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Sodium in PDB 1y9z: Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.14 Nm Resolution

Protein crystallography data

The structure of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.14 Nm Resolution, PDB code: 1y9z was solved by D.Dong, K.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.58 / 1.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 122.090, 138.320, 64.790, 90.00, 97.49, 90.00
R / Rfree (%) 19.7 / 20.7

Other elements in 1y9z:

The structure of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.14 Nm Resolution also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.14 Nm Resolution (pdb code 1y9z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.14 Nm Resolution, PDB code: 1y9z:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1y9z

Go back to Sodium Binding Sites List in 1y9z
Sodium binding site 1 out of 4 in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.14 Nm Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.14 Nm Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:8.8
occ:1.00
O A:VAL174 2.2 10.0 1.0
O A:TYR171 2.3 10.9 1.0
O A:ALA169 2.4 8.9 1.0
NA A:NA608 2.4 17.1 1.0
OE1 A:GLN195 2.4 11.1 1.0
C A:TYR171 3.4 10.3 1.0
C A:VAL174 3.4 9.9 1.0
C A:ALA169 3.5 8.2 1.0
O A:HOH770 3.6 20.2 1.0
CD A:GLN195 3.6 10.1 1.0
N A:TYR171 3.7 9.7 1.0
C A:SER170 3.8 9.8 1.0
CA A:SER170 4.0 8.3 1.0
N A:SER176 4.0 8.9 1.0
N A:VAL174 4.1 10.1 1.0
CA A:VAL174 4.2 10.4 1.0
CB A:SER176 4.2 9.5 1.0
N A:SER170 4.2 8.4 1.0
N A:ASP172 4.2 11.1 1.0
CA A:ASP172 4.3 11.5 1.0
CA A:TYR171 4.3 9.5 1.0
CB A:GLN195 4.3 8.9 1.0
O A:SER170 4.3 11.0 1.0
CB A:VAL174 4.3 9.3 1.0
CG A:GLN195 4.4 9.7 1.0
N A:MET175 4.4 9.4 1.0
NH1 A:ARG395 4.4 12.4 1.0
O A:GLN195 4.4 9.4 1.0
C A:ASP172 4.5 11.3 1.0
C A:MET175 4.5 9.8 1.0
CA A:MET175 4.6 9.2 1.0
OE1 A:GLU197 4.6 15.4 1.0
NE2 A:GLN195 4.6 11.1 1.0
CA A:SER176 4.7 8.9 1.0
CA A:ALA169 4.7 8.3 1.0
O A:ASP172 4.7 11.6 1.0
O A:PRO168 4.8 9.1 1.0

Sodium binding site 2 out of 4 in 1y9z

Go back to Sodium Binding Sites List in 1y9z
Sodium binding site 2 out of 4 in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.14 Nm Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.14 Nm Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na608

b:17.1
occ:1.00
NA A:NA607 2.4 8.8 1.0
O A:GLN195 2.6 9.4 1.0
OE1 A:GLU197 2.8 15.4 1.0
O A:VAL174 3.0 10.0 1.0
N A:SER176 3.0 8.9 1.0
OE1 A:GLN195 3.3 11.1 1.0
CB A:SER176 3.5 9.5 1.0
O A:HOH770 3.5 20.2 1.0
C A:GLN195 3.7 9.5 1.0
O A:HOH769 3.7 20.5 1.0
CB A:GLU197 3.7 13.0 1.0
CA A:SER176 3.8 8.9 1.0
CD A:GLU197 3.9 14.7 1.0
O A:ALA169 3.9 8.9 1.0
C A:MET175 3.9 9.8 1.0
CA A:MET175 3.9 9.2 1.0
NH1 A:ARG395 4.0 12.4 1.0
C A:VAL174 4.1 9.9 1.0
CB A:GLN195 4.2 8.9 1.0
CA A:GLN195 4.2 9.4 1.0
CD A:GLN195 4.3 10.1 1.0
CG A:GLU197 4.3 14.4 1.0
N A:GLU197 4.4 10.7 1.0
N A:MET175 4.5 9.4 1.0
O A:TYR171 4.6 10.9 1.0
O A:SER176 4.7 9.1 1.0
CA A:GLU197 4.7 10.8 1.0
N A:VAL196 4.7 9.7 1.0
OG A:SER176 4.8 9.9 1.0
C A:SER176 4.8 8.9 1.0
C A:VAL196 4.8 10.1 1.0
NH1 A:ARG410 4.8 15.8 1.0
CG A:GLN195 4.9 9.7 1.0
OE2 A:GLU197 4.9 16.5 1.0

Sodium binding site 3 out of 4 in 1y9z

Go back to Sodium Binding Sites List in 1y9z
Sodium binding site 3 out of 4 in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.14 Nm Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.14 Nm Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na609

b:7.2
occ:1.00
O B:VAL174 2.3 7.4 1.0
NA B:NA610 2.3 15.7 1.0
OE1 B:GLN195 2.3 9.4 1.0
O B:TYR171 2.3 8.4 1.0
O B:ALA169 2.4 6.9 1.0
C B:TYR171 3.4 8.7 1.0
C B:VAL174 3.4 6.4 1.0
O B:HOH884 3.5 19.5 1.0
C B:ALA169 3.5 6.7 1.0
CD B:GLN195 3.5 9.6 1.0
N B:TYR171 3.7 8.0 1.0
C B:SER170 3.8 8.1 1.0
CA B:SER170 4.0 7.6 1.0
N B:SER176 4.0 6.9 1.0
N B:VAL174 4.1 7.5 1.0
CA B:VAL174 4.2 7.4 1.0
N B:SER170 4.2 7.1 1.0
CB B:SER176 4.2 7.4 1.0
N B:ASP172 4.2 8.1 1.0
CA B:TYR171 4.3 7.4 1.0
CA B:ASP172 4.3 9.3 1.0
CB B:GLN195 4.3 8.8 1.0
CB B:VAL174 4.3 7.3 1.0
CG B:GLN195 4.3 9.2 1.0
NH1 B:ARG395 4.4 8.9 1.0
O B:SER170 4.4 9.8 1.0
N B:MET175 4.4 6.9 1.0
O B:GLN195 4.4 8.8 1.0
C B:ASP172 4.5 7.5 1.0
C B:MET175 4.5 6.3 1.0
NE2 B:GLN195 4.5 11.4 1.0
OE2 B:GLU197 4.5 12.7 1.0
CA B:MET175 4.6 7.1 1.0
CA B:SER176 4.7 6.4 1.0
CA B:ALA169 4.7 6.5 1.0
O B:ASP172 4.7 8.7 1.0
O B:PRO168 4.9 8.1 1.0
N B:SER173 5.0 7.7 1.0

Sodium binding site 4 out of 4 in 1y9z

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Sodium binding site 4 out of 4 in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.14 Nm Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.14 Nm Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na610

b:15.7
occ:1.00
NA B:NA609 2.3 7.2 1.0
O B:GLN195 2.7 8.8 1.0
OE2 B:GLU197 2.7 12.7 1.0
O B:VAL174 3.0 7.4 1.0
N B:SER176 3.1 6.9 1.0
OE1 B:GLN195 3.3 9.4 1.0
O B:HOH884 3.3 19.5 1.0
CB B:SER176 3.5 7.4 1.0
C B:GLN195 3.7 9.1 1.0
CB B:GLU197 3.8 11.9 1.0
O B:HOH831 3.8 23.6 1.0
O B:ALA169 3.8 6.9 1.0
CA B:SER176 3.9 6.4 1.0
CD B:GLU197 3.9 13.5 1.0
C B:MET175 3.9 6.3 1.0
CA B:MET175 3.9 7.1 1.0
NH1 B:ARG395 3.9 8.9 1.0
C B:VAL174 4.1 6.4 1.0
CB B:GLN195 4.2 8.8 1.0
CA B:GLN195 4.2 8.8 1.0
CD B:GLN195 4.2 9.6 1.0
CG B:GLU197 4.5 12.5 1.0
N B:MET175 4.5 6.9 1.0
O B:TYR171 4.5 8.4 1.0
N B:GLU197 4.6 9.0 1.0
N B:VAL196 4.8 7.7 1.0
O B:SER176 4.8 6.6 1.0
OG B:SER176 4.8 8.2 1.0
CA B:GLU197 4.8 9.1 1.0
CG B:GLN195 4.8 9.2 1.0
C B:SER176 4.9 6.2 1.0
NH1 B:ARG410 4.9 18.2 1.0
C B:VAL196 4.9 7.8 1.0
OE1 B:GLU197 4.9 14.0 1.0

Reference:

D.Dong, K.Watanabe. Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.14 Nm Resolution To Be Published.
Page generated: Tue Dec 15 05:42:10 2020

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