Atomistry » Sodium » PDB 7u34-7v8o » 7v0h
Atomistry »
  Sodium »
    PDB 7u34-7v8o »
      7v0h »

Sodium in PDB 7v0h: Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product

Enzymatic activity of Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product

All present enzymatic activity of Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product:
1.1.1.47;

Protein crystallography data

The structure of Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product, PDB code: 7v0h 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) 49.08 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.72, 116.66, 180.62, 90, 90, 90
R / Rfree (%) 13.9 / 15.9

Other elements in 7v0h:

The structure of Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product (pdb code 7v0h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product, PDB code: 7v0h:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 7v0h

Go back to Sodium Binding Sites List in 7v0h
Sodium binding site 1 out of 10 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


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 Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:3.6
occ:0.58
 NA A:NA305 0.0 3.6 0.6
NA A:NA305 2.0 4.2 0.4
O A:HOH568 2.2 27.6 1.0
O C:HIS240 2.4 9.8 1.0
O C:HOH408 2.5 24.1 1.0
O C:HOH646 3.0 32.7 1.0
OE1 A:GLU239 3.0 16.2 1.0
C C:HIS240 3.5 5.7 1.0
O A:HIS240 4.1 9.8 1.0
CD A:GLU239 4.1 19.3 1.0
O A:HOH612 4.2 34.8 1.0
O C:HOH482 4.3 10.2 0.6
N C:HIS240 4.3 6.4 1.0
O A:HOH501 4.4 12.5 0.6
OE1 C:GLU239 4.4 16.1 1.0
CA C:HIS240 4.4 6.7 1.0
N C:LEU241 4.4 6.0 1.0
CA C:LEU241 4.4 5.4 1.0
O A:HOH401 4.5 26.2 1.0
CB C:HIS240 4.6 7.1 1.0
OE2 A:GLU239 4.6 19.4 1.0
N C:VAL242 4.7 6.6 1.0
O C:HOH605 4.7 11.9 0.5
CG2 C:VAL242 4.9 8.8 1.0

Sodium binding site 2 out of 10 in 7v0h

Go back to Sodium Binding Sites List in 7v0h
Sodium binding site 2 out of 10 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


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 Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:4.2
occ:0.43
 NA A:NA305 0.0 4.2 0.4
NA A:NA305 2.0 3.6 0.6
O A:HIS240 2.3 9.8 1.0
O A:HOH568 2.4 27.6 1.0
O C:HOH408 2.4 24.1 1.0
O A:HOH612 2.7 34.8 1.0
OE1 C:GLU239 3.2 16.1 1.0
C A:HIS240 3.5 6.6 1.0
O C:HIS240 4.1 9.8 1.0
OE1 A:GLU239 4.2 16.2 1.0
O A:HOH501 4.3 12.5 0.6
N A:HIS240 4.3 7.3 1.0
CD C:GLU239 4.3 13.2 1.0
O C:HOH646 4.3 32.7 1.0
CA A:HIS240 4.4 5.6 1.0
O C:HOH482 4.4 10.2 0.6
N A:LEU241 4.4 6.3 1.0
O C:HOH448 4.4 23.5 1.0
CA A:LEU241 4.5 7.2 1.0
CB A:HIS240 4.6 7.3 1.0
N A:VAL242 4.7 6.7 1.0
OE2 C:GLU239 4.8 14.7 1.0
O A:HOH625 4.8 22.7 1.0

Sodium binding site 3 out of 10 in 7v0h

Go back to Sodium Binding Sites List in 7v0h
Sodium binding site 3 out of 10 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


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 Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:4.2
occ:0.58
 NA B:NA304 0.0 4.2 0.6
NA B:NA304 1.9 4.7 0.4
O D:HOH659 2.4 11.9 0.3
O D:HIS240 2.4 9.6 1.0
O D:HOH534 2.4 26.8 1.0
O D:HOH404 2.5 18.6 1.0
OE1 B:GLU239 3.1 17.3 1.0
O D:HOH659 3.2 23.0 0.7
C D:HIS240 3.6 7.2 1.0
O B:HIS240 4.1 11.2 1.0
CD B:GLU239 4.2 16.2 1.0
O B:HOH633 4.3 31.9 1.0
O B:HOH483 4.3 15.9 1.0
OE1 D:GLU239 4.4 16.1 1.0
N D:HIS240 4.4 6.6 1.0
O D:HOH438 4.4 17.5 1.0
CA D:HIS240 4.4 5.3 1.0
N D:LEU241 4.5 5.8 1.0
CA D:LEU241 4.5 7.3 1.0
O B:HOH507 4.5 29.5 1.0
CB D:HIS240 4.6 6.1 1.0
O D:HOH651 4.6 21.8 1.0
N D:VAL242 4.7 6.2 1.0
OE2 B:GLU239 4.7 19.7 1.0
CG2 D:VAL242 5.0 7.9 1.0

Sodium binding site 4 out of 10 in 7v0h

Go back to Sodium Binding Sites List in 7v0h
Sodium binding site 4 out of 10 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


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 Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:4.7
occ:0.42
 NA B:NA304 0.0 4.7 0.4
NA B:NA304 1.9 4.2 0.6
O D:HOH534 2.2 26.8 1.0
O B:HIS240 2.4 11.2 1.0
O D:HOH404 2.4 18.6 1.0
O B:HOH633 2.8 31.9 1.0
OE1 D:GLU239 3.3 16.1 1.0
C B:HIS240 3.5 7.0 1.0
O D:HOH659 3.7 11.9 0.3
O D:HIS240 4.1 9.6 1.0
OE1 B:GLU239 4.2 17.3 1.0
O B:HOH483 4.2 15.9 1.0
N B:HIS240 4.3 6.6 1.0
CD D:GLU239 4.4 14.3 1.0
CA B:HIS240 4.4 5.5 1.0
N B:LEU241 4.4 5.7 1.0
O D:HOH413 4.4 24.2 1.0
CA B:LEU241 4.5 6.8 1.0
O D:HOH438 4.6 17.5 1.0
O D:HOH659 4.6 23.0 0.7
CB B:HIS240 4.6 6.3 1.0
N B:VAL242 4.7 6.1 1.0
O B:HOH636 4.7 23.5 1.0
OE2 D:GLU239 4.9 14.4 1.0

Sodium binding site 5 out of 10 in 7v0h

Go back to Sodium Binding Sites List in 7v0h
Sodium binding site 5 out of 10 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


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 Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na305

b:20.6
occ:1.00
 O B:HOH409 2.2 36.1 1.0
O B:HOH572 2.6 36.1 1.0
OE1 B:GLU106 4.3 32.2 1.0
OE2 B:GLU106 4.5 41.8 1.0
CD B:GLU106 4.8 29.3 1.0

Sodium binding site 6 out of 10 in 7v0h

Go back to Sodium Binding Sites List in 7v0h
Sodium binding site 6 out of 10 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


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 Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na306

b:4.3
occ:0.66
 NA E:NA306 0.0 4.3 0.7
NA E:NA306 2.0 4.0 0.3
O E:HOH483 2.3 27.6 1.0
O G:HIS240 2.4 9.5 1.0
O G:HOH406 2.5 21.5 1.0
OE2 E:GLU239 2.6 8.2 0.5
O E:HOH615 2.6 31.1 1.0
OE1 E:GLU239 2.8 11.1 0.5
CD E:GLU239 3.1 10.9 0.5
OE1 E:GLU239 3.3 11.5 0.5
C G:HIS240 3.5 7.2 1.0
O E:HIS240 4.1 11.3 1.0
O G:HOH445 4.3 16.9 1.0
O E:HOH613 4.3 32.5 1.0
N G:HIS240 4.3 8.8 1.0
OE1 G:GLU239 4.3 15.3 1.0
CA G:HIS240 4.4 6.4 1.0
CD E:GLU239 4.4 11.1 0.5
N G:LEU241 4.4 6.6 1.0
O E:HOH454 4.4 15.3 1.0
CA G:LEU241 4.5 6.0 1.0
CG E:GLU239 4.6 10.5 0.5
O E:HOH403 4.6 25.7 1.0
CB G:HIS240 4.6 6.6 1.0
N G:VAL242 4.7 6.1 1.0
O G:HOH636 4.7 24.2 1.0
OE2 E:GLU239 4.9 12.3 0.5
CG2 G:VAL242 5.0 9.8 1.0

Sodium binding site 7 out of 10 in 7v0h

Go back to Sodium Binding Sites List in 7v0h
Sodium binding site 7 out of 10 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


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 Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na306

b:4.0
occ:0.34
 NA E:NA306 0.0 4.0 0.3
NA E:NA306 2.0 4.3 0.7
O E:HOH483 2.2 27.6 1.0
O G:HOH406 2.4 21.5 1.0
O E:HIS240 2.4 11.3 1.0
O E:HOH613 2.7 32.5 1.0
OE1 E:GLU239 3.0 11.1 0.5
OE1 G:GLU239 3.2 15.3 1.0
C E:HIS240 3.6 7.9 1.0
CD E:GLU239 3.8 10.9 0.5
OE2 E:GLU239 3.9 8.2 0.5
O E:HOH615 4.0 31.1 1.0
O G:HIS240 4.1 9.5 1.0
O G:HOH447 4.1 21.6 1.0
O E:HOH454 4.3 15.3 1.0
CD G:GLU239 4.3 13.6 1.0
N E:HIS240 4.4 8.1 1.0
O G:HOH445 4.4 16.9 1.0
CA E:HIS240 4.4 6.8 1.0
N E:LEU241 4.5 6.0 1.0
OE1 E:GLU239 4.5 11.5 0.5
CA E:LEU241 4.5 8.1 1.0
CB E:HIS240 4.6 9.2 1.0
O E:HOH634 4.7 21.8 1.0
N E:VAL242 4.7 6.5 1.0
OE2 G:GLU239 4.8 17.2 1.0

Sodium binding site 8 out of 10 in 7v0h

Go back to Sodium Binding Sites List in 7v0h
Sodium binding site 8 out of 10 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


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 Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na305

b:3.5
occ:0.53
 NA F:NA305 0.0 3.5 0.5
NA F:NA305 2.0 5.1 0.5
O F:HOH486 2.1 26.5 1.0
O H:HIS240 2.4 11.0 1.0
O H:HOH406 2.5 18.9 1.0
OE2 F:GLU239 2.6 9.2 0.4
OE1 F:GLU239 2.7 9.4 0.4
O H:HOH639 3.0 31.9 1.0
CD F:GLU239 3.0 10.4 0.4
OE1 F:GLU239 3.3 10.8 0.6
C H:HIS240 3.5 8.1 1.0
O F:HIS240 4.1 9.6 1.0
OE1 H:GLU239 4.3 14.4 1.0
N H:HIS240 4.4 7.0 1.0
O F:HOH483 4.4 17.3 1.0
O F:HOH407 4.4 30.3 1.0
O F:HOH626 4.4 32.8 1.0
O H:HOH439 4.4 17.1 1.0
CA H:HIS240 4.4 7.1 1.0
CD F:GLU239 4.4 7.9 0.6
N H:LEU241 4.4 7.1 1.0
CA H:LEU241 4.5 6.9 1.0
CG F:GLU239 4.5 9.0 0.4
CB H:HIS240 4.6 6.4 1.0
N H:VAL242 4.6 7.7 1.0
O H:HOH647 4.7 25.0 1.0
OE2 F:GLU239 4.9 9.6 0.6
CG2 H:VAL242 5.0 8.4 1.0

Sodium binding site 9 out of 10 in 7v0h

Go back to Sodium Binding Sites List in 7v0h
Sodium binding site 9 out of 10 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na305

b:5.1
occ:0.47
 NA F:NA305 0.0 5.1 0.5
NA F:NA305 2.0 3.5 0.5
O F:HOH486 2.2 26.5 1.0
O H:HOH406 2.4 18.9 1.0
O F:HIS240 2.4 9.6 1.0
O F:HOH626 2.7 32.8 1.0
OE1 F:GLU239 2.9 9.4 0.4
OE1 H:GLU239 3.2 14.4 1.0
C F:HIS240 3.6 7.6 1.0
CD F:GLU239 3.9 10.4 0.4
OE2 F:GLU239 4.0 9.2 0.4
O H:HIS240 4.1 11.0 1.0
O F:HOH483 4.2 17.3 1.0
CD H:GLU239 4.3 14.8 1.0
O H:HOH639 4.3 31.9 1.0
N F:HIS240 4.4 8.0 1.0
O H:HOH429 4.4 22.5 1.0
CA F:HIS240 4.4 5.8 1.0
O H:HOH439 4.5 17.1 1.0
N F:LEU241 4.5 5.8 1.0
CA F:LEU241 4.5 5.8 0.6
CA F:LEU241 4.5 5.8 0.4
OE1 F:GLU239 4.6 10.8 0.6
CB F:HIS240 4.6 6.3 1.0
O F:HOH633 4.7 21.7 1.0
N F:VAL242 4.7 6.6 1.0
OE2 H:GLU239 4.8 18.0 1.0
CD2 F:LEU241 5.0 8.8 0.4
CG2 F:VAL242 5.0 8.0 1.0

Sodium binding site 10 out of 10 in 7v0h

Go back to Sodium Binding Sites List in 7v0h
Sodium binding site 10 out of 10 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na306

b:20.3
occ:1.00
 O F:HOH415 2.3 27.4 1.0
O F:HOH506 2.6 34.4 1.0
OE2 F:GLU106 4.4 28.6 1.0
OE1 F:GLU106 4.5 23.7 1.0
CD F:GLU106 4.9 21.8 1.0

Reference:

J.Abendroth, N.D.Debouwer, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product To Be Published.
Page generated: Wed Oct 9 09:17:10 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