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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

Go back to Sodium Binding Sites List in 3pnx
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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