.9 17.3 1.0
C C:GLU236 4.9 17.3 1.0
O D:HOH517 4.9 19.2 1.0

Calcium binding site 3 out of 4 in 7y6m

Go back to Calcium Binding Sites List in 7y6m
Calcium binding site 3 out of 4 in the Intracellular Subtilisin From Bacillus Sp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Intracellular Subtilisin From Bacillus Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:48.2
occ:1.00
 OE2 D:GLU205 2.6 22.5 1.0
OD1 D:ASP198 2.6 33.5 1.0
O D:ASP200 2.9 22.4 1.0
N D:ASP198 3.2 21.6 1.0
OE1 D:GLU205 3.2 19.8 1.0
CD D:GLU205 3.2 20.5 1.0
OG1 D:THR203 3.3 21.1 1.0
O D:THR203 3.3 24.0 1.0
N D:ASP200 3.4 24.4 1.0
C D:ASP200 3.6 26.2 1.0
CG D:ASP198 3.6 26.6 1.0
CB D:ALA233 3.9 17.0 1.0
N D:GLY199 3.9 27.1 1.0
C D:ASP198 3.9 26.4 1.0
CA D:ASP198 3.9 27.8 1.0
CA D:ASP200 4.0 22.6 1.0
CA D:GLY197 4.0 20.9 1.0
C D:GLY197 4.1 19.1 1.0
CB D:ASP198 4.3 22.0 1.0
C D:GLY199 4.3 28.6 1.0
OD2 D:ASP198 4.4 29.8 1.0
C D:THR203 4.4 19.9 1.0
CB D:ASP200 4.4 25.0 1.0
O D:ASP198 4.5 26.0 1.0
N D:GLU201 4.6 25.3 1.0
CA D:GLY199 4.6 23.9 1.0
CB D:THR203 4.6 25.6 1.0
N D:ALA233 4.7 25.1 1.0
CG D:GLU205 4.7 22.6 1.0
CD2 D:LEU309 4.8 28.9 1.0
O D:SER231 4.8 25.0 1.0
CA D:ALA233 4.9 21.7 1.0
CA D:THR203 5.0 23.8 1.0

Calcium binding site 4 out of 4 in 7y6m

Go back to Calcium Binding Sites List in 7y6m
Calcium binding site 4 out of 4 in the Intracellular Subtilisin From Bacillus Sp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Intracellular Subtilisin From Bacillus Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca403

b:38.6
occ:1.00
 O1 D:PEG401 2.2 20.4 1.0
O2 D:PEG401 2.5 28.9 1.0
O D:VAL215 2.5 27.8 1.0
C2 D:PEG401 2.5 23.9 1.0
C3 D:PEG401 2.5 25.8 1.0
O D:ASN213 2.5 21.6 1.0
C1 D:PEG401 2.6 26.1 1.0
OD2 D:ASP238 2.7 22.0 1.0
C D:VAL215 3.1 20.1 1.0
CG D:ASP238 3.3 21.6 1.0
OD1 D:ASP238 3.3 19.4 1.0
N D:ILE216 3.5 23.4 1.0
CA D:ILE216 3.6 21.7 1.0
C D:ASN213 3.7 21.2 1.0
C4 D:PEG401 3.8 26.1 1.0
N D:VAL215 3.9 24.7 1.0
C D:GLU214 3.9 20.8 1.0
O D:GLU214 4.0 19.5 1.0
CA D:VAL215 4.1 22.3 1.0
N D:ALA217 4.4 22.0 1.0
CG1 D:ILE216 4.5 18.6 1.0
O4 D:PEG401 4.5 28.9 1.0
C D:ILE216 4.6 26.2 1.0
CA D:GLU214 4.6 20.6 1.0
N D:GLU214 4.6 17.2 1.0
CA D:ASN213 4.6 19.4 1.0
CB D:ILE216 4.7 20.3 1.0
O D:TYR212 4.7 33.1 1.0
CB D:ASP238 4.7 22.1 1.0
OH D:TYR293 4.7 24.9 1.0
CE1 D:TYR293 4.8 16.8 1.0

Reference:

N.Hussin, H.Jamaluddin, M.A.Jonet. Intracellular Subtilisin From Bacillus Sp. To Be Published.
Page generated: Thu Jul 10 02:36:01 2025

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