Atomistry » Sodium » PDB 5jiq-5kc1 » 5jyd
Atomistry »
  Sodium »
    PDB 5jiq-5kc1 »
      5jyd »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy