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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

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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

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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

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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

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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

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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

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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

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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

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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

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