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Sodium in PDB 2wwt: 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: 2wwt was solved by J.Vevodova, 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) 105.57 / 2.68
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 121.640, 121.640, 106.201, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 25.2

Sodium Binding Sites:

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

Sodium binding site 1 out of 5 in 2wwt

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Sodium binding site 1 out of 5 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
B:Na401

b:37.8
occ:1.00
 O B:ALA97 2.2 46.8 1.0
O B:VAL103 2.4 44.2 1.0
OG1 B:THR99 2.5 53.6 1.0
O B:SER101 2.6 51.6 1.0
OD1 B:ASP58 2.6 50.9 1.0
N B:THR99 3.3 52.1 1.0
C B:ALA97 3.3 46.3 1.0
C B:VAL103 3.5 43.7 1.0
CB B:THR99 3.6 54.9 1.0
C B:SER101 3.7 53.0 1.0
CG B:ASP58 3.7 48.1 1.0
N B:VAL103 3.7 47.3 1.0
CG2 B:THR99 4.0 54.2 1.0
CA B:THR99 4.0 54.2 1.0
CA B:GLU98 4.1 47.9 1.0
N B:GLU98 4.1 47.1 1.0
C B:GLU98 4.1 51.1 1.0
N B:SER101 4.3 54.2 1.0
CA B:VAL103 4.3 44.5 1.0
N B:ALA97 4.3 43.7 1.0
CB B:ASP58 4.4 46.7 1.0
CA B:ALA97 4.4 44.7 1.0
C B:GLY102 4.5 49.1 1.0
N B:VAL104 4.5 41.8 1.0
CA B:SER101 4.5 54.8 1.0
N B:GLY102 4.6 53.3 1.0
N B:GLY100 4.7 54.4 1.0
OD2 B:ASP58 4.7 49.8 1.0
CA B:GLY102 4.7 51.6 1.0
CA B:VAL104 4.7 40.9 1.0
CB B:VAL104 4.7 41.7 1.0
C B:THR99 4.7 55.2 1.0
CA B:ASP58 4.7 48.1 1.0
C B:ALA96 4.9 41.3 1.0
CB B:SER101 4.9 56.7 1.0

Sodium binding site 2 out of 5 in 2wwt

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Sodium binding site 2 out of 5 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
C:Na401

b:22.2
occ:1.00
 O C:HOH2002 2.3 25.2 1.0
O C:ALA97 2.3 29.6 1.0
OD1 C:ASP58 2.4 33.3 1.0
O C:VAL103 2.4 29.1 1.0
O C:SER101 2.5 35.2 1.0
OG1 C:THR99 2.9 34.8 1.0
CG C:ASP58 3.3 30.8 1.0
N C:VAL103 3.3 29.9 1.0
C C:VAL103 3.4 27.9 1.0
C C:ALA97 3.6 29.6 1.0
C C:SER101 3.6 35.5 1.0
N C:THR99 3.7 32.8 1.0
OD2 C:ASP58 3.9 31.5 1.0
CB C:THR99 3.9 33.9 1.0
C C:GLY102 4.0 32.0 1.0
CG2 C:THR99 4.1 31.5 1.0
CA C:VAL103 4.1 28.0 1.0
CA C:GLY102 4.2 32.8 1.0
N C:VAL104 4.3 27.2 1.0
CB C:ASP58 4.3 28.3 1.0
N C:GLY102 4.4 34.6 1.0
CA C:THR99 4.4 33.9 1.0
N C:ALA97 4.4 29.4 1.0
N C:GLU98 4.4 29.7 1.0
CA C:GLU98 4.5 30.5 1.0
N C:SER101 4.5 36.7 1.0
CA C:VAL104 4.5 26.2 1.0
CA C:ALA97 4.6 28.9 1.0
C C:GLU98 4.6 31.9 1.0
N C:GLY100 4.7 35.3 1.0
CA C:ASP58 4.7 29.1 1.0
CA C:SER101 4.7 36.4 1.0
C C:ALA96 4.8 29.2 1.0
CB C:VAL104 4.8 26.9 1.0
O C:GLY102 5.0 32.9 1.0

Sodium binding site 3 out of 5 in 2wwt

Go back to Sodium Binding Sites List in 2wwt
Sodium binding site 3 out of 5 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
D:Na401

b:37.4
occ:1.00
 O D:VAL103 2.2 40.9 1.0
OD1 D:ASP58 2.4 51.4 1.0
O D:SER101 2.5 49.9 1.0
O D:ALA97 2.5 43.7 1.0
OG1 D:THR99 2.5 50.5 1.0
CG D:ASP58 3.3 45.5 1.0
C D:VAL103 3.3 40.2 1.0
N D:VAL103 3.4 43.5 1.0
N D:THR99 3.5 49.7 1.0
C D:ALA97 3.7 42.3 1.0
CB D:THR99 3.7 51.4 1.0
C D:SER101 3.7 51.2 1.0
OD2 D:ASP58 3.8 46.1 1.0
CA D:VAL103 3.9 41.1 1.0
CG2 D:THR99 4.1 48.3 1.0
CA D:THR99 4.1 51.6 1.0
C D:GLY102 4.2 45.8 1.0
CB D:ASP58 4.3 41.9 1.0
N D:VAL104 4.3 38.9 1.0
CA D:GLU98 4.4 45.5 1.0
C D:GLU98 4.4 48.2 1.0
CA D:GLY102 4.4 48.3 1.0
N D:GLU98 4.4 43.6 1.0
N D:SER101 4.5 54.9 1.0
N D:GLY102 4.5 50.9 1.0
CA D:ASP58 4.6 42.3 1.0
N D:ALA97 4.7 36.9 1.0
CA D:VAL104 4.7 37.1 1.0
CA D:SER101 4.7 54.0 1.0
CA D:ALA97 4.7 39.5 1.0
C D:THR99 4.7 54.0 1.0
N D:GLY100 4.8 53.8 1.0

Sodium binding site 4 out of 5 in 2wwt

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Sodium binding site 4 out of 5 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
E:Na401

b:33.2
occ:1.00
 O E:VAL103 2.2 40.8 1.0
OD1 E:ASP58 2.3 46.2 1.0
O E:ALA97 2.5 42.5 1.0
O E:SER101 2.5 46.7 1.0
OG1 E:THR99 2.7 51.0 1.0
N E:THR99 3.2 48.1 1.0
CG E:ASP58 3.3 44.0 1.0
C E:VAL103 3.3 40.1 1.0
N E:VAL103 3.5 42.4 1.0
C E:ALA97 3.7 41.9 1.0
C E:SER101 3.7 47.6 1.0
OD2 E:ASP58 3.8 47.3 1.0
CA E:GLU98 3.8 44.9 1.0
CB E:THR99 3.9 51.0 1.0
C E:GLY102 4.0 43.9 1.0
C E:GLU98 4.0 47.2 1.0
CA E:VAL103 4.0 40.9 1.0
CA E:THR99 4.1 50.7 1.0
N E:GLU98 4.2 43.2 1.0
CG2 E:THR99 4.3 50.7 1.0
N E:VAL104 4.3 38.9 1.0
CA E:GLY102 4.4 45.1 1.0
CB E:ASP58 4.4 41.6 1.0
N E:SER101 4.5 50.4 1.0
N E:GLY102 4.5 47.3 1.0
O E:GLY102 4.5 44.2 1.0
CA E:VAL104 4.6 38.4 1.0
N E:GLY100 4.6 51.6 1.0
CA E:SER101 4.8 49.6 1.0
CA E:ALA97 4.9 40.0 1.0
C E:THR99 4.9 52.4 1.0
CA E:ASP58 4.9 42.4 1.0
CB E:VAL104 4.9 39.1 1.0
N E:ALA97 5.0 37.7 1.0

Sodium binding site 5 out of 5 in 2wwt

Go back to Sodium Binding Sites List in 2wwt
Sodium binding site 5 out of 5 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
F:Na401

b:44.5
occ:1.00
 O F:ALA97 2.4 52.9 1.0
O F:SER101 2.4 52.0 1.0
OD1 F:ASP58 2.4 47.6 1.0
O F:VAL103 2.5 44.0 1.0
OG1 F:THR99 2.5 54.9 1.0
N F:VAL103 3.3 46.6 1.0
N F:THR99 3.3 55.3 1.0
C F:VAL103 3.3 43.2 1.0
CG F:ASP58 3.4 47.3 1.0
C F:SER101 3.6 52.8 1.0
C F:ALA97 3.6 51.9 1.0
CB F:THR99 3.7 57.6 1.0
C F:GLY102 3.8 48.1 1.0
OD2 F:ASP58 3.8 48.7 1.0
CA F:VAL103 3.9 44.1 1.0
CA F:GLY102 4.0 50.3 1.0
CA F:THR99 4.0 57.2 1.0
N F:GLY102 4.2 52.3 1.0
N F:VAL104 4.3 41.9 1.0
C F:GLU98 4.3 55.4 1.0
CA F:GLU98 4.3 53.5 1.0
CG2 F:THR99 4.4 57.0 1.0
N F:GLU98 4.4 52.5 1.0
N F:ALA97 4.6 49.2 1.0
CA F:VAL104 4.6 42.2 1.0
CB F:ASP58 4.6 47.3 1.0
O F:GLY102 4.7 48.0 1.0
N F:SER101 4.7 55.9 1.0
CA F:ALA97 4.7 50.9 1.0
CA F:SER101 4.7 54.8 1.0
C F:THR99 4.8 58.5 1.0
N F:GLY100 4.9 57.2 1.0
CB F:VAL104 4.9 42.5 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 0969-2126
PubMed: 20541512
DOI: 10.1016/J.STR.2010.03.008
Page generated: Mon Oct 7 04:58:55 2024

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