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Sodium in PDB 5jyd: Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia

Protein crystallography data

The structure of Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia, PDB code: 5jyd was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.94 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.800, 107.820, 117.690, 90.00, 97.63, 90.00
R / Rfree (%) 14.1 / 17.4

Other elements in 5jyd:

The structure of Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms
Iodine (I) 54 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia (pdb code 5jyd). 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 A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia, PDB code: 5jyd:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5jyd

Go back to Sodium Binding Sites List in 5jyd
Sodium binding site 1 out of 4 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na910

b:10.8
occ:1.00
 O B:VAL304 2.2 11.1 1.0
O A:VAL304 2.2 8.7 1.0
O B:HOH1204 2.3 12.6 1.0
O A:PHE314 2.5 12.5 1.0
O B:PHE314 2.5 10.2 1.0
C A:PHE314 3.3 14.2 1.0
C B:PHE314 3.4 12.3 1.0
C B:VAL304 3.4 10.2 1.0
C A:VAL304 3.5 7.6 1.0
CA A:PHE314 3.9 11.2 1.0
CA B:PHE314 4.0 10.2 1.0
CG2 A:VAL304 4.0 7.8 0.2
CB A:PHE314 4.0 11.5 1.0
CB B:PHE314 4.0 12.0 1.0
CA A:TRP305 4.2 8.8 1.0
CA B:TRP305 4.2 9.0 1.0
OXT A:PHE314 4.2 12.8 1.0
N B:TRP305 4.3 10.1 1.0
OXT B:PHE314 4.3 11.9 1.0
N A:TRP305 4.3 10.2 1.0
CA B:VAL304 4.4 9.2 1.0
N A:GLY306 4.5 8.0 1.0
CA A:VAL304 4.5 8.6 0.2
N B:GLY306 4.5 10.7 1.0
CA A:VAL304 4.5 8.2 0.8
CB B:VAL304 4.5 10.7 1.0
CB A:VAL304 4.6 10.0 0.8
N B:VAL304 4.6 10.2 1.0
CD1 B:TRP305 4.6 10.3 1.0
CB A:VAL304 4.7 9.7 0.2
N A:VAL304 4.7 8.2 1.0
CD1 A:TRP305 4.7 9.1 1.0
O B:HOH1081 4.7 15.7 1.0
O A:HOH1143 4.8 19.7 1.0
CD1 B:PHE314 4.8 10.4 1.0
C A:TRP305 4.8 9.2 1.0
CD1 A:PHE314 4.9 9.7 1.0
C B:TRP305 4.9 10.4 1.0
CG B:PHE314 5.0 11.9 1.0
CG A:PHE314 5.0 9.8 1.0

Sodium binding site 2 out of 4 in 5jyd

Go back to Sodium Binding Sites List in 5jyd
Sodium binding site 2 out of 4 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na909

b:10.6
occ:1.00
 O C:VAL304 2.2 8.9 1.0
O D:VAL304 2.2 9.4 1.0
O D:HOH1252 2.3 11.0 1.0
O D:PHE314 2.5 10.5 1.0
O C:PHE314 2.5 10.4 1.0
C C:PHE314 3.4 8.9 1.0
C D:PHE314 3.4 12.2 1.0
C D:VAL304 3.5 7.7 1.0
C C:VAL304 3.5 6.7 1.0
CA C:PHE314 3.9 8.6 1.0
CA D:PHE314 4.0 8.7 1.0
CB C:PHE314 4.0 9.7 1.0
CB D:PHE314 4.1 11.3 1.0
CA C:TRP305 4.2 7.2 1.0
CA D:TRP305 4.3 7.0 1.0
OXT D:PHE314 4.3 11.3 1.0
OXT C:PHE314 4.3 10.5 1.0
N D:TRP305 4.3 8.8 1.0
N C:TRP305 4.3 8.5 1.0
CA D:VAL304 4.4 7.1 1.0
CA C:VAL304 4.4 7.0 1.0
N C:GLY306 4.5 8.0 1.0
N D:GLY306 4.5 7.7 1.0
CB D:VAL304 4.6 8.9 1.0
CB C:VAL304 4.6 11.1 1.0
N C:VAL304 4.6 6.5 1.0
N D:VAL304 4.6 7.4 1.0
CD1 D:TRP305 4.7 6.8 1.0
CD1 C:TRP305 4.7 8.7 1.0
O D:HOH1068 4.8 17.3 1.0
O C:HOH1086 4.8 18.7 1.0
CD1 D:PHE314 4.8 11.2 1.0
CD1 C:PHE314 4.9 10.2 1.0
C C:TRP305 4.9 7.8 1.0
C D:TRP305 4.9 7.2 1.0
CG C:PHE314 5.0 8.5 1.0
CG D:PHE314 5.0 9.4 1.0

Sodium binding site 3 out of 4 in 5jyd

Go back to Sodium Binding Sites List in 5jyd
Sodium binding site 3 out of 4 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na913

b:11.5
occ:1.00
 O F:VAL304 2.2 13.6 1.0
O E:VAL304 2.2 10.0 1.0
O F:HOH1170 2.3 13.8 1.0
O F:PHE314 2.5 15.2 1.0
O E:PHE314 2.5 12.1 1.0
C E:PHE314 3.4 12.7 1.0
C F:PHE314 3.4 15.4 1.0
C F:VAL304 3.4 14.3 1.0
C E:VAL304 3.4 9.2 1.0
CA F:PHE314 4.0 12.2 1.0
CA E:PHE314 4.0 10.3 1.0
CB F:PHE314 4.0 12.8 1.0
CB E:PHE314 4.1 12.5 1.0
CA E:TRP305 4.2 12.4 1.0
CA F:TRP305 4.2 9.6 1.0
OXT E:PHE314 4.2 13.8 1.0
N E:TRP305 4.3 10.6 1.0
N F:TRP305 4.3 11.1 1.0
OXT F:PHE314 4.3 15.3 1.0
CA F:VAL304 4.4 12.8 1.0
CA E:VAL304 4.5 9.0 1.0
N F:GLY306 4.5 11.2 1.0
N E:GLY306 4.5 11.0 1.0
CB F:VAL304 4.5 16.2 1.0
CB E:VAL304 4.6 13.9 1.0
N F:VAL304 4.6 13.6 1.0
N E:VAL304 4.6 9.6 1.0
CD1 E:TRP305 4.7 11.2 1.0
CD1 F:TRP305 4.7 10.5 1.0
O F:HOH1088 4.8 20.2 1.0
O E:HOH1053 4.8 20.2 1.0
CD1 F:PHE314 4.8 12.0 1.0
C F:TRP305 4.8 12.9 1.0
C E:TRP305 4.9 10.3 1.0
CD1 E:PHE314 4.9 16.2 1.0
CG F:PHE314 5.0 12.5 1.0

Sodium binding site 4 out of 4 in 5jyd

Go back to Sodium Binding Sites List in 5jyd
Sodium binding site 4 out of 4 in the Crystal Structure of A Putative Short Chain Dehydrogenase From Burkholderia Cenocepacia


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 Short Chain Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na910

b:16.4
occ:1.00
 O H:VAL304 2.2 16.4 1.0
O G:VAL304 2.3 13.7 1.0
O G:HOH1211 2.4 15.1 1.0
O H:PHE314 2.4 14.3 1.0
O G:PHE314 2.5 18.2 1.0
C H:PHE314 3.3 17.6 1.0
C G:PHE314 3.4 15.6 1.0
C H:VAL304 3.4 18.1 1.0
C G:VAL304 3.5 14.2 1.0
CA H:PHE314 3.9 15.4 1.0
CA G:PHE314 4.0 15.9 1.0
CB H:PHE314 4.0 19.5 1.0
OXT H:PHE314 4.2 16.4 1.0
CB G:PHE314 4.2 16.3 1.0
CA H:TRP305 4.2 18.4 1.0
CA G:TRP305 4.2 16.2 1.0
OXT G:PHE314 4.3 18.6 1.0
N H:TRP305 4.3 15.0 1.0
N G:TRP305 4.3 13.7 1.0
CA H:VAL304 4.4 18.6 1.0
N H:GLY306 4.5 17.2 1.0
CA G:VAL304 4.5 11.9 1.0
N G:GLY306 4.5 13.8 1.0
CB H:VAL304 4.6 17.8 1.0
N H:VAL304 4.6 15.8 1.0
CB G:VAL304 4.6 16.7 1.0
N G:VAL304 4.7 13.2 1.0
O H:HOH1096 4.7 24.7 1.0
CD1 H:TRP305 4.7 14.4 1.0
CD1 G:TRP305 4.7 15.3 1.0
CD1 H:PHE314 4.8 16.6 1.0
O G:HOH1152 4.8 23.9 1.0
C H:TRP305 4.9 21.3 1.0
CD1 G:PHE314 4.9 15.2 1.0
C G:TRP305 4.9 15.0 1.0
CG H:PHE314 4.9 19.9 1.0

Reference:

Ssgcid, J.Y.Yano, D.Lorimer, T.E.Edwards. Tbd To Be Published.
Page generated: Mon Oct 7 21:58:39 2024

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