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Sodium in PDB 3pnx: Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution, PDB code: 3pnx was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.45 / 1.92
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.416, 76.504, 127.652, 90.00, 93.08, 90.00
R / Rfree (%) 19 / 21.5

Other elements in 3pnx:

The structure of Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution (pdb code 3pnx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution, PDB code: 3pnx:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 3pnx

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Sodium binding site 1 out of 10 in the Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A 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 A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na164

b:56.6
occ:1.00
 O C:HOH187 2.1 48.8 1.0
OE2 A:GLU62 2.4 55.5 1.0
O A:GLU125 2.4 52.0 1.0
O A:ILE126 2.6 50.6 1.0
OE1 C:GLU98 2.7 59.2 1.0
C A:ILE126 3.2 49.9 1.0
CD A:GLU62 3.3 57.8 1.0
O A:HOH245 3.4 60.2 1.0
C A:GLU125 3.5 51.5 1.0
CA A:ILE126 3.5 49.5 1.0
CG A:GLU62 3.6 55.9 1.0
CD C:GLU98 3.6 57.8 1.0
N A:GLY128 4.0 54.1 1.0
N A:ILE126 4.0 49.8 1.0
CG C:GLU98 4.1 56.0 1.0
N A:MSE127 4.2 49.6 1.0
CA A:GLY128 4.2 56.3 1.0
O C:MSE94 4.3 50.3 1.0
OE1 A:GLU62 4.5 58.4 1.0
C A:MSE127 4.5 52.5 1.0
OE1 C:GLU97 4.5 65.3 1.0
OE2 C:GLU98 4.6 59.6 1.0
CB C:GLU98 4.7 54.7 1.0
CA A:MSE127 4.8 50.4 1.0
CA A:GLU125 4.8 52.1 1.0
CB A:ILE126 4.9 48.5 1.0

Sodium binding site 2 out of 10 in 3pnx

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Sodium binding site 2 out of 10 in the Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A 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 A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na166

b:36.9
occ:1.00
 O B:GLN156 2.2 36.1 1.0
O A:GLN156 2.2 36.8 1.0
O C:GLN156 2.3 37.0 1.0
C B:GLN156 3.4 37.0 1.0
C A:GLN156 3.4 36.8 1.0
C C:GLN156 3.5 37.8 1.0
OE1 A:GLN156 4.0 52.5 1.0
OE1 C:GLN156 4.1 51.9 1.0
OE1 B:GLN156 4.1 52.1 1.0
CB B:GLN156 4.2 39.2 1.0
CA B:GLN156 4.2 38.3 1.0
CA A:GLN156 4.2 37.9 1.0
CD2 A:LEU157 4.2 32.6 1.0
CB C:GLN156 4.2 40.5 1.0
CA C:GLN156 4.3 39.0 1.0
CB A:GLN156 4.3 39.4 1.0
N A:GLN156 4.3 38.6 1.0
N B:GLN156 4.3 38.5 1.0
CD2 C:LEU157 4.3 33.0 1.0
N C:GLN156 4.3 40.0 1.0
N B:LEU157 4.4 36.7 1.0
N A:LEU157 4.4 36.2 1.0
CD2 B:LEU157 4.4 32.9 1.0
N C:LEU157 4.5 36.4 1.0
CA A:LEU157 4.5 34.8 1.0
CA B:LEU157 4.6 35.5 1.0
CA C:LEU157 4.6 35.9 1.0
CL A:CL161 4.7 34.0 1.0
CD A:GLN156 5.0 47.7 1.0

Sodium binding site 3 out of 10 in 3pnx

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Sodium binding site 3 out of 10 in the Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A 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 A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na170

b:33.0
occ:1.00
 O B:PHE158 2.2 33.9 1.0
O A:PHE158 2.3 33.7 1.0
O C:PHE158 2.3 33.7 1.0
O2 B:GOL172 2.6 51.3 0.5
O2 B:GOL172 2.7 47.3 0.5
CL A:CL161 2.9 34.0 1.0
C B:PHE158 3.4 34.5 1.0
C A:PHE158 3.4 34.9 1.0
C C:PHE158 3.4 35.4 1.0
CB B:PHE158 3.8 34.2 1.0
CB A:PHE158 3.8 35.0 1.0
C2 B:GOL172 3.9 47.8 0.5
CB C:PHE158 3.9 36.0 1.0
C2 B:GOL172 3.9 52.6 0.5
CA A:PHE158 3.9 34.5 1.0
CA B:PHE158 4.0 34.2 1.0
N A:PHE158 4.0 34.3 1.0
CA C:PHE158 4.0 35.4 1.0
N C:PHE158 4.0 35.2 1.0
N B:PHE158 4.0 34.5 1.0
C3 B:GOL172 4.1 47.6 0.5
CD1 B:PHE158 4.2 35.9 1.0
CD1 A:PHE158 4.2 34.2 1.0
CD1 C:PHE158 4.2 34.0 1.0
N B:ILE159 4.5 35.0 1.0
N A:ILE159 4.5 35.5 1.0
CG B:PHE158 4.5 35.1 1.0
CG A:PHE158 4.5 33.9 1.0
CG C:PHE158 4.5 36.4 1.0
N C:ILE159 4.5 35.9 1.0
C3 B:GOL172 4.7 51.3 0.5
CA B:ILE159 4.9 36.3 1.0
O3 B:GOL172 4.9 49.2 0.5
O1 B:GOL172 4.9 52.6 0.5
CA A:ILE159 4.9 36.0 1.0
CA C:ILE159 4.9 36.5 1.0
C1 B:GOL172 4.9 52.4 0.5

Sodium binding site 4 out of 10 in 3pnx

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Sodium binding site 4 out of 10 in the Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A 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 A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na162

b:57.6
occ:1.00
 O A:HOH289 2.0 46.3 1.0
OE2 B:GLU62 2.3 51.4 1.0
O B:GLU125 2.3 46.8 1.0
OE2 A:GLU98 2.5 54.6 1.0
O B:ILE126 2.7 46.9 1.0
C B:ILE126 3.2 46.9 1.0
CD B:GLU62 3.3 52.9 1.0
CD A:GLU98 3.3 53.9 1.0
C B:GLU125 3.4 46.7 1.0
CG A:GLU98 3.5 50.5 1.0
CA B:ILE126 3.5 45.9 1.0
CG B:GLU62 3.8 51.3 1.0
N B:GLY128 3.9 52.1 1.0
N B:ILE126 3.9 45.4 1.0
CA B:GLY128 4.1 54.2 1.0
N B:MSE127 4.2 47.2 1.0
O A:MSE94 4.4 46.0 1.0
OE1 B:GLU62 4.4 53.5 1.0
OE1 A:GLU98 4.5 55.2 1.0
C B:MSE127 4.5 50.7 1.0
OE1 A:GLU97 4.5 64.8 1.0
CA B:GLU125 4.7 47.6 1.0
CA B:MSE127 4.8 48.8 1.0
CB A:GLU98 5.0 50.2 1.0
CB B:ILE126 5.0 45.4 1.0

Sodium binding site 5 out of 10 in 3pnx

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Sodium binding site 5 out of 10 in the Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na169

b:56.4
occ:1.00
 O B:HOH277 2.1 45.9 1.0
OE2 C:GLU62 2.3 49.4 1.0
O C:GLU125 2.5 43.9 1.0
O C:ILE126 2.7 43.6 1.0
OE1 B:GLU98 2.7 58.9 1.0
CD C:GLU62 3.3 49.7 1.0
C C:ILE126 3.3 43.5 1.0
O C:HOH357 3.4 57.1 1.0
C C:GLU125 3.6 44.0 1.0
CA C:ILE126 3.6 42.5 1.0
CG C:GLU62 3.7 48.8 1.0
CD B:GLU98 3.7 56.5 1.0
N C:ILE126 4.1 41.9 1.0
N C:GLY128 4.1 48.2 1.0
O B:MSE94 4.2 46.5 1.0
CG B:GLU98 4.2 53.2 1.0
CA C:GLY128 4.3 49.5 1.0
N C:MSE127 4.4 43.8 1.0
CB B:GLU98 4.4 51.6 1.0
OE1 C:GLU62 4.4 49.7 1.0
OE2 B:GLU98 4.6 60.2 1.0
C C:MSE127 4.7 47.0 1.0
CA C:GLU125 4.9 44.6 1.0
CA C:MSE127 5.0 45.4 1.0
C B:MSE94 5.0 47.2 1.0

Sodium binding site 6 out of 10 in 3pnx

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Sodium binding site 6 out of 10 in the Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na165

b:46.0
occ:1.00
 OE2 D:GLU62 2.2 45.8 1.0
O E:HOH337 2.2 46.7 1.0
O D:ILE126 2.4 44.0 1.0
O D:GLU125 2.5 46.0 1.0
OE2 E:GLU98 2.5 59.8 1.0
C D:ILE126 3.1 44.5 1.0
CD D:GLU62 3.2 47.5 1.0
CD E:GLU98 3.3 59.9 1.0
CG E:GLU98 3.4 56.6 1.0
O D:HOH240 3.5 47.8 1.0
CG D:GLU62 3.5 46.8 1.0
CA D:ILE126 3.5 44.8 1.0
C D:GLU125 3.5 46.3 1.0
N D:GLY128 3.8 47.5 1.0
N D:ILE126 4.0 45.4 1.0
CA D:GLY128 4.1 48.8 1.0
N D:MSE127 4.1 44.2 1.0
O E:MSE94 4.3 49.1 1.0
OE1 D:GLU62 4.3 46.3 1.0
C D:MSE127 4.4 46.9 1.0
OE1 E:GLU98 4.5 63.7 1.0
CA D:MSE127 4.6 45.3 1.0
OE1 E:GLU97 4.7 53.4 1.0
CA D:GLU125 4.9 47.3 1.0
CB E:GLU98 4.9 56.0 1.0
CB D:ILE126 4.9 44.4 1.0

Sodium binding site 7 out of 10 in 3pnx

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Sodium binding site 7 out of 10 in the Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na167

b:43.3
occ:1.00
 O E:GLN156 2.2 42.8 1.0
O F:GLN156 2.3 44.5 1.0
O D:GLN156 2.3 42.4 1.0
C E:GLN156 3.4 43.6 1.0
C F:GLN156 3.4 44.7 1.0
C D:GLN156 3.5 43.8 1.0
OE1 F:GLN156 4.1 57.3 1.0
OE1 E:GLN156 4.1 59.9 1.0
CB F:GLN156 4.1 47.9 1.0
OE1 D:GLN156 4.2 55.8 1.0
CB E:GLN156 4.2 46.6 1.0
CA F:GLN156 4.2 46.5 1.0
CA E:GLN156 4.2 45.3 1.0
CD2 E:LEU157 4.2 39.4 1.0
CA D:GLN156 4.2 45.0 1.0
CB D:GLN156 4.3 46.4 1.0
N F:GLN156 4.3 47.7 1.0
N D:GLN156 4.3 46.0 1.0
CD2 F:LEU157 4.3 38.7 1.0
N E:GLN156 4.3 45.8 1.0
N E:LEU157 4.4 42.4 1.0
CD2 D:LEU157 4.4 39.6 1.0
N F:LEU157 4.4 42.7 1.0
N D:LEU157 4.5 42.5 1.0
CA E:LEU157 4.5 41.6 1.0
CA F:LEU157 4.6 41.9 1.0
CA D:LEU157 4.6 41.5 1.0
CL D:CL160 4.7 39.6 1.0

Sodium binding site 8 out of 10 in 3pnx

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Sodium binding site 8 out of 10 in the Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na171

b:38.5
occ:1.00
 O D:PHE158 2.3 38.1 1.0
O F:PHE158 2.3 39.8 1.0
O E:PHE158 2.3 39.0 1.0
O2 D:GOL173 2.6 49.5 0.5
O2 D:GOL173 2.7 45.9 0.5
CL D:CL160 2.8 39.6 1.0
C E:PHE158 3.4 39.3 1.0
C F:PHE158 3.4 40.2 1.0
C D:PHE158 3.4 39.6 1.0
CB F:PHE158 3.8 40.1 1.0
C2 D:GOL173 3.8 51.7 0.5
CB D:PHE158 3.8 40.1 1.0
CB E:PHE158 3.9 39.7 1.0
C1 D:GOL173 3.9 49.8 0.5
CA F:PHE158 4.0 40.0 1.0
CA D:PHE158 4.0 39.6 1.0
CA E:PHE158 4.0 39.8 1.0
N F:PHE158 4.0 40.3 1.0
N D:PHE158 4.0 40.6 1.0
C2 D:GOL173 4.0 47.2 0.5
N E:PHE158 4.1 40.3 1.0
CD1 F:PHE158 4.2 40.9 1.0
CD1 E:PHE158 4.2 40.3 1.0
CD1 D:PHE158 4.3 40.6 1.0
C3 D:GOL173 4.3 46.9 0.5
O3 D:GOL173 4.5 50.6 0.5
CG F:PHE158 4.5 39.6 1.0
N E:ILE159 4.5 40.3 1.0
N F:ILE159 4.5 40.3 1.0
N D:ILE159 4.5 39.6 1.0
CG E:PHE158 4.5 39.5 1.0
CG D:PHE158 4.5 40.0 1.0
C3 D:GOL173 4.7 51.5 0.5
O3 D:GOL173 4.7 43.0 0.5
CA E:ILE159 4.9 40.4 1.0
CA D:ILE159 4.9 40.1 1.0
C1 D:GOL173 4.9 46.7 0.5
CA F:ILE159 4.9 41.0 1.0

Sodium binding site 9 out of 10 in 3pnx

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Sodium binding site 9 out of 10 in the Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na168

b:52.0
occ:1.00
 OE2 E:GLU62 2.3 49.3 1.0
O F:HOH231 2.3 49.8 1.0
O E:ILE126 2.5 49.5 1.0
O E:GLU125 2.5 52.0 1.0
OE1 F:GLU98 2.6 62.4 1.0
C E:ILE126 3.2 49.8 1.0
CD E:GLU62 3.2 51.5 1.0
O E:HOH242 3.5 57.0 1.0
CG E:GLU62 3.5 51.1 1.0
CA E:ILE126 3.6 49.9 1.0
C E:GLU125 3.6 51.6 1.0
CD F:GLU98 3.6 62.8 1.0
N E:GLY128 4.0 52.9 1.0
N E:ILE126 4.1 50.3 1.0
N E:MSE127 4.2 49.6 1.0
CA E:GLY128 4.2 55.1 1.0
CG F:GLU98 4.2 61.2 1.0
O F:MSE94 4.3 53.0 1.0
OE1 E:GLU62 4.4 52.4 1.0
CB F:GLU98 4.4 60.1 1.0
C E:MSE127 4.5 51.8 1.0
OE2 F:GLU98 4.5 65.6 1.0
OE1 F:GLU97 4.7 60.4 1.0
CA E:MSE127 4.8 49.9 1.0
CA E:GLU125 4.9 52.5 1.0
CB E:ILE126 4.9 49.0 1.0
CB F:MSE94 5.0 52.4 1.0

Sodium binding site 10 out of 10 in 3pnx

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Sodium binding site 10 out of 10 in the Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of A Putative Sulfurtransferase Dsre (SWOL_2425) From Syntrophomonas Wolfei Str. Goettingen at 1.92 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na163

b:65.3
occ:1.00
 OE2 F:GLU62 2.1 51.3 1.0
O D:HOH338 2.1 53.2 1.0
OE2 D:GLU98 2.5 50.6 0.5
O F:GLU125 2.6 49.2 1.0
O F:ILE126 2.7 48.0 1.0
CD F:GLU62 3.1 50.0 1.0
O F:HOH241 3.2 56.3 1.0
CD D:GLU98 3.4 53.4 0.5
C F:ILE126 3.4 48.1 1.0
CG D:GLU98 3.5 54.5 0.5
CG F:GLU62 3.5 49.9 1.0
C F:GLU125 3.7 49.2 1.0
CG D:GLU98 3.7 57.8 0.5
CA F:ILE126 3.8 47.9 1.0
N F:GLY128 4.0 53.9 1.0
OE2 D:GLU98 4.1 60.6 0.5
OE1 F:GLU62 4.1 50.3 1.0
CA F:GLY128 4.2 55.1 1.0
N F:ILE126 4.2 48.1 1.0
O D:MSE94 4.3 53.4 1.0
N F:MSE127 4.3 48.7 1.0
CD D:GLU98 4.4 58.8 0.5
OE1 D:GLU98 4.5 51.7 0.5
C F:MSE127 4.5 52.3 1.0
OE1 D:GLU97 4.8 69.8 1.0
CA F:MSE127 4.9 50.4 1.0
CA F:GLU125 5.0 50.1 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Mon Oct 7 12:21:22 2024

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