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Sodium in PDB 2x8j: Intracellular Subtilisin Precursor From B. Clausii

Enzymatic activity of Intracellular Subtilisin Precursor From B. Clausii

All present enzymatic activity of Intracellular Subtilisin Precursor From B. Clausii:
3.4.21.62;

Protein crystallography data

The structure of Intracellular Subtilisin Precursor From B. Clausii, PDB code: 2x8j was solved by J.Vedodova, M.Gamble, A.Ariza, E.Dodson, D.D.Jones, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.98 / 1.56
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 125.659, 125.659, 106.141, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 23

Sodium Binding Sites:

The binding sites of Sodium atom in the Intracellular Subtilisin Precursor From B. Clausii (pdb code 2x8j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Intracellular Subtilisin Precursor From B. Clausii, PDB code: 2x8j:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 2x8j

Go back to Sodium Binding Sites List in 2x8j
Sodium binding site 1 out of 6 in the Intracellular Subtilisin Precursor From B. Clausii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Intracellular Subtilisin Precursor From B. Clausii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1317

b:30.1
occ:1.00
 OD1 A:ASP58 2.3 31.4 1.0
O A:SER101 2.3 32.7 1.0
O A:ALA97 2.4 28.7 1.0
OG1 A:THR99 2.4 37.2 1.0
O A:VAL103 2.4 25.2 1.0
O A:HOH2099 2.5 39.4 1.0
CG A:ASP58 3.3 27.7 1.0
CB A:THR99 3.5 34.9 1.0
N A:THR99 3.5 35.1 1.0
C A:VAL103 3.5 23.1 1.0
C A:SER101 3.6 35.0 1.0
C A:ALA97 3.6 27.9 1.0
CG2 A:THR99 3.7 34.7 1.0
O A:HOH2094 3.8 32.8 1.0
N A:VAL103 3.8 27.9 1.0
OD2 A:ASP58 3.9 30.1 1.0
C A:GLY102 4.1 29.4 1.0
O A:HOH2100 4.1 51.9 1.0
CA A:THR99 4.1 35.9 1.0
CA A:GLY102 4.2 31.9 1.0
CB A:ASP58 4.3 28.0 1.0
CA A:VAL103 4.4 26.2 1.0
CA A:GLU98 4.4 30.9 1.0
C A:GLU98 4.4 33.2 1.0
N A:GLY102 4.4 32.9 1.0
N A:GLU98 4.4 29.6 1.0
N A:SER101 4.5 37.5 1.0
N A:VAL104 4.6 23.7 1.0
CA A:ALA97 4.6 27.6 1.0
CA A:SER101 4.7 36.8 1.0
N A:ALA97 4.7 25.1 1.0
CA A:ASP58 4.7 28.0 1.0
O A:GLY102 4.7 29.6 1.0
N A:GLY100 4.8 37.5 1.0
CA A:VAL104 4.8 23.7 1.0
C A:THR99 4.8 36.8 1.0

Sodium binding site 2 out of 6 in 2x8j

Go back to Sodium Binding Sites List in 2x8j
Sodium binding site 2 out of 6 in the Intracellular Subtilisin Precursor From B. Clausii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Intracellular Subtilisin Precursor From B. Clausii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1317

b:26.3
occ:1.00
 OD1 B:ASP58 2.3 28.6 1.0
O B:SER101 2.4 27.6 0.5
O B:ALA97 2.4 25.7 1.0
O B:SER101 2.4 27.8 0.5
O B:VAL103 2.4 22.7 1.0
OG1 B:THR99 2.4 35.4 1.0
O B:HOH2080 2.6 28.6 1.0
CG B:ASP58 3.3 27.6 1.0
C B:VAL103 3.5 25.6 1.0
CB B:THR99 3.5 31.4 1.0
C B:SER101 3.6 26.9 0.5
C B:SER101 3.6 26.8 0.5
N B:VAL103 3.6 25.6 1.0
C B:ALA97 3.6 24.9 1.0
N B:THR99 3.7 32.4 1.0
CG2 B:THR99 3.8 30.5 1.0
C B:GLY102 3.9 27.6 1.0
OD2 B:ASP58 3.9 31.1 1.0
O B:HOH2054 3.9 33.3 1.0
CA B:GLY102 4.0 27.2 1.0
CA B:VAL103 4.2 25.4 1.0
CB B:ASP58 4.2 26.3 1.0
CA B:THR99 4.2 32.4 1.0
N B:GLY102 4.2 27.3 1.0
CA B:GLU98 4.4 28.3 1.0
C B:GLU98 4.5 30.7 1.0
N B:GLU98 4.5 26.7 1.0
N B:VAL104 4.5 23.8 1.0
O B:GLY102 4.5 26.6 1.0
CA B:ASP58 4.6 27.0 1.0
N B:ALA97 4.7 24.9 1.0
CA B:ALA97 4.7 25.0 1.0
N B:SER101 4.7 27.3 0.5
N B:SER101 4.7 27.4 0.5
CA B:SER101 4.8 27.2 0.5
CA B:SER101 4.8 27.4 0.5
O B:HOH2081 4.8 43.5 1.0
CA B:VAL104 4.9 21.8 1.0
C B:THR99 4.9 32.8 1.0

Sodium binding site 3 out of 6 in 2x8j

Go back to Sodium Binding Sites List in 2x8j
Sodium binding site 3 out of 6 in the Intracellular Subtilisin Precursor From B. Clausii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Intracellular Subtilisin Precursor From B. Clausii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1317

b:23.0
occ:1.00
 OD1 C:ASP58 2.3 27.8 1.0
O C:VAL103 2.4 21.5 1.0
O C:ALA97 2.4 20.7 1.0
O C:SER101 2.4 25.9 1.0
OG1 C:THR99 2.4 29.9 1.0
O C:HOH2107 2.5 30.2 1.0
CG C:ASP58 3.2 24.4 1.0
C C:VAL103 3.5 23.0 1.0
C C:ALA97 3.6 22.4 1.0
CB C:THR99 3.6 29.6 1.0
C C:SER101 3.6 27.6 1.0
N C:VAL103 3.6 23.1 1.0
N C:THR99 3.7 27.2 1.0
OD2 C:ASP58 3.8 29.0 1.0
CG2 C:THR99 3.9 28.4 1.0
O C:HOH2059 3.9 34.6 1.0
C C:GLY102 4.0 22.5 1.0
CA C:VAL103 4.2 22.7 1.0
CB C:ASP58 4.2 21.1 1.0
CA C:THR99 4.3 29.2 1.0
CA C:GLY102 4.3 25.0 1.0
CA C:GLU98 4.3 24.2 1.0
N C:GLU98 4.4 22.5 1.0
N C:GLY102 4.4 24.8 1.0
C C:GLU98 4.4 25.8 1.0
N C:SER101 4.5 30.8 1.0
N C:VAL104 4.5 21.4 1.0
O C:GLY102 4.6 25.4 1.0
CA C:ALA97 4.7 20.3 1.0
N C:ALA97 4.7 19.2 1.0
CA C:SER101 4.7 30.1 1.0
CA C:ASP58 4.7 20.7 1.0
CA C:VAL104 4.8 20.5 1.0
N C:GLY100 4.9 31.8 1.0
C C:THR99 4.9 31.2 1.0

Sodium binding site 4 out of 6 in 2x8j

Go back to Sodium Binding Sites List in 2x8j
Sodium binding site 4 out of 6 in the Intracellular Subtilisin Precursor From B. Clausii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Intracellular Subtilisin Precursor From B. Clausii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1317

b:30.1
occ:1.00
 O D:VAL103 2.4 27.1 1.0
OG1 D:THR99 2.4 38.0 1.0
OD1 D:ASP58 2.4 35.5 1.0
O D:ALA97 2.4 29.8 1.0
O D:SER101 2.4 34.9 1.0
O D:HOH2073 2.5 31.9 1.0
C D:VAL103 3.4 28.8 1.0
CG D:ASP58 3.5 30.8 1.0
CB D:THR99 3.5 38.3 1.0
N D:THR99 3.6 36.9 1.0
C D:ALA97 3.6 30.6 1.0
C D:SER101 3.6 37.2 1.0
N D:VAL103 3.7 31.4 1.0
CG2 D:THR99 3.8 36.9 1.0
C D:GLY102 3.9 32.9 1.0
O D:HOH2070 4.0 33.7 1.0
OD2 D:ASP58 4.0 34.3 1.0
CG2 D:VAL104 4.1 30.1 1.0
CA D:VAL103 4.1 29.1 1.0
CA D:THR99 4.1 38.4 1.0
CA D:GLY102 4.2 35.0 1.0
C D:GLU98 4.2 34.9 1.0
CA D:GLU98 4.2 32.9 1.0
N D:GLY102 4.4 35.5 1.0
N D:VAL104 4.4 28.3 1.0
N D:GLU98 4.4 31.6 1.0
CB D:ASP58 4.6 34.3 1.0
O D:GLY102 4.6 33.8 1.0
N D:SER101 4.7 40.5 1.0
CA D:VAL104 4.7 28.2 1.0
CA D:ALA97 4.8 30.6 1.0
CA D:SER101 4.8 38.9 1.0
N D:ALA97 4.8 29.8 1.0
O D:HOH2074 4.9 40.4 1.0
C D:THR99 5.0 40.1 1.0
CA D:ASP58 5.0 33.4 1.0

Sodium binding site 5 out of 6 in 2x8j

Go back to Sodium Binding Sites List in 2x8j
Sodium binding site 5 out of 6 in the Intracellular Subtilisin Precursor From B. Clausii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Intracellular Subtilisin Precursor From B. Clausii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1317

b:19.0
occ:1.00
 OD1 E:ASP58 2.3 24.3 1.0
O E:ALA97 2.3 15.0 1.0
O E:VAL103 2.3 17.8 1.0
OG1 E:THR99 2.4 19.2 1.0
O E:HOH2098 2.4 20.6 1.0
O E:SER101 2.6 28.9 1.0
CG E:ASP58 3.4 24.1 1.0
C E:VAL103 3.4 17.4 1.0
C E:ALA97 3.5 16.4 1.0
CB E:THR99 3.6 19.2 1.0
N E:THR99 3.6 15.9 1.0
N E:VAL103 3.6 17.5 1.0
C E:SER101 3.9 23.2 1.0
CG2 E:THR99 4.0 20.0 1.0
CB E:ASP58 4.1 21.0 1.0
C E:GLY102 4.1 18.3 1.0
CA E:THR99 4.1 19.0 1.0
CA E:VAL103 4.2 17.8 1.0
CA E:GLY102 4.3 19.9 1.0
CA E:GLU98 4.3 16.9 1.0
C E:GLU98 4.4 18.7 1.0
N E:GLU98 4.4 16.4 1.0
OD2 E:ASP58 4.4 33.7 1.0
CA E:ASP58 4.4 21.2 1.0
N E:ALA97 4.4 16.1 1.0
N E:VAL104 4.5 16.7 1.0
CA E:ALA97 4.5 16.2 1.0
CG2 E:VAL104 4.5 21.9 1.0
N E:GLY102 4.6 21.4 1.0
O E:THR99 4.6 21.5 1.0
O E:HOH2019 4.7 34.3 1.0
O E:HOH2055 4.7 36.6 1.0
C E:THR99 4.7 19.3 1.0
CA E:VAL104 4.7 16.8 1.0
O E:GLY102 4.8 18.1 1.0
C E:ALA96 4.9 14.8 1.0
CB E:ALA96 4.9 14.3 1.0

Sodium binding site 6 out of 6 in 2x8j

Go back to Sodium Binding Sites List in 2x8j
Sodium binding site 6 out of 6 in the Intracellular Subtilisin Precursor From B. Clausii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Intracellular Subtilisin Precursor From B. Clausii within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1317

b:22.3
occ:1.00
 OD1 F:ASP58 2.3 25.4 1.0
O F:ALA97 2.4 19.9 1.0
O F:VAL103 2.4 22.0 1.0
O F:SER101 2.4 23.7 1.0
OG1 F:THR99 2.5 24.9 1.0
O F:HOH2119 2.6 21.5 1.0
CG F:ASP58 3.3 26.1 1.0
C F:VAL103 3.6 22.0 1.0
C F:ALA97 3.6 18.6 1.0
CB F:THR99 3.6 23.4 1.0
C F:SER101 3.6 25.5 1.0
N F:THR99 3.7 24.5 1.0
N F:VAL103 3.8 22.3 1.0
CG2 F:THR99 3.8 23.4 1.0
O F:HOH2074 3.9 29.2 1.0
C F:GLY102 4.0 24.0 1.0
OD2 F:ASP58 4.1 28.2 1.0
CA F:GLY102 4.2 24.4 1.0
CB F:ASP58 4.2 22.9 1.0
CA F:THR99 4.3 24.8 1.0
CA F:VAL103 4.3 22.7 1.0
N F:GLY102 4.4 23.0 1.0
CA F:GLU98 4.4 21.6 1.0
N F:GLU98 4.4 21.4 1.0
C F:GLU98 4.5 23.1 1.0
O F:HOH2120 4.6 39.1 1.0
N F:ALA97 4.6 19.6 1.0
CA F:ALA97 4.6 18.1 1.0
N F:SER101 4.6 25.6 1.0
N F:VAL104 4.6 21.3 1.0
O F:GLY102 4.6 24.3 1.0
CA F:ASP58 4.6 22.5 1.0
CA F:SER101 4.7 25.4 1.0
CA F:VAL104 4.8 20.9 1.0
N F:GLY100 5.0 26.4 1.0
C F:THR99 5.0 24.7 1.0

Reference:

J.Vevodova, M.Gamble, G.Kunze, A.Ariza, E.Dodson, D.D.Jones, K.S.Wilson. Crystal Structure of An Intracellular Subtilisin Reveals Novel Structural Features Unique to This Subtilisin Family. Structure V. 18 744 2010.
ISSN: ISSN 1878-4186
PubMed: 20541512
DOI: 10.1016/J.STR.2010.03.008
Page generated: Mon Oct 7 05:06:20 2024

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