Atomistry » Sodium » PDB 4q3a-4qm6 » 4qku
Atomistry »
  Sodium »
    PDB 4q3a-4qm6 »
      4qku »

Sodium in PDB 4qku: Crystal Structure of A Putative Hydrolase From Burkholderia Cenocepacia

Protein crystallography data

The structure of Crystal Structure of A Putative Hydrolase From Burkholderia Cenocepacia, PDB code: 4qku 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) 50.00 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.640, 110.550, 116.160, 90.00, 106.61, 90.00
R / Rfree (%) 20.8 / 24.9

Sodium Binding Sites:

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

Sodium binding site 1 out of 4 in 4qku

Go back to Sodium Binding Sites List in 4qku
Sodium binding site 1 out of 4 in the Crystal Structure of A Putative Hydrolase 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 Hydrolase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:16.4
occ:1.00
O A:ALA271 2.3 14.8 1.0
O A:TRP249 2.4 15.7 1.0
O A:LYS268 2.4 17.0 1.0
OD1 A:ASP248 2.5 18.1 1.0
OG1 A:THR272 2.9 13.4 1.0
N A:TRP249 3.3 16.8 1.0
C A:ALA271 3.3 15.1 1.0
C A:LYS268 3.3 17.1 1.0
C A:TRP249 3.4 15.8 1.0
C A:ASP248 3.5 17.7 1.0
CG A:ASP248 3.6 18.4 1.0
CA A:LYS268 3.7 18.0 1.0
CA A:TRP249 3.7 16.0 1.0
CA A:ASP248 3.9 17.9 1.0
CB A:LYS268 3.9 18.8 1.0
CB A:TRP249 4.0 15.7 1.0
CB A:THR272 4.0 13.5 1.0
CA A:THR272 4.0 13.9 1.0
N A:THR272 4.0 14.7 1.0
O A:ASP248 4.1 19.0 1.0
N A:ALA271 4.3 15.8 1.0
CB A:ASP248 4.4 18.6 1.0
CA A:ALA271 4.4 16.2 1.0
OD2 A:ASP248 4.5 19.4 1.0
O A:HOH718 4.5 11.8 1.0
N A:GLY269 4.5 16.2 1.0
O A:HOH653 4.6 22.6 1.0
N A:SER250 4.6 15.6 1.0
CG2 A:THR272 4.7 13.6 1.0
O A:HOH658 4.7 24.2 1.0
CD1 A:TRP249 4.9 15.3 1.0
CG A:TRP249 4.9 15.6 1.0
O A:ASN247 5.0 18.0 1.0
CD A:LYS268 5.0 21.5 1.0

Sodium binding site 2 out of 4 in 4qku

Go back to Sodium Binding Sites List in 4qku
Sodium binding site 2 out of 4 in the Crystal Structure of A Putative Hydrolase 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 Hydrolase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:15.6
occ:1.00
O B:ALA271 2.3 11.4 1.0
OD1 B:ASP248 2.4 16.9 1.0
O B:TRP249 2.4 16.4 1.0
O B:LYS268 2.5 17.2 1.0
OG1 B:THR272 2.8 11.3 1.0
N B:TRP249 3.2 15.1 1.0
C B:ALA271 3.3 11.5 1.0
C B:LYS268 3.4 16.6 1.0
C B:TRP249 3.4 15.9 1.0
C B:ASP248 3.5 15.8 1.0
CG B:ASP248 3.6 16.3 1.0
CA B:LYS268 3.7 17.9 1.0
CA B:TRP249 3.8 15.3 1.0
CA B:ASP248 3.8 15.5 1.0
CB B:THR272 3.9 11.0 1.0
CA B:THR272 3.9 11.0 1.0
CB B:LYS268 4.0 18.9 1.0
N B:THR272 4.0 11.2 1.0
CB B:TRP249 4.0 14.7 1.0
O B:ASP248 4.1 16.0 1.0
O B:HOH692 4.3 26.1 1.0
CB B:ASP248 4.3 15.8 1.0
N B:ALA271 4.4 12.5 1.0
OD2 B:ASP248 4.4 16.4 1.0
CA B:ALA271 4.5 12.0 1.0
N B:GLY269 4.6 15.5 1.0
O B:HOH646 4.6 6.2 1.0
CG2 B:THR272 4.6 10.9 1.0
N B:SER250 4.7 16.7 1.0
O B:HOH666 4.8 10.9 1.0
CD1 B:TRP249 4.9 13.1 1.0
O B:ASN247 4.9 13.8 1.0
CG B:TRP249 4.9 13.8 1.0

Sodium binding site 3 out of 4 in 4qku

Go back to Sodium Binding Sites List in 4qku
Sodium binding site 3 out of 4 in the Crystal Structure of A Putative Hydrolase 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 Hydrolase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:23.1
occ:1.00
O C:ALA271 2.3 13.2 1.0
O C:LYS268 2.4 16.1 1.0
OD1 C:ASP248 2.4 17.7 1.0
O C:TRP249 2.6 15.6 1.0
OG1 C:THR272 2.7 11.4 1.0
C C:ALA271 3.3 12.7 1.0
C C:LYS268 3.4 15.8 1.0
N C:TRP249 3.4 16.9 1.0
CG C:ASP248 3.6 17.5 1.0
C C:TRP249 3.6 16.5 1.0
C C:ASP248 3.6 16.8 1.0
CA C:LYS268 3.7 16.9 1.0
CB C:THR272 3.8 11.5 1.0
CA C:THR272 3.9 12.1 1.0
CA C:ASP248 3.9 16.6 1.0
CA C:TRP249 3.9 16.8 1.0
N C:THR272 3.9 12.5 1.0
CB C:LYS268 4.0 17.4 1.0
CB C:TRP249 4.2 17.0 1.0
O C:ASP248 4.2 16.7 1.0
O C:HOH717 4.3 26.4 1.0
CB C:ASP248 4.4 16.8 1.0
N C:ALA271 4.4 12.9 1.0
CA C:ALA271 4.4 13.1 1.0
OD2 C:ASP248 4.5 18.9 1.0
O C:HOH754 4.5 15.8 1.0
CG2 C:THR272 4.5 11.6 1.0
N C:GLY269 4.5 14.6 1.0
O C:HOH626 4.8 14.2 1.0
N C:SER250 4.8 16.3 1.0
O C:ASN247 4.9 14.2 1.0
CD1 C:TRP249 4.9 16.8 1.0
CG C:TRP249 5.0 17.1 1.0
CA C:GLY269 5.0 13.9 1.0

Sodium binding site 4 out of 4 in 4qku

Go back to Sodium Binding Sites List in 4qku
Sodium binding site 4 out of 4 in the Crystal Structure of A Putative Hydrolase 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 Hydrolase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:21.9
occ:1.00
O D:ALA271 2.3 11.2 1.0
OD1 D:ASP248 2.3 18.2 1.0
O D:LYS268 2.5 19.5 1.0
O D:TRP249 2.5 13.1 1.0
OG1 D:THR272 2.8 9.6 1.0
N D:TRP249 3.3 13.3 1.0
C D:ALA271 3.3 11.0 1.0
C D:LYS268 3.4 19.2 1.0
C D:TRP249 3.5 13.7 1.0
C D:ASP248 3.5 14.1 1.0
CG D:ASP248 3.5 17.5 1.0
CA D:LYS268 3.8 20.7 1.0
CA D:TRP249 3.8 13.1 1.0
CA D:ASP248 3.8 14.7 1.0
CB D:THR272 3.9 9.6 1.0
CA D:THR272 3.9 9.8 1.0
N D:THR272 4.0 10.2 1.0
CB D:LYS268 4.0 21.4 1.0
CB D:TRP249 4.1 12.5 1.0
O D:ASP248 4.1 14.1 1.0
O D:HOH677 4.2 14.4 1.0
CB D:ASP248 4.3 16.1 1.0
N D:ALA271 4.4 12.0 1.0
OD2 D:ASP248 4.4 19.0 1.0
CA D:ALA271 4.5 11.6 1.0
O D:HOH619 4.5 8.2 1.0
CG2 D:THR272 4.5 9.4 1.0
N D:GLY269 4.6 18.1 1.0
O D:HOH629 4.7 10.7 1.0
N D:SER250 4.7 14.7 1.0
CD1 D:TRP249 4.9 11.6 1.0
O D:ASN247 4.9 12.7 1.0
CG D:TRP249 4.9 12.0 1.0

Reference:

T.E.Edwards, J.W.Fairman, Seattle Structural Genomics Center For Infectious Disease. Crystal Structure of A Putative Hydrolase From Burkholderia Cenocepacia To Be Published.
Page generated: Tue Dec 15 07:05:53 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy