Atomistry » Sodium » PDB 4mfc-4mzx » 4mow
Atomistry »
  Sodium »
    PDB 4mfc-4mzx »
      4mow »

Sodium in PDB 4mow: Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315

Enzymatic activity of Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315

All present enzymatic activity of Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315:
1.1.1.47;

Protein crystallography data

The structure of Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315, PDB code: 4mow 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) 20.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.990, 82.380, 168.350, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315 (pdb code 4mow). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315, PDB code: 4mow:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4mow

Go back to Sodium Binding Sites List in 4mow
Sodium binding site 1 out of 8 in the Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315


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 Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:24.6
occ:1.00
 O D:HOH443 2.3 25.7 1.0
O A:HOH430 2.4 22.3 1.0
O A:HOH413 2.4 13.3 1.0
OD1 A:ASN248 2.4 18.7 1.0
O A:ASN248 2.5 16.0 1.0
O D:HOH426 2.7 17.8 1.0
NA A:NA302 3.1 20.4 1.0
C A:ASN248 3.2 16.4 1.0
CG A:ASN248 3.5 18.4 1.0
N A:ASN248 3.8 15.5 1.0
OXT A:ASN248 3.9 18.7 1.0
CA A:ASN248 4.0 15.8 1.0
O A:HOH441 4.1 22.7 1.0
O D:HOH432 4.3 25.6 1.0
ND2 A:ASN248 4.3 19.6 1.0
CB A:ASN248 4.3 16.5 1.0
O A:HOH442 4.4 21.1 1.0
O D:ILE146 4.6 14.9 1.0
O D:SER145 4.7 15.9 1.0
O D:HOH439 4.8 30.4 1.0
O A:HOH529 4.8 31.3 1.0
O A:HOH528 4.8 30.4 1.0
O D:HOH435 4.8 28.6 1.0
O B:HOH411 4.9 18.5 1.0
O A:GLY246 4.9 14.2 1.0
CD1 B:LEU170 4.9 16.6 1.0
CA D:ILE146 4.9 16.9 1.0

Sodium binding site 2 out of 8 in 4mow

Go back to Sodium Binding Sites List in 4mow
Sodium binding site 2 out of 8 in the Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315


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 Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:20.4
occ:1.00
 O A:HOH528 2.1 30.4 1.0
O D:SER145 2.3 15.9 1.0
O D:HOH435 2.3 28.6 1.0
OD1 A:ASN248 2.4 18.7 1.0
O D:HOH426 2.5 17.8 1.0
O A:HOH430 2.5 22.3 1.0
NA A:NA301 3.1 24.6 1.0
CG A:ASN248 3.4 18.4 1.0
C D:SER145 3.5 16.9 1.0
O D:HOH441 3.9 24.9 1.0
ND2 A:ASN248 4.0 19.6 1.0
O A:HOH568 4.1 37.1 1.0
CA D:ILE146 4.2 16.9 1.0
O B:HOH465 4.2 23.5 1.0
O A:HOH425 4.2 21.0 1.0
N D:ILE146 4.3 16.1 1.0
OXT A:ASN248 4.3 18.7 1.0
C A:ASN248 4.4 16.4 1.0
OG1 D:THR147 4.5 16.9 1.0
C D:ILE146 4.5 15.8 1.0
O A:ASN248 4.5 16.0 1.0
CA D:SER145 4.5 16.8 1.0
CB A:ASN248 4.6 16.5 1.0
O B:HOH411 4.6 18.5 1.0
O D:HOH443 4.7 25.7 1.0
OXT D:ASN248 4.7 16.6 1.0
O D:ILE146 4.7 14.9 1.0

Sodium binding site 3 out of 8 in 4mow

Go back to Sodium Binding Sites List in 4mow
Sodium binding site 3 out of 8 in the Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315


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 Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:29.1
occ:1.00
 O C:HOH453 2.1 27.6 1.0
O C:HOH455 2.3 21.8 1.0
OD1 B:ASN248 2.6 20.0 1.0
O C:HOH464 2.6 26.0 1.0
O B:HOH412 2.7 16.2 1.0
O B:ASN248 2.8 18.7 1.0
NA B:NA302 3.0 23.4 1.0
C B:ASN248 3.4 20.2 1.0
CG B:ASN248 3.7 20.2 1.0
N B:ASN248 4.0 18.9 1.0
OXT B:ASN248 4.1 20.0 1.0
O C:HOH451 4.1 30.6 1.0
CA B:ASN248 4.2 19.5 1.0
O B:HOH474 4.2 28.1 1.0
O B:HOH473 4.4 32.9 1.0
CB B:ASN248 4.5 19.0 1.0
ND2 B:ASN248 4.5 20.0 1.0
O C:ILE146 4.5 17.0 1.0
O C:SER145 4.6 16.9 1.0
O C:HOH502 4.7 30.9 1.0
CA C:ILE146 4.8 18.0 1.0
O C:HOH456 4.8 28.7 1.0
O A:HOH424 4.9 18.2 1.0
CD1 A:LEU170 4.9 19.9 1.0

Sodium binding site 4 out of 8 in 4mow

Go back to Sodium Binding Sites List in 4mow
Sodium binding site 4 out of 8 in the Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315


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 Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:23.4
occ:1.00
 O C:HOH464 2.3 26.0 1.0
O C:HOH454 2.3 27.5 1.0
O C:SER145 2.4 16.9 1.0
O C:HOH455 2.4 21.8 1.0
OD1 B:ASN248 2.4 20.0 1.0
O C:HOH456 2.6 28.7 1.0
NA B:NA301 3.0 29.1 1.0
CG B:ASN248 3.4 20.2 1.0
C C:SER145 3.6 17.6 1.0
O C:HOH424 4.0 22.1 1.0
ND2 B:ASN248 4.1 20.0 1.0
CA C:ILE146 4.2 18.0 1.0
O C:HOH501 4.2 35.5 1.0
O B:HOH437 4.2 21.5 1.0
O C:HOH484 4.3 31.4 1.0
O A:HOH459 4.3 31.3 1.0
N C:ILE146 4.4 16.4 1.0
OXT B:ASN248 4.4 20.0 1.0
C B:ASN248 4.5 20.2 1.0
C C:ILE146 4.5 18.0 1.0
CB B:ASN248 4.5 19.0 1.0
OG1 C:THR147 4.6 19.4 1.0
O B:ASN248 4.6 18.7 1.0
CA C:SER145 4.6 16.8 1.0
O A:HOH424 4.6 18.2 1.0
O C:HOH453 4.7 27.6 1.0
OXT C:ASN248 4.7 23.8 1.0
O C:ILE146 4.7 17.0 1.0
O C:HOH418 5.0 24.1 1.0

Sodium binding site 5 out of 8 in 4mow

Go back to Sodium Binding Sites List in 4mow
Sodium binding site 5 out of 8 in the Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315


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 Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:23.4
occ:1.00
 O B:HOH456 2.2 28.4 1.0
OD1 C:ASN248 2.3 21.7 1.0
O B:SER145 2.3 18.9 1.0
O B:HOH441 2.4 22.5 1.0
O C:HOH425 2.5 23.6 1.0
O B:HOH447 2.5 30.5 1.0
NA C:NA302 3.1 27.7 1.0
CG C:ASN248 3.3 21.1 1.0
C B:SER145 3.6 16.9 1.0
ND2 C:ASN248 3.8 24.0 1.0
O B:HOH435 4.1 27.6 1.0
O C:HOH418 4.1 24.1 1.0
O B:HOH506 4.1 38.2 1.0
CA B:ILE146 4.2 18.8 1.0
OXT C:ASN248 4.3 23.8 1.0
O D:HOH453 4.3 25.4 1.0
N B:ILE146 4.4 17.4 1.0
C C:ASN248 4.4 21.1 1.0
CB C:ASN248 4.4 20.5 1.0
O C:ASN248 4.5 20.7 1.0
C B:ILE146 4.5 18.8 1.0
OG1 B:THR147 4.6 18.1 1.0
O D:HOH418 4.6 23.6 1.0
O B:HOH475 4.6 36.3 1.0
CA B:SER145 4.7 16.6 1.0
O B:ILE146 4.7 20.4 1.0
OXT B:ASN248 4.7 20.0 1.0

Sodium binding site 6 out of 8 in 4mow

Go back to Sodium Binding Sites List in 4mow
Sodium binding site 6 out of 8 in the Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315


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 Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na302

b:27.7
occ:1.00
 O B:HOH475 2.2 36.3 1.0
OD1 C:ASN248 2.3 21.7 1.0
O C:HOH425 2.3 23.6 1.0
O C:HOH420 2.5 15.9 1.0
O C:ASN248 2.6 20.7 1.0
O B:HOH441 2.8 22.5 1.0
NA C:NA301 3.1 23.4 1.0
C C:ASN248 3.3 21.1 1.0
CG C:ASN248 3.4 21.1 1.0
N C:ASN248 3.8 18.6 1.0
OXT C:ASN248 4.0 23.8 1.0
CA C:ASN248 4.0 20.1 1.0
ND2 C:ASN248 4.2 24.0 1.0
CB C:ASN248 4.3 20.5 1.0
O C:HOH451 4.4 30.6 1.0
O C:HOH483 4.5 35.5 1.0
O B:HOH474 4.5 28.1 1.0
O B:ILE146 4.7 20.4 1.0
O B:SER145 4.7 18.9 1.0
O B:HOH535 4.8 35.8 1.0
O D:HOH418 4.8 23.6 1.0
O B:HOH447 4.8 30.5 1.0
CD1 D:LEU170 4.8 24.1 1.0
O B:HOH456 4.9 28.4 1.0
O C:GLY246 4.9 16.0 1.0
CA B:ILE146 5.0 18.8 1.0

Sodium binding site 7 out of 8 in 4mow

Go back to Sodium Binding Sites List in 4mow
Sodium binding site 7 out of 8 in the Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315


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 Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:19.0
occ:1.00
 O D:HOH430 2.2 19.9 1.0
O A:HOH417 2.3 17.2 1.0
O A:SER145 2.3 15.7 1.0
O A:HOH438 2.3 25.8 1.0
OD1 D:ASN248 2.4 18.9 1.0
O D:HOH414 2.5 20.2 1.0
NA D:NA302 3.3 26.3 1.0
CG D:ASN248 3.4 20.1 1.0
C A:SER145 3.5 14.6 1.0
ND2 D:ASN248 3.9 21.0 1.0
O D:HOH444 4.0 29.5 1.0
O A:HOH421 4.0 23.6 1.0
CA A:ILE146 4.1 15.8 1.0
O D:HOH416 4.2 20.9 1.0
O A:HOH490 4.2 30.3 1.0
O C:HOH438 4.2 24.9 1.0
N A:ILE146 4.3 15.1 1.0
OXT D:ASN248 4.4 16.6 1.0
C D:ASN248 4.5 19.1 1.0
OG1 A:THR147 4.5 14.5 1.0
O C:HOH428 4.5 20.5 1.0
C A:ILE146 4.5 15.4 1.0
CB D:ASN248 4.5 19.1 1.0
CA A:SER145 4.6 13.8 1.0
O D:ASN248 4.7 17.7 1.0
OXT A:ASN248 4.7 18.7 1.0
O A:ILE146 4.7 15.7 1.0
O A:HOH533 4.8 30.4 1.0
O A:HOH425 5.0 21.0 1.0

Sodium binding site 8 out of 8 in 4mow

Go back to Sodium Binding Sites List in 4mow
Sodium binding site 8 out of 8 in the Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315


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 Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:26.3
occ:1.00
 O A:HOH533 2.3 30.4 1.0
O D:HOH417 2.4 13.9 1.0
OD1 D:ASN248 2.4 18.9 1.0
O D:HOH414 2.4 20.2 1.0
O D:ASN248 2.7 17.7 1.0
O A:HOH417 2.8 17.2 1.0
NA D:NA301 3.3 19.0 1.0
C D:ASN248 3.3 19.1 1.0
CG D:ASN248 3.5 20.1 1.0
N D:ASN248 3.7 18.2 1.0
CA D:ASN248 4.0 18.4 1.0
OXT D:ASN248 4.1 16.6 1.0
O D:HOH432 4.2 25.6 1.0
ND2 D:ASN248 4.3 21.0 1.0
CB D:ASN248 4.3 19.1 1.0
O A:HOH441 4.4 22.7 1.0
O D:HOH421 4.5 31.7 1.0
O C:HOH428 4.6 20.5 1.0
O A:HOH502 4.7 28.5 1.0
O A:ILE146 4.7 15.7 1.0
O A:HOH438 4.8 25.8 1.0
O D:GLY246 4.8 15.9 1.0
O A:SER145 4.8 15.7 1.0
CD1 C:LEU170 4.9 17.9 1.0
C D:LEU247 4.9 18.0 1.0
CA A:ILE146 5.0 15.8 1.0

Reference:

C.M.Lukacs, J.W.Fairman, T.E.Edwards, D.Lorimer. Crystal Structure of A Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia J2315 To Be Published.
Page generated: Mon Oct 7 17:03:28 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy